P-PHENYLENE ETHYNYLENE COMPOUNDS AS BIOACTTVE AND

DETECTION AGENTS

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of the filing dates of U.S.

Provisional Application No. 61/953,31 1, filed on March 14, 2014, U.S.

Provisional Application No. 61/954,923, filed on March 18, 2014, U.S.

Provisional Application No. 61 /955,522, filed on March 19, 2014, and U.S.

Provisional Application No. 62/012,780, filed on June 16, 2014, the disclosures of which are incorporated by reference herein in their entireties.

STATEMENT OF GOVERNMENT SUPPORT

[0002] This invention was made with Government support under

HDTRA-1 1-1-0004 awarded by the Defense Threat Reduction Agency (DTRA), under DMR 1207362 and CBET-1 150855 awarded by the National Science Foundation (NSF), and under R21 NS07708 awarded by the National Institutes certain rights in this invention.

[ΘΘ03] Agents that can kill the viable bacteria, such as antibiotics, can be ineffective to terminate the viability of the bacterial spores, making populations of such bacteria difficult to control. Even if the entire mature population is killed, viable spores are still available for germination to restore a potentially pathogenic bacterial population.

[0004] Detecting enzymes, proteins, or chemical agents can be valuable for a wide variety of uses. For example, abnormal formation and deposition of amyloid protein aggregates is associated with a number of neurodegenerative diseases, including, but not limited to, Alzheimer's disease, Parkinson's disease, Huntington's disease, systemic amyloidosis and inherited organ-specific amyloidoses, and transmissible prion diseases such as bovine spongiform encephalopat hy, chronic wasting disease, and sheep scrapie. Each of these diseases is characterized by symptoms including cross- -sheet rich aggregates. formed from characteristic proteins depending upon the specific disease.

Understanding, diagnosing, and treating these diseases require tools to locate and track the formation of amyloid aggregates in living organisms, particularly the putative toxic aggregate forms. The primary method for amyloid detection is histopathological staining of tissue sections with fluorescent dyes, of which the commonest currently is Thioflavin T. Existing dyes have limitations; they target primarily mature aggregates and they cannot distinguish between amyloids with differing conformations, particularly oligomeric / pre-fribillar aggregates that are considered the primary toxic species.

SUMMARY OF THE INVENTION

10005] In various embodiments, the present invention provides a method of inducing germination of microbial spores including contacting the microbial spores with a p-phenylene ethynylene compound.

[0006] In various embodiments, the present invention provides a method for detecting an enzyme. The method includes (i) introducing an enzyme to a composition including a p-phenylene ethynylene compound and an enzyme substrate. The method also includes (ii) analyzing the change in fluorescence of the p-phenylene ethynylene compound following introduction of the enzyme.

[0007] In various embodiments, the present invention provides a method for detecting an enzyme. The method includes (i) introducing an enzyme to a composition including a. p-phenylene ethynylene compound and an enzyme substrate; and (ii) analyzing the change in fluorescence of the p-phenylene ethynylene compound following introduction of the enzyme. The p-phenylene ethynylene compound has the structure:

/

The variable s is about 1 to about 3. The enzyme substrate is 1 ,2-dilauroyi-sn- glycero-phospho-(l '-rac-glycerol). The enzyme is at least one of phospholipase Al , phospholipase A2, and phospholipase C. [0008] In various embodiments, the present invention provides a method for detecting an enzyme. The method includes (i) introducing an enzyme to a composition including a p-phenylene ethynylene compound and an enzyme substrate. The method also includes (ii) analyzing the change in fluorescence of the p-phenylene ethynylene compound following introduction of the enzyme. The p-phenylene ethynylene compound has the structure:

The variable t is about 1 to about 3. The enzyme substrate is lauroyl choline. The enzyme is acetylcholinesterase.

[0009] In various embodiments, the present invention provides a sensor.

The sensor includes a p-phenylene ethynylene compound and an enzyme substrate.

|00i0] In various embodiments, the present invention provides a sensor.

The sensor includes a cationic p-phenylene ethynylene compound and an anionic enzyme substrate. The p-phenylene ethynylene compound has the structure:

The variable s is about I to about 3. The anionic enzyme substrate is 1,2- dilauroyl-sn-glycero-phospho-( -rac-glycerol).

[θθίί] In various embodiments, the present invention provides a sensor, The sensor includes a p-phenylene ethynylene compound and an enzyme substrate. The p-phenylene ethynylene compound has the structure:

The variable t is about 1 to about 3, The enzyme substrate is lauroyi choline, [0012] In various embodiments, the present invention provides a method for protein analysis. The method includes (i) introducing a p-phenylene ethynylene compound to a biological sample including at least one protein. The method also includes (ii) analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample including the at least one protein.

[ΘΘΪ3] In various embodiments, the present invention provides a method for protein analysis. The method includes (i) analyzing the fluorescence of a p- phenylene ethynylene compound. The method includes (ii) introducing the p- phenylene ethynylene compound to a biological sample including at least one protein. The method includes (iii) analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample including the at least one protein. The method also includes (iv) determining the morphology of the at feast one protein in the biological sample by analyzing spectral changes between the fluorescence of the p-phenylene ethyny lene compound of step (i) and the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample including the at feast one protein of step (iii). The p- phenylene ethynylene compound has the structure:

The variable s is L The protein is at least one of an amyloid beta protein, Αβ-40, Αβ-42, tau, and a-synuclein, islet amyloid precursor protein, Huntingtin, prion, lysozyme, TDP-43 (transactive response DNA-binding protein 43), FUS (fused in sarcoma), and insulin.

[0014] In various embodiments, the present invention provides a method for detecting a chemical agent. The method includes (i) exposing a sensor composition including a complex including a p-phenylene ethynylene compound and an enzyme substrate to a sample. The method includes (ii) introducing an enzyme to the sensor composition of step (i). The method also includes (iii) analyzing the change in fluorescence of the p-phenylene ethynylene compound between the exposing step (i) and the introducing an enzyme step (ii).

[0015] In various embodiments, the present invention provides a method for detecting a chemical agent. The method includes (i) exposing a sensor composition including a complex including a p-phenyiene ethynylene compound and an enzyme substrate to a sample. The method includes (ii) introducing an enzyme to the sensor composition of step (i). The method also includes (iii) analyzing the change in fluorescence of the p-phenylene ethynylene compound between the exposing step (i) and the introducing an enzyme step (ii). The p- phenylene ethynylene compound has the structure:

The variable t is about 1 to about 3. The enzyme substrate is lauroyi choline. A change in fluorescence between the exposing step (i) and the introducing an enzyme step (ii) indicates the presence of a chemical agent that does interact with the enzyme.

[0016] In various embodiments, the present invention provides a sensor for detecting the presence of a chemical agent. The sensor includes a sensor composition including a complex including a p-phenylene ethynylene compound and an enzyme substrate.

[0017] In various embodiments, the present invention provides a sensor for detecting the presence of a chemical agent. The sensor includes a sensor composition including a complex including a p-phenylene ethynylene compound and an enzyme substrate. The p-phenylene ethynylene compound has the structure

The variable t is about 1 to about 3. The enzyme substrate is lauroyi choline. BRIEF DESCRIPTION OF THE FIGURES

[0018] The drawings illustrate generally, by way of example, but not by way of limitation, various embodiments discussed in the present document.

[0019] FIGS. 1A-D illustrate flow eytometry-reported fluorescence of stained B. atrophaeus vegetative cells following various treatment conditions, in accordance with various embodiments.

[ΘΘ2Θ] FIGS. 2A-D illustrate flow eytometry-reported germination ofB. atrophaeus spores under various treatment conditions, in accordance with various embodiments.

[ΘΘ21] FIGS. 3A-E illustrate scanning electron microscope images of B, atrophaeus spores and vegetative cells, in accordance with various

embodiments.

[0022] FIG. 4 illustrates B, anthracis Sterne vegetative cell viability with and without exposure to a PE, in accordance with various embodiments.

[0023] FIG. 5 illustrates B. anthracis Sterne spore and germinated vegetative cell viability as a function of starting concentration, in accordance with various embodiments.

[0024] FIGS. 6A-D illustrate absorbance and fluorescence of various p- phenylene ethynylene compounds (PEs) versus wavelength in the presence of varying amounts of 1 ,2-dilauroyl-sn-glycero-3-phospho-(l -rac-glycerol)

(DLPG) or lauroyl choline (LaC ), in accordance with various embodiments.

[0025] FIGS. 7A-B illustrate integrated fluorescence versus absorbance for various PEs, in accordance with various embodiments.

[0026] FIGS. 8A-D illustrate fluorescence versus time for PE with various concentrations of DLPG and PLA1 or PLA2, in accordance with various embodiments.

[0027] FIGS. 9A-C illustrate absorbance or fluorescence versus substrate concentration for various sensors, in accordance with various embodiments.

[0028] FIGS. 10A-B illustrate loss of fluorescence over time and velocity versus substrate concentration, in accordance with various

embodiments. [0029] FIGS, 11A-B illustrate absorbance and fluorescence versus time after addition of various concentrations of substrate, in accordance with various embodiments.

[0030] FIGS. 12A-C illustrate fluorescence versus time for a PE/LaCh sensor over time with and without inhibitor, in accordance with various embodiments.

[0031] FIGS. 13A-B illustrate absorbance and fluorescence versus wavelength for a PE alone, with LaCh, and with various inhibitors, in accordance with various embodiments.

[ΘΘ32] FIGS. 14A-B illustrate absorbance and fluorescence of a PE with various concentrations of DLPG, in accordance with various embodiments.

[0033] FIG. 15 illustrates fluorescence enhancement versus hen egg white lysozyme (FIEWL) incubation time, in accordance with various embodiments.

[0034] FIG. 16 illustrates mean molar ellipticity versus wavelength for

FIEWL incubated for various times, in accordance with various embodiments, in accordance with various embodiments.

[0035] FIG. 17 illustrates transmission electron spectroscopy and atomic force microscopy images of HEWL incubated for various times, in accordance with various embodiments.

[0036] FIGS. 18A-H illustrate fluorescence versus wavelength for various PEs, in accordance with various embodiments.

[0037] FIG. 19 illustrates fluorescence versus PE concentration in the presence ofFTEWL monomers, in accordance with various embodiments.

[0038] FIG. 20 illustrates HEWL/PE Forster resonance energy transfer

(FRET) efficiencies for various PEs calculated from spectral data, in accordance with various embodiments.

[0039] FIG. 21 illustrates modes of interaction between PEs and HEWL monomers and amyloids, in accordance with various embodiments.

DETAILED DESCRIPTION OF THE INVENTION

[0040] Reference will now be made in detail to certain embodiments of the disclosed subject matter, examples of which are illustrated in part in t he accompanying drawings. While the disclosed subject matter will be described in conjunction with the enumerated claims, it will be understood that the exemplified subject matter is not intended to limit the claims to the disclosed subject matter.

[ΘΘ41] Throughout this document, values expressed in a range format should be interpreted in a flexible manner to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range is explicitly recited. For example, a range of "about 0.1 % to about 5%" or "about 0. 1 % to 5%" should be interpreted to include not just about 0, 1 % to about 5%, but also the individual values (e.g., 1%, 2%, 3%, and 4%) and the sub-ranges (e.g., 0.1% to 0.5%, 1.1% to 2.2%, 3.3% to 4.4%) within the indicated range. The statement "about X to Y" has the same meaning as "about X to about Y," unless indicated otherwise. Likewise, the statement "about X, Y, or about Z" has the same meaning as "about X, about Y, or about Z," unless indicated otherwise.

[0042] In this document, the terms "a," "an," or "the" are used to include one or more than one unless the context dearly dictates otherwise. The term "or" is used to refer to a nonexclusive "or" unless otherwise indicated. The statement "at least one of A and B" has the same meaning as "A, B, or A and B." In addition, it is to be understood that the phraseology or terminology employed herein, and not otherwise defined, is for the purpose of description only and not of limitation. Any use of section headings is intended to aid reading of the document and is not to be interpreted as limiting; information that is relevant to a section heading may occur within or outside of that particular section. A comma can be used as a delimiter or digit group separator to the left or right of a decimal mark; for example, "0.000, 1" is equivalent to "0.0001."

10043] In the methods of manufacturing described herein, the acts can be carried out in any order without departing from the principles of the invention, except when a temporal or operational sequence is explicitly recited.

Furthermore, specified acts can be carried out concurrently unless explicit claim language recites that they be carried out separately. For example, a claimed act of doing X and a claimed act of doing Y can be conducted simultaneously within a single operation, and the resulting process will fall within the literal scope of the claimed process. [0044] The term "about" as used herein can allow for a degree of variability in a value or range, for example, within 10%, within 5%, or within 1% of a stated value or of a stated limit of a range, and includes the exact stated value or range.

10045] The term "substantially" as used herein refers to a majority of, or mostly, as in at least about 50%, 60° ,. 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, 99.99%, or at least about 99.999% or more, or 100%.

[0046] The term "organic group" as used herein refers to any carbon- containing functional group. For example, an oxygen-containing group such as an alkoxy group, aryloxy group, aralkyioxy group, oxo(carbonyl) group, a carboxyl group including a carboxylic acid, carboxylate, and a carboxylate ester; a sulfur-containing group such as an alkyl and aryi sulfide group; and other heteroatom-contaimng groups. Non-limiting examples of organic groups include OR, OOR, OC(0)N(R) ₂ , CN, CF ₃ , OCF ₃ , R, C(O), methylenedioxy, ethylenedioxy, N(R) ₂ , SR, SOR, S0 ₂ R, S0 ₂ N(R) ₂ , S0 ₃ R, C(0)R, C(0)C(0)R, C(0)CH ₂ C(0)R, C(S)R, C(0)OR, OC(0)R, C(0)N(R) ₂ , OC(0)N(R) ₂ , C(S)N(R) ₂₎ (CH ₂ ) ₀ . ₂ N(R)C(O)R, (CH ₂ ) ₀ -. ₂ N(R)N(R) ₂ , N(R)N(R)C(0)R, N(R)N(R)C(0)OR, N(R)N(R)CON(R) ₂ , N(R)S0 ₂ R, N(R)S0 ₂ N(R) ₂ ,

N(R)C(0)OR, N(R)C(Q)R, N(R)C(S)R, N(R)C(0)N(R) ₂ , N(R)C(S)N(R) ₂ , N(COR)COR, N(OR)R, C(=NH)N(R) ₂ , C(0)N(OR)R, C(=NOR)R, and substituted or unsubstituted (C i -C ioo)hydrocarbyl, wherein R can be hydrogen (in examples that include other carbon atoms) or a carbon-based moiety, and wherein the carbon-based moiety can be substituted or unsubstituted.

[0047] The term "substituted" as used herein in conjunction with a molecule or an organic group as defined herein refers to the state in which one or more hydrogen atoms contained therein are replaced by one or more non- hydrogen atoms. The term "functional group" or "substituent" as used herein refers to a group that can be or is substituted onto a molecule or onto an organic group. Examples of substituents or functional groups include, but are not limited to, a halogen (e.g., F, CI, Br, and I); an oxygen atom in groups such as hydroxy groups, alkoxy groups, aryloxy groups, aralkyioxy groups, oxo(carbonyl) groups, carboxyl groups including carboxylic acids, carboxylases, and carboxylate esters; a sulfur atom in groups such as thiol groups, alkyl and aryl sulfide groups, sulfoxide groups, sulfone groups, sulfonyl groups, and sulfonamide groups; a nitrogen atom in groups such as amines, hydroxyamines, nitriles, nitro groups, N-oxides, hydrazides, azides, and enamines; and other heteroaioms in various other groups. Non-limiting examples of substituenis that can be bonded to a substituted carbon (or other) atom include F, CI, Br, I, OR, OC(0)N(R) ₂ , CN, NO, N0 ₂ , ON0 ₂ , azido, CF ₃ , OCF ₃ , R, O (oxo), S (thiono), C(O), S(O), methylenedioxy, ethylenedioxy, N(R) ₂ , SR, SOR, S0 ₂ R,

SO .Ni R ) .. S0 ₃ R, C(0)R, C(0)C(0)R, C(0)CH ₂ C(0)R, C(S)R, C(0)OR, OC(0)R, C(0)N(R) ₂ , OC(Q)N(R) ₂ , C(S)N(R) ₂₎ (CH ₂ ) _0-2 N(R)C(O)R, (CH ₂ ) _{0- 2} N(R)N(R) ₂ , N(R)NiR)C(0)R, N(R)N(R)C(0)OR, N(R)N(R)CON(R) ₂ , N(R)S0 ₂ R, N(R)S0 ₂ N(R) ₂ , N(R)C(0)OR, N(R)C(0)R, N(R)C(S)R,

N(R)C(0)N(R) ₂ , N(R)C(S)N(R) ₂ , N(COR)COR, N(OR)R, C(=NH)N(R) ₂ , C(0)N(OR)R, and ( ^' ( \OR )R. wherein R can be hydrogen or a carbon-based moiety; for example, R can be hydrogen, (C 1 -C ioo)hydrocarbyl, alkyl, acyl, cycloalkyl, aryl, aralkyl, heterocyelyl, heteroaryl, or heteroarylalkyl; or wherein two R groups bonded to a nitrogen atom or to adjacent nitrogen atoms can together with the nitrogen atom or atoms form a heterocyclyl.

[0048] The term "alkyl" as used herein refers to straight chain and branched alkyl groups and cycloalkyl groups having from 1 to 40 carbon atoms, 1 to about 20 carbon atoms, 1 to 12 carbons or, in some embodiments, from 1 to 8 carbon atoms. Examples of straight chain alkyl groups include those with from 1 to 8 carbon atoms such as methyl, ethyl, n-propyl, n-butyl, n-pentyf, n- hexyi, n-heptyl, and n-octyi groups. Examples of branched alkyl groups include, but are not limited to, isopropyl, iso-butyl, sec-butyl, t-butyl, neopentyl, isopentyl, and 2,2-dimethylpropyl groups. As used herein, the term "alkyl" encompasses n-alkyl, isoalkyl, and anteisoalkyl groups as well as other branched chain forms of alkyl. Representative substituted alkyl groups can be substituted one or more times with any of the groups listed herein, for example, amino, hydroxy, cyano, carboxy, nitro, t io, alkoxy, and halogen groups.

[0049] The term "alkenyi" as used herein refers to straight and branched chain and cyclic alkyl groups as defined herein, except that at least one double bond exists between two carbon atoms. Thus, alkenyi groups have from 2 to 40 carbon atoms, or 2 to about 20 carbon atoms, or 2 to 12 carbons or, in some embodiments, from 2 to 8 carbon atoms. Examples include, but are not limited to vinyl, -C! i ( I li Ci h i. -CIT-C(CH ₃ ) ₂ , -CK i l n C i h. -O C! i CS K C! ί .- }. - C(CH ₂ CH3)=CH ₂ , cyclohexenyl, eyclopentenyl, cyclohexadienyl, butadienyl, pentadienyl, and hexadienyl among others.

[0050] The term "alkynyl" as used herein refers to straight and branched chain alkyl groups, except that at least one triple bond exists between two carbon atoms. Thus, alkynyl groups have from 2 to 40 carbon atoms, 2 to about 20 carbon atoms, or from 2 to 12 carbons or, in some embodiments, from 2 to 8 carbon atoms. Examples include, but are not limited to ~-C=CH, -C=C(CH ₃ ), - C=C(CH ₂ CH ₃ ), -CI 1 . ⁽ . ^' ( I I. - Ci hC ( ^' ( ( ^' ! I ; !. and -CH ₂ G≡C(CH ₂ CH ₃ ) among others.

[0051] The term "a.cyi" as used herein refers to a group containing a carbonyl moiety wherein the group is bonded via the carbonyl carbon atom. The carbonyl carbon atom is bonded to a hydrogen forming a "formyl" group or is bonded to another carbon atom, which can be part of an alkyl, aryl, aralkyl cycloalkyl, cycloalkylalkyl, heteroeyciyi, heierocyclylalkyl, heteroaryl, heteroarylalkyl group or the like. An acyl group can include 0 to about 12, 0 to about 20, or 0 to about 40 additional carbon atoms bonded to the carbonyl group. An acyl group can include double or triple bonds within the meaning herein. An acryloyl group is an example of an acyl group. An acyl group can also include heteroatoms within the meaning herein. A nicotinoyl group (pyridyl-3-carbony3) is an example of an acyl group within the meaning herein. Other examples include acetyl, benzoyl, phenylaceiyl, pyridylaceiyl, cinnamoyi, and acryloyl groups and the like. When the group containing the carbon atom that is bonded to the carbonyl carbon atom contains a halogen, the group is termed a "haloacyl" group. An example is a trifiuoroaeetyl group.

[0052] The term "aryl" as used herein refers to cyclic aromatic hydrocarbons that do not contain heteroatoms in the ring. Thus aryl groups include, but are not limited to, phenyl, azulenyl, heptalenyl, biphenyl, indacenyi, fluorenyl, phenanthrenyl, triphenylenyl, pyrenyl, naphthacenyl, chrysenyl, biphenyienyl, anthracenyl, and napht yl groups. In some embodiments, aryl groups contain about 6 to about 14 carbons in the ring portions of the groups, Aryl groups can be unsubsiituied or substituted, as defined herein.

Representative substituted aryl groups can be mono-substituted or substituted more than once, such as, but not limited to, 2-, 3-, 4-, 5-, or 6-substituted phenyl

I I or 2-8 substituted naplithyl groups, which can be substituted with carbon or non- carbon groups such as those listed herein.

[0053] The term "heterocyclyl" as used herein refers to aromatic and non-aromatic ring compounds containing three or more ring members, of which one or more is a heteroatom such as, but not limited to, N, (3, and S.

10054] The term "alkoxy" as used herein refers to an oxygen atom connected to an alkyi group, including a eycloalkyl group, as are defined herein. Examples of linear alkoxy groups include but are not limited to methoxy, ethoxy, propoxy, butoxy, pentyloxy, hexyloxy, and the like. Examples of branched alkoxy include but are not limited to isopropoxy, sec -butoxy, tert- butoxy, isopentyloxy, isohexyfoxy, and the like. Examples of cyclic alkoxy include but are not limited to cyclopropyloxy, cyclobutyloxy, cyclopentyloxy, cyclohexyloxy, and the like. An alkoxy group can include one to about 12-20 or about 12-40 carbon atoms bonded to the oxygen atom, and can further include double or triple bonds, and can also include heteroatoms. For example, an allyloxy group is an alkoxy group within the meaning herein. A methoxyethoxy group is also an alkoxy group within the meaning herein, as is a methylenedioxy group in a context where two adjacent atoms of a structure are substituted therewith.

[0055] The term "amine" as used herein refers to primary, secondary, and tertiary amines having, e.g., the formula N(group) 3 wherein each group can independently be H or non-H, such as alkyl, aryl, and the like. Amines include but are not limited to R-NH2, for example, alkyiamines, arylamines, alkylarylamines; R .> \ ! i wherein each R is independently selected, such as dialkylamines, diary-famines, aralkylamines, heterocycfylamines and the like; and R ₃ N wherein each R is independently selected, such as trialkylamines, dialkylarylamines, alkyldiarylamines, triarylamines, and the like. The term "amine" also includes ammonium ions as used herein.

[ΘΘ56] The term "amino group" as used herein refers to a substituent of the form -NIT?; -NHR, -NR ₂ , -NR3 ⁴ , wherein each R is independently selected, and protonated forms of each, except for -NR ₃ ¹ , which cannot be protonated. Accordingly, any compound substituted with an amino group can be viewed as an amine. An "amino group" within the meaning herein can be a primary, secondary, tertiary, or quaternary amino group. An "alkylamino" group includes a monoalkylamino, dialkylamino, and trialkylamino group.

[0057] The terms "halo," "halogen," or "halide" group, as used herein, by themselves or as part of another substituent, mean, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom.

10058] The term "hydrocarbon" or "hydrocarbyl" as used herein refers to a molecule or functional group, respectively, that includes carbon and hydrogen atoms. The term can also refer to molecule or functional group that normally includes both carbon and hydrogen atoms but wherein all the hydrogen atoms are substituted with other functional groups,

[ΘΘ59] As used herein, the term "hydrocarbyl" refers to a functional group derived from a straight chain, branched, or cyclic hydrocarbon, and can be alkyl, alkenyl, alkynyl, aryl, cycloalkyi, acyl, or any combination thereof.

Hydrocarbyl groups can be shown as (C _a ~C _b )hyxlroearbyl, wherein a and b are integers and mean having any of a to b number of carbon atoms. For example, (Cj -C/j hydrocarbyl means the hydrocarbyl group can be methyl (C _f ), ethyl (C ₂ ), propyl (C ₃ ), or butyl (C ₄ ). (Co-Ct _> )hydrocarby3 means in certain embodiments there is no hydrocarbyl group.

[0060] The term "solvent" as used herein refers to a liquid that can dissolve a solid, another liquid, or a gas. Non-limiting examples of solvents are silicones, organic compounds, water, alcohols, ionic liquids, and supercritical fluids.

[0061] The term "number-average molecular weight" as used herein refers to the ordinary arithmetic mean of the molecular weight of individual molecules in a sample. It is defined as the total weight of all molecules in a sample divided by the total number of molecules in the sample. Experimentally, the number-average molecular weight (M„) is determined by analyzing a sample divided into molecular weight fractions of species I having ¾ molecules of molecular weight M; through the formula. M„ = ΣΜ;η; / Ση,. The number- average molecular weight can be measured by a variety of well-known methods including gel permeation chromatography, spectroscopic end group analysis, and osmometry. If unspecified, molecular weights of polymers given herein are number-average molecular weights.

1.3 [0062] The term "room temperature" as used herein refers to a temperature of about 15 °C to about 28 °C.

[0063] As used herein, "degree of polymerization" is the number of repeating units in a polymer.

[0064] As used herein, the term "polymer" refers to a molecule having at least one repeating unit and can include copolymers. As used herein, the term "oligomer" refers to a relatively low molecular weight polymer in which the number of repeating units can be, for example, from 1 to 10. The properties of the oligomer can vary with the removal of one or a fe of the units.

[ΘΘ65] The term "copolymer" as used herein refers to a polymer that includes at feast two different repeating units. A copolymer can include any suitable number of repeating units.

[0066] The polymers described herein can terminate in any suitable way.

In some embodiments, the polymers can terminate with an end group that is independently chosen from a suitable polymerization initiator, -H, -OH, a substituted or unsubstituted (C i -C ₂ o)hydrocarbyl (e.g., (C i -C io)alkyl, ((V

:, }ai i. or an alkyne) interrupted with 0, 1, 2, or 3 groups independently selected from -0-, substituted or unsubstituted -NH-, and -S-, a polyfsubstituted or unsubstituted (Ci -C ₂ o)hydrocarbyloxy), a poly( substituted or unsubstituted (Ci -C2o)hydrocarbylamino) and a halogen,

[0067] In various embodiments, salts having a positively charged counterion can include any suitable positively charged counterion. For example, the counterion can be ammonium(NH ₄ ⁺ ), or an alkali metal such as sodium (Na ^" ), potassium (K ), or lithium (Lf ). In some embodiments, the counterion can have a positive charge greater than +1, which can in some embodiments complex to multiple ionized groups, such as Zn ^7'+ , ΑΓ ⁺ , or alkaline earth metals such as Ca ^2i~ or Mg ^{2 '} .

[0068] In various embodiments, salts having a negatively charged counterion can include any suitable negatively charged counterion. For example, the counterion can be a haiide, such as fluoride, chloride, iodide, or bromide. In other examples, the counterion can be nitrate, hydrogen sulfate, dihydrogen phosphate, bicarbonate, nitrite, perchiorate, iodate, chlorate, bromate, chlorite, hypochlorite, hypobromite, cyanide, amide, cyanate, hydroxide, permanganate. The counterion can be a conjugate base of any carboxylic acid, such as acetate or formate. In some embodiments, a count erion can have a negative charge greater than -1, which can in some embodiments complex to multiple ionized groups, such as oxide, sulfide, nitride, arsenate, phosphate, arsenite, hydrogen phosphate, sulfate, thiosulfate, sulfite, carbonate, chromate, dichromate, peroxide, or oxalate.

10069] The p-phenylene ethynylene compounds described herein can include counterfoils. For example, a p-phenylene ethynylene compound bearing a -N ^T (CH ₃ )3 can have a negatively charged counterfoil, such as Br ^" or Γ, associated with it.

[ΘΘ70] As used herein, the term "3-methylimidazolium" refers to a substituent having the structure

The wavy line indicates the point of attachment to the rest of the molecule.

[0071] As used herein, the term "(d -C ₁ o)alkyl-(l ,4-substituted 1 ,4- diazabicyclo[2.2.2]octane- l,4-diium)~" refers to a substituent having the structure

I— — (C ^c io)a!ky!

\ /

The wavy line indicates the point of attachment to the rest of the molecule.

[0072] As used herein, a "cationic p-phenylene ethynylene compound" refers to a p-phenylene ethynylene compound that has a net positive charge.

[0073] As used herein, the term "anionic enzyme substrate" refers to an enzyme substrate that has a net negative charge.

[0074] As used herein, an "anionic ρ-phenylene ethynylene compound" refers to a p-phenylene ethynylene compound that has a net negative charge.

[0075] As used herein, the term "biological sample" includes, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof and other biological fluids.

[0076] As used herein, the term "microbial spore" can refer to any suitable microbial spore, such as a eukaryotic spore or a bacterial spore. [0077] As used herein, the term "anionic enzyme substrate" can refer to any suitable anionic enzyme substrate that can be used as described herein. The anionic enzyme substrate can be a substrate that is sufficiently hydrophobic but is not so large that it cannot form a complex with an oligomer. The anionic enzyme substrate can be a. phospholipid. The anionic enzyme substrate can be a lipopolysaccharide or other hybrid species that can be a component of a membrane. The anionic enzyme substrate can be an anionic peptide or a small protein with a net-negative patch. The anionic enzyme substrate can be D A. The anionic enzyme substrate can be l,2-dilaui yl-sn-glycero-phospho-( l '-rac- glycerol) (DLPG).

[0078] As used herein, the term "cationic enzyme substrate" can refer to any suitable caiionic enzyme substrate that can be used as described herein. The cationic enzyme substrate can be a substrate that is not so large that it cannot form a complex with an oligomer. The cationic enzyme substrate can be a suitable cleavable amphophilic substrate. The cationic enzyme substrate can be a cationic phospholipid, such as cationic dimyristoyltrimethylammonium propane (DMTAP). The cationic enzyme substrate can be a cationic peptide or a small protein with a net -positive patch. The cationic enzyme substrate can be DNA. The cationic enzyme substrate can be lauroyi choline. The cationic enzyme substrate can be acetylcholine.

[0079] As used herein, the term "phenolate" refers to a p-phenolate, e.g., a phenolate attached via the 4-position. p-Phenylene Ethynylene Compounds for Inducing Germination of Microtia! Spores.

[0080] In various embodiments, a method for inducing the germination of microbial spores with a p-phenylene ethynylene compound is described herein. The microbial spores can be at least one of a Bacillus anthracis, a Bacillus atrophaeus, a. Bacillus cereus, and a. Bacillus subtilis,

[0081] In various embodiments, the p-phenylene ethynylene compound includes a repeating u it which can have the structure: The variable can have the structure:

i...Z-~L ² -- R ²

The variable Z, at each occurrence, can be independently chosen from -CH ₂ -, - 0-, -S-, and -NH-. The variable L ² can be independently chosen from a (C< - C5o)hydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R at each occurrence, can be independently chosen from -H, (Ci-C5)alkyi, -SO ₃ ^" , -CO?. ^" , ^■■ H2PO4 ^" , HPO4 ^{2 "} , P0 ₄ ^3" , phenolate, « V ⁽ Y-, )alkv l-{ -siibsi iniied 1,4- diazabicyclo [2.2.2] octane- 1 ,4-diium)-, 3 -methylimidazolium and -N ⁺ (R ^a )J wherein at each occurrence R ^/ is independently (Ci -Cs)aikyl. The variable V, at each occurrence can be independently chosen from a bond and

The variable j can be about 0 to about 4,

[0082] In various embodiments, the p-phenyfene ethynylene compoun can include a repeating unit having the structure:

The variable R: , can be independently chosen from -Ν (¾)3,

The variable n can be about 2 to about 4.

[0083] In various embodiments, the p-phenyfene ethynylene compound can have the structure:

The variable R can have the structure: The variable Z, at each occurrence, can be independently chosen from -CH ₂ ~, ^■■ 0-, -S-, and -NH-. The variable L ² , at each occurrence, can be independently chosen from a (C i -C5o)hydrocarbylene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R , at each occurrence, can be independently chosen from -H, (Ci-Cs)alkyl, (Ci- Cio)alkyl-(l ,4-substituted l,4-diazabicyclo[2.2.2]octane-l,4-dimm)-, 3- methylimidazolium and N ¹ (R ^'v )i wherein at each occurrence R' ¹ is independently (Ci-Cs)alkyl. The variable j can be about 0 to about 4. The variable L ^! , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(0)0-(Ci-Cio)hydrocarbyl, -C(0) ^' NH-(Ci - Cjo)hydrocarbyl, and C(0)OH. The variable m can be about 1 to about Li [0084] In various embodiments, the p-phenylene ethynylene compound can have the structure:

The variable R ^J , at each occurrence, can be independently chosen from - N ⁺ (CH ₃ ) ₃ ,

The variable n can be about 2 to about 4. The variable A, at each occurrence can be independently chosen from -H and -C(0)0-(Ci-Cs)alkyl. In various embodiments, the variable A can be -C(0)OCH ₂ CH ₃ . The variable q can be about 1 to about 50, about 1 to about 40, about 1 to about 30, about 1 to about 20, about 1 to about 10, about 1 to about 5, about 1 to about 3, and about 1, 2, 3, 4, 5, 7, 10, 20, 30, 40, and about 50 or greater. [0085] In various embodiments the p-phenyiene ethynylene compound can have the structure:

The variable R ¹ , at each occurrence can have the structure:

— Z— L ² — R ²

5

The variable Z, at each occurrence, can be independently chosen from -CH ₂ -, -

0-, -S-, and -NH-. The variable L ^7' , at each occurrence, can be a (Ci -

Csojhydrocarby!ene internipted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NB-. The variable R ² , at each occurrence can be independently chosen from ^" (R ^' )3 , (Ci -Cio)aikyl-(l,4- substituted 1 ,4-diazabicyclo [2.2.2]octane- 1 ,4-diium)-, and 3-methylimidazolium. The variable R ^A , at each occurrence, can be independently (Ci-Cs)alkyl. The variable p can be about 1 to about 10, about 1 to about 7, about 1 to about 5, about 1 to about 3, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

10086] In various embodiments, the variable Z, at each occurrence, can be -0-. The variable ΙΛ at each occurrence, can independently be a (Ci- C5)alkyl. The variable R ² , at each occurrence, can be independently chosen from -N ^"h fCH ^{3 )} ₃ ,

The variable p can be about 1 to about 5, about 1 to about 3, or about 1 , 2, 3, 4, or about 5 or greater.

10087] In various embodiments, the p-phenylene ethynylene compound can have the structure: The variable P can be about 1, 2. 3, 4, or about 5 or sreater. Method for Detecting Enzymes

[0088] In various embodiments, a method for detecting enzymes is described herein. The method includes (i) introducing an enzyme to a composition including a p-phenylene ethynylene compound and an enzyme substrate; and (ii) analyzing the change in fluorescence of the p-phenylene ethynylene compound following introduction of the enzy me. The introducing step (i) can include introducing the p-phenylene ethynylene compound and the enzyme substrate to a sample which includes an enzyme. Further, the introducing step (i) can include introducing a sample which includes an enzyme to the p-phenylene ethynylene compound and the enzyme substrate. In various embodiments, the p-phenylene ethynylene compound and the enzyme substrate form a complex. In various embodiments, the introduction step (i) and the analyzing step (ii) occur in an aqueous environment.

[0089] In various embodiments, the fluorescence of the p-phenylene ethynylene compound can decrease following the introduction of the enzyme. The fluorescence can decrease due to a molecular transformation of the enzyme substrate to an entity or entities that do not complex with the p-phenylene ethynylene compound.

[0090] In various embodiments, the the p-phenylene ethynylene compound can be a cationic p-phenylene ethynylene compound. In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable R can have the structure:

— Z— i ^~ — F¾ ^~

5

The variable Z, at each occurrence, can be independently chosen from -CH ₂ -, - 0-, -S-, and -NH-. The variable L ^"' , at each occurrence, can be independently chosen from (Ci -Csojhydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (C _t -C5)alkyl, -SO ₃ ^" , - CO . . -H ₂ PO ₄ ^" , l i PO. . i'0., \ phenolate, -TT(R ^A ) ₃ , i ( _r ( i^a !kyi-i i .4- substituted 1 ,4-diazabicyclo[2.2.2]octane- 1 ,4-diium)-, and 3-methylimidazolium. The variable R ^A , at each occurrence, can be independently (C i -Cs ^' Jalkyl.

Further, at least one R ² can be independently chosen froni (R ^A )3 , ί ( ^' i ··

Cio)alkyl-(l ,4-substituted l,4-diazabicyclo[2.2.2]octane-l ,4-diium)-, and 3- methylimidazoiium, such that the cationic p-phenylene ethvnylene compound has a net positive charge. The variable j can be about 0 to about 4, about 1 to about 2, or 0, i, 2, 3, or 4. The variable L ¹ , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or imsubstituted -C(O)O-(Ci-C ₁₀ )hydrocarbyl, and -C(0) H-(Ci- C io)hydrocarbyl. The variable m can be about 1 to about 10, about 1 to about 7 about 1 to about 5, about 1 to about 3 or about 1 , 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[00 1] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, is independently chosen from -H and - C(0)0-(C ₁ -C5)alkyl. The variable q is about 1 to about 5, about 1 to about 3, or about 1 , 2, 3, 4, or about 5 or greater.

[0092] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure: CH ₃ CH CH CHQ

The variable s can be about 1 to about 3, or about 1 , 2, or about 3 or greater. 10093] In various embodiments, the enzyme substrate can be an anionic enzyme substrate. For example, the anionic enzyme substrate can be 1,2- dilauroyl-sn-glycero-phospho-( -rac-glycerol) (DLPG), having the structure:

In various embodiments, the p-phenyiene ethynylene compound is an anionic p-phenyiene ethynylene compound. In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable R can have the structure:

— Z— L ² — R ²

The variable Z, at each occurrence, can be independently chosen from -CH ₂ -, - 0-, -S-, and -NH-. The variable ΙΛ at each occurrence, can be independently chosen from (Ci -Cso)hydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ci-C5)alky1, -SO ₃ ^" , - C0 ₂ ^" , -H2PO4 ^" , HPO4 ^2" , P04 ^"5' , and phenolate. Further, at least one R" can be an anionic group such as SO3 ^" , -CO?. ^" , -H2PO4 ^" , HPO4 ^2" , PO4 ^' ' ^" , or phenolate, such that the anionic p-phenyiene ethynylene compound can have a net negative charge. The variable j can be about 0 to about 4, about 1 to about 2, or 0, 1, 2, 3, or 4. The variable L ^! , at each occurrence, can be independently chosen from a bond and ' \...

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(0)0-(C _} -C-.o)hydrocarbyi, and -C(0)NH-(Ci - C io)hydrocarbyL The variable m can be about 1 to about 10, about 1 to about 7 about 1 to about 5, about 1 to about 3 or about 1 , 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable R ³ , at each occurrence, can be independently chosen from SO ₃ ^" , - C0 ₂ ^" , -H2PO4 ^" , HPO ₄ ^2" , PO ₄ ^3" , and phenolate. The variable R ^J can be -SO ₃ ^' . The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, is independently chosen from -H and - C(0)0-(Ci-C5 )a3kyl. The variable q is about I to about 5, about 1 to about 3, or about 1, 2, 3, 4, or about 5 or greater.

[0096] In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3 or about 1, 2 or about 3 or greater. [ΘΘ97] In various embodiments, the enzyme substrate can be a cationic enzyme substrate. The cationic enzyme substrate can be a substituted or unsubstituted

The cationic enzyme substrate can be a substituted or unsubstituted (Ci- C ₂ 5)alkyi-C(0)0-(C < -C ₄ iH lky l -N i C ^' i 1 > ) ·.. In various embodiments the cationic enzyme substrate can be chosen from lauroyl choline and acetylcholine. The cationic enzyme substrate can be lauroyl choline, [0098] In various embodiments, the enzyme can be any suitable enzyme.

For example, the enzyme can be a protolytic enzyme, a DNA restriction enzyme, a phosphatase, or a kinase. In various embodiments, the enzyme can be chosen from p ospho lipase Al, phospholipase A2, phospholipase C, and acetyl cholinesterase,

10099] In various embodiments, the method includes (i) introducing an enzyme to a composition including a p-phenyiene ethynylene compound and an enzyme substrate; and (ii) analyzing the change in fluorescence of the p- phenylene ethynylene compound following introduction of the enzyme. The p- phenyle

The variable s can be about 1 to about 3, or about I, 2 or about 3 or greater. The enzyme substrate can be l ,2-dilauroyl-sn-glycero-phospho-( -rac-glycerol). In various embodiments, the enzyme can be any suitable enzyme. For example, the enzyme can be a protolytic enzyme, a DNA restriction enzyme, a phosphatase, or a kinase. The enzyme can be at least one of phospholipase Al , phospholipase A2, and phospholipase C.

[00100] In various embodiments, the method can include (i) introducing an enzyme to a composition including a p-phenyiene ethynylene compound and an enzyme substrate; and (ii) analyzing the change in fluorescence of the p- phenylene ethynylene compound following introduction of the enzyme. The p- phenyle

The variable s can be about 1 to about 3, or about 1 , 2 or about 3 or greater. The enzyme substrate can be lauroyl choline. The enzyme can be any suitable enzyme. The enzyme can be a phospholipase (e.g., PLA1 , PLA2, PLC, PLB). The enzyme can be butyrylcholinesterase. The enzyme can be

acetylcholinesterase.

Sensor for Detecting Enzymes

[00101] In various embodiments a sensor is described herein. The sensor may be a sensor for the detection of enzymes. The sensor inc ludes a p- phenylene ethynylene compound and an enzyme substrate. In various embodiments, the ρ-phenylene ethynylene compound can be a charged p- phenylene ethynylene compound and the enzyme substrate can be an oppositely charged enzyme substrate. In various embodiments, the p-phenylene ethynylene compound and the enzyme substrate form a complex.

[00102] In various embodiments, the the p-phenylene ethynylene compound can be a cationic p-phenylene ethynylene compound. In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable R can have the structure:

— Z— L ² — R ²

The variable Z, at each occurrence, can be independently chosen from -CH ₂ -, - 0-, -S-, and -NH-. The variable L ² , at each occurrence, can be independently chosen from (Ci -Cso jhydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -Nil-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ct-C5)alkyl, -SO ₃ ^" , - C0 ₂ ^" , -H2PO4 ^" , HPO4 ^2" , P0 ₄ ^3" , phenolate, -> ( ^A )3 , (Ci -C _{! 0} )alkyl-(1 ,4- substituted l ,4-diazabicycio[2,2.2]octane- l ,4-diium)-, and 3-methylimidazolium. The variable R ^A , at each occurrence, can be independently (C i -Cs)a]kyl.

Further, at least one R can be independently chosen from N ^÷ (R ^A )3 , (C i ~ Cio)alkyl-(l ,4-substituted l,4-diazabicyclo[2.2.2]octane- l ,4-diium)-, and 3- methylimidazolium, such that the cationic p-phenylene ethynylene compound has a net positive charge. The variable j can be about 0 to about 4, about 1 to about 2, or 0, 1, 2, 3, or 4. The variable L , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, cars be independently chosen from -H, substituted or unsubstituted -C(0)0-(C i -C io)hydrocarbyl, and -C(0) H-(Ci- Cio)hydroca.rbyl. The variable m can be about 1 to about 10, about 1 to about 7 about 1 to about 5, about 1 to about 3 or about 1 , 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[00103] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable R', at each occurrence, can be independently chosen from - N ( C M , ⁾ , .

The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, can be independently chosen from -H and ^■■ C(0)0-(Ci-Cs)a3kyl. The variable q can be about 1 to about 5, about 1 to about 3, or about 1 , 2, 3, 4, or about 5 or greater,

[ΘΘ104] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3, or about 1, 2 or about 3 or greater. [00105] In various embodiments, the enzyme substrate can be an anionic enzyme substrate. For example, the anionic enzyme substrate can be 1 ,2- dilauroyl-sn-glycero-phospho-(l '-rae-glyceroi).

[ΘΘΪ 06] In various embodiments, the p-phenylene ethynylene compound can be an anionic p-phenylene ethynylene compound. In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable R can have the structure:

1— Z— L ² — R ²

The variable Z, at each occurrence, can be independently chosen from -CH ₂ -, - 0-, -S-, and -NH-. The variable L\ at each occurrence, can be independently chosen from (Ci -C5o)hydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -8-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ci-Cj jalkyl, -SO-, ^" , - C0 ₂ ^" , -H2PO4 ^" , HPO ₄ ^2" , PO ₄ ^"5' , and p enolate. Further, at least one R ^" can be an anionic substituent such as -SO3 ^" , -C0 ₂ ^" , -H ₂ PCV, HP(V ^~ , PCV ^" , or phenolate, such that the anionic p-phenylene ethynylene compound can have a net negative charge. The variable j can be about 0 to about 4, about 1 to about 2, or 0, 1, 2, 3, or 4. The variable L ¹ , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(0)0~(Ci-Cio)hydrocarbyl, and -C(0)NH-(Ci- CjojhydrocarbyL The variable m can be about 1 to about 10, about 1 to about 7 about 1 to about 5, about 1 to about 3 or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[ΘΘΪ 07] In various embodiments, the anionic p-pheny3ene ethynylene compound can have the structure:

The variable R ³ , at each occurrence, can be independently chosen from -SO ₃ ^" , - C0 ₂ ^" , -H2PO4 ^" , HPO ₄ ^2" , PO ₄ ^3" , and phersolate. The variable R ^J can be -SO3 ^" . The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, can be independently chosen from -H and ^■ · C(0)0-(Ci -C5 )a1ky1. The variable q can be about i to about 5, about 1 to about 3 , or about 1, 2, 3, 4, or about 5 or greater.

[00108] In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3 or about 1, 2 or about 3 or greater. [ΘΘ109] In various embodiments, the enzyme substrate can be a cationic enzyme substrate. The cationic enzyme substrate can be a substituted or unsubstituted

The cationic enzyme substrate can be a substituted or unsubstituted i ( ^' > ··

C ₂ s)alkyl-C(0)0-(C■ -C ₄ )alkyl-N ^1" (CH ₃ )3. In various embodiments the cationic enzyme substrate can be chosen from lauroyi choline and acetylcholine. The cationic enzyme substrate can be lauroyi choline.

[ΘΘ110] In various embodiments the sensor includes a cationic p- phenylene ethynylene compound and an anionic enzyme substrate. The p- phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3, or about 1, 2 or about 3 or greater. The anionic enzyme substrate can be l,2-dilaiiroyl-sn-glycero-phospho-( -rac- glycerol).

[00111 ] In various embodiments the sensor includes a p-plienylene ethynyiene compound and an enzyme substrate. The p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3, or about 1, 2 or about 3 or greater. The enzyme substrate can be lauroyl choline.

Method of Protein Analysis

100112] In various embodiments, a method for protein analysis is described herein. The method includes (i) introducing a p-phenylene ethynylene compound to a biological sample including at least one protein and (ii) analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample including the at least one protein.

[00113] It has been unexpectedly discovered that p-phenylene ethynylene compounds can be employed for the selective detection of proteins in biological samples. For example, p-phenylene ethynylene compounds can be used to detect the presence of amyloids in tissue samples. Further, it has been unexpectedly discovered that p-phenylene ethynylene compounds display a distinguishable response to monomeric and fibrillary proteins. For example, p-phenylene ethynyiene compounds show display a distinguishable response to monomeric and fibrillary Αβ-40 amyloid and a-symiclein.

[00114] In various embodiments, the fluorescence of the p-phenylene ethynylene compound is analyzed prior to being introduced to the biological sample including the at least one protein. In various embodiments, analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample including the at least one protein includes analyzing the spectral changes between the fluorescence of the p-phenylene ethynylene compound of step (i) and the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample including the at least one protein of step (ii). In various embodiments, the morphology of the protein in the biological sample is determined by analyzing spectral changes between the fluorescence of the p-phenylene ethynylene compound of step (i) and the fluorescence of the p-phenyiene et hynylene compound in the presence of t he biological sample including the at least one protein of step (ii). In various embodiments, the spectral changes in the fluorescence of the p-phenylene ethynylene compound between step (i) and step (ii) are induced by changes in the conformational freedom of the p-phenylene ethynylene compound between step (i) and step (ii).

fOOiiS] In various embodiments, the p-phenyiene ethynylene compound can have the structure:

The variable R can have the structure:

Z-~L ² ~~R ²

The variable Z, at each occurrence, can be independently chosen from -CH ₂ ~, - 0-, -S-, and -NH-. The variable L ² , at each occurrence, can be independently chosen from (C ₁ -Cso)hydrocarby3ene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ci-C5)alkyl, -SO ₃ ^" , - CO2 ^" , -H2PO4 ^" , HPO4 ^2" , phenolate, -N ⁺ (R ^A ) ₃ , (Ci-Ci ₀ )a1kyl-(1,4- substituted l,4-diazabicyclo[2.2.2]octane-l ,4-diium)-, and 3-methylimidazoIium. The variable R ^A , at each occurrence, can be independently (C i-C5)alkyl. The variable ] can be about 0 to about 4, about 1 to about 2, or 0, 1 , 2, 3, or 4. The variable ίΛ at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(Q)0-(Ci-Cio)hydrocarbyl, and -C(0)NH-(Ci - C io)hydrocarbyL The variable m can be about ! to about 10, about 1 to about about 1 to about 5, about 1 to about 3 or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[00116] In various embodiments, the p-phenylene ethynylene compound can have the structure:

The variable R ^J , at each occurrence, can be independently chosen from ^{■ T} _—c- _R 6H' Ί _{1 !} 3,

The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, can be independently chosen from -H and - C(0)0-(Ci -C5)a1kyl. The variable q can be about 1 to about 5, about 1 to about 3, or about 1, 2, 3, 4, or about 5 or greater

[00117] In various embodiments, the p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3, or about 1 , 2 or about 3 or greater.

[00118] In various embodiments, the protein can be at least one of an amyloid beta protein, Αβ-40, Αβ-42, tau, and a-synuclein, islet amyloid precursor protein, Huntingdn, prio , !ysozyme, TDP-43 (transactive response DNA-binding protein 43), FUS (fused in sarcoma), and insulin.

[00119] In various embodiments, the method includes (i) analyzing the fluorescence of a p-phenylene ethynylene compound; (ii) introducing the p- phenylene ethynylene compound to a biological sample including at least one protein; (iii) analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample including the at least one protein; and (iv) determining the morphology of the at least one protein in the biological sample by analyzing spectral changes between the fluorescence of the p-pheny!ene ethynylene compound of step (i) and the fluorescence of the p- phenylene ethynylene compound in the presence of the biological sample including the at least one protein of step (iii). The p-phenylene ethynylene compound can have the structure:

/

The variable s can be about 1 to about 3, such as about 1. The protein can be at least one of an amyloid beta protein, Αβ-40, Αβ-42, tau, and a-syrmelein, islet amyloid precursor protein, Huntingtin, prion, lysozyme, TDP-43 (transactive response DNA-binding protein 43), FUS (fused in sarcoma), and insulin.

Method of Detecting Chemical Agents

[00120] In various embodiments, a method for detecting a chemical agent is described herein. The method includes (i) exposing a sensor composition including a complex including a p-phenylene ethynylene compound and an enzyme substrate to a sample; (ii) introducing an enzyme to the sensor composition of step (i); and (iii) analyzing the change in fluorescence of the p- pheny lene ethynylene compound between the exposing step (i) and the introducing an enzyme step (ii).

[00121] The sample may be, but is not limited to, any solution that has been exposed to a potential chemical agent. Chemical agents include, without limitation, organophosphate nerve agents (e.g. sarin, soman, tabun, VX, and VR) and G-type nerve agents (e.g. diethyl phosphoramidate). The chemical agent can be a pesticide or insecticide, such as an organophosphate pesticide or insecticide, such as malathion (e.g.. Diethyl 2-

[(dimethoxyphosphorothioyl)sulfanyl]butanedioate)or chiorpyrifos (e.g., Ο,Ο- diethyl 0-3,5,6-trichioropyridin-2-yl phosphorofhioate). In various embodiments, a. change in fluorescence between the exposing step (i) and the introducing an enzyme step (ii) indicates the presence of a chemical agent that does interact with the enzyme. In various embodiments, a minimal change in fluorescence between the exposing step (i) and the introducing an enzyme step (ii) indicates the presence of a chemical agent thai does interact with the enzyme.

[00123] In various embodiments, the p-phenylene ethynylene compound can be a cationic p-phenylene ethynylene compoimd. In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable R ¹ can have the structure:

|_Z_L ² -R ²

The variable Z, at each occurrence, can be independently chosen from - ^■ €¾ - , - 0-, -S-, and -NH-. The variable L ² , at each occurrence, can be independently chosen from (Ci ~C5o)hydroearbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ci -Cs jalkyl, -8€V, ^■■ CO . . -H2PO4 ^" , HPO4 ^2" , P0 ₄ ^3" , phenolate, - ^r (R ^A ) ₃ , (Ci -C i ₀ )alkyl-(1 ,4- substituted l ,4-diazabicycio[2,2.2]octane- l ,4-diium)-, and 3-methylimidazoliiim. The variable R ^A at each occurrence, can be independently (C i -C5 )alkyl.

Further, at least one R ^7' can be independently chosen from ^÷ (R ^A )3 , i C ^' 1 ··

C io)alkyl-(l ,4-substituted l,4-diazabicyclo[2.2.2]octane- l ,4-diium)-, and 3- methylimidazolium, such that the cationic p-phenylene ethynylene compound has a net positive charge. The variable j can be about 0 to about 4, about 1 to about 2, or 0, I, 2, .3, or 4. The variable L ¹ , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(0)0-(C _} -C-. o)hydrocarbyi, and -C(0)NH-(Cj - C io)hydrocarbyl. The variable m can be about 1 to about 10, about 1 to about

3.3 about 1 to about 5, about 1 to about 3 or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[00124] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable R ^J , at each occurrence, can be independently chosen from ^{■ T} _—c- _R 6H' Ί _{1 !} 3,

The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, can be independently chosen from -H and - C(0)0-(Ci -C5)a1kyl. The variable q can be about 1 to about 5, about 1 to about 3, or about 1, 2, 3, 4, or about 5 or greater,

[00125] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3, or about 1 , 2 or about 3 or greater.

[00126] In various embodiments, the enzyme substrate can be an anionic enzyme substrate. For example, the anionic enzyme substrate can be 1,2- dilauroyl-sn-giycero-phospho-( i '-rac-glyceroi). In various embodiments, the enzyme can be any suitable enzyme. For example, the enzyme can be a protolytic enzyme, a DNA restriction enzyme, a phosphatase, or a kinase. In various embodiments the enzyme is chosen from phospho lipase Al , phosphoiipase A2 and phosphoHpase C. [00127] In various embodiments, the p-phenylene ethynylene compound is an anionic p-phenylene ethynylene compound. In various embodiments, the anionic p-phenylene ethynylene compound can have the structure: The variable R ¹ can have the structure:

The variable Z, at each occurrence, can be independently chosen from -CH?-, - 0-, -S-, and -NH-. The variable L ² , at each occurrence, can be independently chosen from (Ci -Cso jhydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ci-Cs)alkyl, -SO3 ^" , - CO2 ^" , -H2PO4 ^" , HPO4 ^2" , PO4 ^3" , and phenolate. Further, at least one R ² can be an anionic group such as -SO3 ^" , -CO?. ^" , -H2PO4 ^" , HP0 ₄ ^2~ , P0 ₄ ^3" , or phenoiate, such that the anionic p-phenylene ethynylene compound can have a net negative charge. The variable ] can be about 0 to about 4, about 1 to about 2, or 0, 1 , 2, 3, or 4. The variable L ¹ , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(0)0-(C 1 -C io)hydrocarbyl, and -C(0) H-(Ci- Cio)hydroca.rbyl. The variable m can be about 1 to about 10, about 1 to about 7 about 1 to about 5, about 1 to about 3 or about 1 , 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[00128] In various embodiments, the anionic p-phenylene ethynylene compound can have the structure: The variable R , at each occurrence, can independently be chosen from -SO3 ^" , - CO/, -H ₂ P0 ₄ ^" , HPO4 ^2" , Pi) i ^: . and phenolate. The variable R ³ can be -SO3 ^" . The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, can be independently chosen from -H and - C(0)0-(Ci -C5)alkyl. The variable q can be about 1 to about 5, about I to about 3, or about 1, 2, 3, 4, or about 5 or greater.

[00129] In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3 or about 1 , 2 or about 3 or greater.

[00130] In various embodiments, the enzyme substrate can be a cationic enzyme substrate. The cationic enzyme substrate can be a substituted or unsubstituted (C 1 -C ₂₅ )hydrocarbyl-C(0)0-(C 1 -C io)alkyl-N ⁺ ((C 1 -C ₅ )alkyl) ₃ . The cationic enzyme substrate can be a substituted or unsubstituted (Q- C ₂ 5)a!kyl-C(0)0-(Ci-C i )alkyl-N ^" (CH ₃ ) ₃ . in various embodiments the cationic enzyme substrate can be chosen from lauroyi chohne and acetylcholine. The cationic enzyme substrate can be lauroyi choline.

[00131] The enzyme can be any suitable enzyme. The enzyme can be a phosphoiipase (e.g., PLA1, PLA2, PLC, PLB). The enzyme can be

butyrylcholinest erase. In various embodiments, the enzyme can be

acetylcholinesterase.

[00132] In various embodiments includes (i) exposing a sensor composition including a complex including a p-phenylene ethynylene compound and an enzyme substrate to a sample; (ii) introducing an enzyme to the sensor composition of step (i); and (iii) analyzing the change in fluorescence of the p- phenylene ethynylene compound between the exposing step (i) and the introducing an enzyme step (ii). The p-phenylene ethynylene compound can have the structure:

The variable s can be 1. The enzyme substrate can be lauroyl choline. A change in fluorescence between the exposing step (i) and the introducing an enzyme step (ii) can indicate the presence of a chemical agent that does interact with the enzyme.

Sensor for Detecting the Presence of a Chemical Agent

|00133] In various embodiments, a sensor for detecting the presence of a chemical agent is described herein. The sensor including a sensor composition including a complex including a p-phenylene ethynylene compound and an enzyme substrate.

[00134] In various embodiments, the the ρ-phenylene ethynylene compound can be a cationic p-phenylene ethynylene compound. In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable R ¹ can have the structure:

— Z— L ² — R ²

The variable Z, at each occurrence, can be independently chosen from -CH?-, - 0-, -S-, and -NH-. The variable L ^' , at each occurrence, can be independently chosen from (Ci -Cso)hydrocarby1ene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ci-Cs)alkyl, -SO3 ^" , - CO?/, - I h PO.i . HPO4 ^2" , P(V\ phenolate, -N ⁺ (R ^A ) ₃ , i C C ^' i.-. ialkyM 1 .4 - substituted l,4-diazabicyclo[2.2.2]octane-l ,4-diium)-, and 3-methylimidazolium. The variable R ^A , at each occurrence, can be independently iC Cs)alky3.

Further, at least one R ² can be independently chosen from N ^'!' (R ^A )3, (Ci- C io)alkyl-( 1 ,4-substituted 1 ,4-diazabicyclo[2.2.2]octane-l ,4-diium)-, and 3- meihylimidazoiitmi such thai the cationic p-phenylene ethynylene compound has a net positive charge. The variable ] can be about 0 to about 4, about 1 to about 2, or 0, 1, 2, 3, or 4. The variable L ¹ , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(0)0-(Ci -Cio)hydrocarbyl, and -C(0)NH-(Ci- CiojhydrocarbyL The variable m can be about 1 to about 10, about 1 to about 7 about 1 to about 5, about 1 to about 3 or about 1 , 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[00135] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable R ^J , at each occurrence, can be independently chosen from - N ( CS ! : ,. , . a anndil

The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, can be independently chosen from -H and - C(0)0-(Ci -C5)a1kyl. The variable q can be about 1 to about 5, about 1 to about 3, or about 1, 2, 3, 4, or about 5 or greater,

[00136] In various embodiments, the cationic p-phenylene ethynylene compound can have the structure:

The variable s can be about 1 to about 3, or about 1, 2 or about 3 or greater.

[00137] In various embodiments, the enzyme substrate can be an anionic enzyme substrate. For example, the anionic enzyme substrate can be 1 ,2- dilauroy1-so-glycero-phospho-( 1 '-rac-glycerol).

[00138] In various embodiments, the p-phenyiene ethynylene compound can be an anionic p-phenylene ethynylene compound. In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable R ^l can have the structure

The variable Z, at each occurrence, can be independently chosen from -CH?.-, - 0-, -S-, and -NH-. The variable ΙΛ at each occurrence, can be independently chosen from (Ci -Cso)hydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-. The variable R ² , at each occurrence, can be independently chosen from -H, (Ci-C5)alky1, -SO ₃ ^" , - C0 ₂ ^" , -H ₂ P0 ₄ \ HPO ₄ ^2" , P0 ₄ ^3" , and phenolate. Further, at least one R can be an anionic group such as -SO3 -CO? ^" , -i I > ΡΟ· . HP0 ₄ ^2" , PQ4 ^J" , or phenolate, such that the anionic p-phenylene ethynylene compound can have a net negative charge. The variable j can be about 0 to about 4, about 1 to about 2, or 0, 1, 2, 3, or 4. The variable L ^! , at each occurrence, can be independently chosen from a bond and

The variable A, at each occurrence, can be independently chosen from -H, substituted or unsubstituted -C(0)0-(C ₁ -C ₁ o)hydrocarbyl, and -C(0)NH-(Cj - Cio)hydrocarbyl. The variable m can be about 1 to about 10, about 1 to about 7 about 1 to about 5, about 1 to about 3 or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or about 10 or greater.

[00139] In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

The variable R ^" , at each occurrence, can be independently chosen from -SO ₃ ^" , - C0 ₂ ^" , -H2PO4 ^" , HPO ₄ ^2" , PO4 ^3" , and phenolate. The variable R ^J can be -SO3 ^" . The variable n can be about 2 to about 4, or about 2, 3, or about 4 or greater. The variable A, at each occurrence, can be independently chosen from -H and ^■ · C(0)0-(Ci -C5 )a1ky1. The variable q can be about i to about 5, about 1 to about 3 , or about 1, 2, 3, 4, or about 5 or greater.

[00140] In various embodiments, the anionic p-phenylene ethynylene compound can have the structure:

-SO,

The variable s can be about 1 to about 3 or about 1 , 2 or about 3 or greater.

[ΘΘ141] In various embodiments, the enzyme substrate can be a cationic enzyme substrate. The cationic enzyme substrate can be a substituted or ^substituted (C 1 -C ₂₅ )hydrocarbyl-C(0)0-(C 1 -C ₁₀ jalky 1- ^; ((C i -C ₅ )alkyl) ₃ . The cationic enzyme substrate can be a substituted or unsubstituted (Ci- C25)a1kyl-C(0)0-(C 1 -C ₄ )alk l-N ⁺ (CH ₃ )3. In various embodiments the cationic enzyme substrate can be chosen from lauroyl choline and acetylcholine. The cationic enzyme substrate can be lauroyl choline.

[00142] In various embodiments, the sensor includes a sensor composition including a complex including a p-phenylene ethynylene compound and an enzyme substrate. The p-phenylene ethynylene compound can have the structure:

The variable s can be 1. The enzyme substrate can be lauroyl choline.

Examples

[ΘΘ143] Various embodiments of the present invention can be better understood by reference to the following Examples which are offered by way of illustration. The present invention is not limited to the Examples given herein. Example 1

Example 1.1.

[00144] Growth and Preparation of Bacillus airophaeus spores.

Bacillus airophaeus (ATCC #9372) spores were obtained from 20% glycerol- suspended spore stock stored at -70 °C. A working batch of B, airophaeus spores was obtained by induced germination and subsequent sporulation on sporulation agar. Using a sterile inoculation loop, spore colonies were scraped off the sporulation agar, suspended in sterile DT water, and filtered through glass wool Spores were then washed three times via centrifugation (15 minutes, 4.4k RPM), with the pellet being resuspended in 50% ethanoi, and stored at 4 °C for 12 hours to provide time for vegetative cell death. Spores were then washed another three times via centrifugation and resu sponsion in sterile DI water. Spores were then aliquoted into glass vials and stored at 4 °C until use. The concentration of spores in these aliquots was determined with a hemocytometer. Example 1.2

[00145] Growth and Preparation ot Bacillus airophaeus vegetative cells. Bacillus airophaeus vegetative cells were obtained by adding 1 mL of prepared spore aliquot to 50 mL Bacto tryptic soy broth (TSB; Beekton

Dickinson), which was then incubated for 18 hours at 30 °C with shaking (250 RPM), Vegetative ceils were prepared for analysis by a triple-wash step consisting of three centrifiigations of 4.4k RPM for 15 minutes each; with pellets resuspended in 0.85% aCl (physiological saline solution). The resulting cell concentrations were determined with a hemocytometer.

Example 1.3

[00146] Bacillus airophaeus viability testing. Viability testing was carried out at concentrations of 10' bacteria/mL in 0.85% NaCL p-Phenyiene ethynylene compound ("PE") concentrations of 10 i;g mi . and 20 μg/nlL were used to target B. airophaeus vegetative cells and spores, respectively. Samples were prepared at volumes of I ml_ in 0.5 -dram glass vials (VWR; Radnor, PA), and exposed to light or dark conditions for varying time periods. Light experiments were carried out in a 10-iamp LZC-ORG phoioreactor (Luzchem Research; Ontario, Canada) fitted with UVA lamps (Hitachi FL8BL-B) exhibiting a power density of 0,975 mW/cm ² , over a wavelength range of 316- 400 nm (centered at 350 nm). Samples were loaded into a rotating carousel in the center of the phoioreactor to ensure uniform light exposure. Following light exposure, samples were stained with a membrane -permeable stain, SYTO 21 (Life Technologies; Carlsbad, CA), and a membrane-impermeable stain, propidmm iodide (PT; Life Technologies). Membrane-permeable nucleic acid dyes such as SYTO 21 stain nucleic acids throughout a bacterium, independent of membrane damage. On the other hand, membrane- impermeable stains such as propidmm iodide selectively stain nucleic acids in bacteria with compromised membranes. Vegetative cell samples were permitted 15 minutes to stain at room temperature (in the dark), while spores were allowed 45 minutes to stain at room temperature (also in the dark). Staining of spores with hydrophilic nucleic acid stains, such as propidmm iodide, takes longer than that of vegetative cells due to the fact that a spore's UNA is supercoiled within the inner membrane, which is inherently impermeable to hydrophilic molecules.

[00147] Stained samples were then evaluated with an Accuri C6 (Becton

Dickinson) flow cytometer equipped with a 488 nm, 50 mW laser. SYTO 21 fluorescence was quantified with the FL1 detector at 530 ± 15 nm; PI fluorescence was quantified with the FL3 detector at wavelengths exceeding 670 nm.

[00148] Two thresholds were used in viability analysis; the first was a forward scatter (FSC) threshold that ensured that only events exceeding 50,000 FSC units were included in the data sets. Lowering the forward scatter threshold to 50,000 helps ensure that small Bacillus spores aren't omitted as events. The second threshold was specific to the FL1 detector, and ensured that only events exhibiting some degree of SYTO 21 uptake (at least 250 fluorescence units) were included as data points. Bacteria were analyzed at a nominal flow rate of 14 μί/ιηίη, with a stream core diameter of 10 μιη. All samples were evaluated until at least 10,000 events had been recorded. Using B. atrophaeus vegetative cells, the live gate was based on untreated negative controls, while the dead gate was based on positive controls exposed to 70% ethanol for 60 minutes. An additional gate was obtained to denote the fluorescence regions of viable, untreated spores.

Example 1.4

[00149] SEM of Bacillus atrophaeus vegetative cells and spores. Spores exposed to EO-PE (Th,C2), or simply 0.85% NaCl as a negative control, were examined by scanning electron spectroscopy (SEM) (Quanta 250 FEG SEM; FEI; Hillsboro, OR). Samples were fixed in 2,5% glutaraldehyde overnight at room temperature, rinsed in phosphate-buffered saline (PBS), and subsequently dehydrated in ethanol. Dehydrated samples were sputercoated in approximately 12 nm of gold and palladium under vacuum and subsequently analyzed by SEM. Example 1.5

[00150] Growth and Preparation of Bacillus anthracis Sterne. BSL2 agent B. anthracis Sterne was not permitted for use in flow cytometry facilities and thus was prepared and evaluated differently from the aforementioned B. atrophaeus. B. anthracis Sterne spore stocks were prepared as previously described. Briefly, spores were prepared in phage assay broth; sporulation was subsequently confirmed with phase-contrast microscopy, and any remaining vegetative cells were killed with a 40 minute, 68 °C heat treatment. Bacteria were then washed and resuspended in Dulbecco's phosphate-buffered saline (DPBS; Gibco), tittered, aliquoted, and stored at -80 °C, Colony growth of aliquots was evaluated before and after heat treatment (40 minutes at 68 °C) to ensure the absence of vegetative cells.

[00151 ] B. anthracis Sterne vegetative cells were prepared exclusively for the experiments described herein. B. anthracis Sterne spores were removed from frozen storage and thawed at room temperature before 20 μΕ of suspension was streaked onto a tryptic soy agar (TSA) plate. TSA plates were incubated for 16 hours at 37 °C. A sterile inoculation loop was then used to transfer 2 colonies from the TSA plate into 40 mL of brain heart infusion (BHl), along with 200 uL of glycerol. The flask was then aerobically incubated for 16 hours at 37 °C with 250 RPM shaking. To ensure sterility of BHl a second flask was aerobically incubated with 10 mL BHL Following verification of sterility, 200 μL of the inoculated BHl was added to 800 ^iL sterile BHl, vortexed, and subsequently transferred to a disposable cuvette. The absorbance of the cuvette was measured

4.3 at 600 relative to sterile BHL A subculture was then prepared at an OD of 0.1 and aerobieally incubated at 37 °C with shaking until the subculture' s OD reached 1.0 indicating a vegetative cell concentration of 2 x 10' CFU/mL

(confirmed by colony growth on TSA).

[00152] Saline-washed B. anthracis Sterne vegetative cells were exposed to 10 p,g/mL EO-PE (Th,C2) in light and dark conditions for varying time durations, diluted, and streaked onto TSA plates. TSA plates were incubated at 37 °C for 18 hours and the colonies counted to estimate viability. B. anthracis Sterne spores were evaluated by a similar technique, albeit with the

implementation of heat treatment. In this case, samples were diluted, plated, and subsequently heat-treated to kill vegetative cells. Heat treatment is applied via a 68 °C water bath for 30 minutes, such that B. airophaeus vegetative cells are killed; presumably, any resulting colony growth would result from spores and not vegetative cells. Heat-treated samples were also diluted and plated— the difference of colony growt between the heat-treated and non-heat treated samples was used to gauge the percentage of sample which was vegetative cells. Negative controls contained no PE, while heat treatment consisted of submersion in a 68 °C water bath for 30 minutes. Equations 1 .1, 1.2, and 1.3 were used to infer sample populations based on colony growth:

% of CPUs that are Viable Vegetative Cells = 100 X ^CFU - ^CFU » ^T

° CFU

(1. 1 )

% of CPUs that are Viable Spores = 100 x -— ~

^ CFU

(1 .2)

% of CPUs that are nonviable re!ativeve to negative control 00 x

CFU _NC --CFU

CFU _NC

(1.3)

[00153] As used herein, "CPUs" and "CFU" refer to the number of colony forming units on TSA prior to Heat Treatment, CFUHT is the number of colony forming units on TSA after Heat Treatment, and CFUNC is the number of colony forming units on TSA in the negative control (no heat treatment). These equations are implemented in FIG, 5 as a means to monitor viability and germination, under the assumption that heat treated vegetative cells lose their ability to form colonies. All B. anlhracis Sterne experiments (those shown in FIGS. 4 and 5) were conducted in triplicate.

Example 1.5

[00154] Results. PE-indueed cell death was inferred using a

complementary set of nucleic acid stains such that bacteria with intact cell membranes exhibit uptake of SYTO 21, while only cells with compromised membranes exhibit uptake of PL In these studies, flow cytometry was utilized to gauge cell viability by rapid interrogation of dual-stain fluorescence. FIGS. 1A- D illustrate flow cytometry-reported viability of 10,000 B. atrophaeus vegetative cells determined by changes in PI (X-axis) and SYTO 21 (Y-axis) fluorescence; the L Gate represents the live vegetative cells and the D gate represents the dead vegetative cells; B. atrophaeus vegetative were cells suspended in physiological saline solution for 1 hr; A: negative control (0 .ug/mL PE); B: 10 .ug/mL PE in the dark; C: negative control (0 .ug/mL,) in UVA light; D; 10 pg/mL PE in UVA light.

[00155] FIG. ! A illustrates fluorescence emitted from untreated B.

atrophaeus vegetative cells: 1 hr in physiological saline solution at a temperature of 28.5 °C, Under these conditions, 100% of untreated B, atrophaeus vegetative cells retained their ability to form colonies and exhibit greater uptake of SYTO 21 (~10 ³ arbitrary fluorescence units) than PI (~10 ⁴ arbitrary fluorescence units). In this case, cellular membranes remained intact, limiting propidium iodide uptake. The addition of a known membrane-disrupting agent, such as EO-PE (Th,C2), results in a noticeable fluorescence shift (FIG. I B). The structure of EO-PE (Th,C2) is depicted below in Scheme 1 . Following an hour's exposure to this PE at a concentration of 10 μ^ητΐ,, B. atrophaeus cells exhibit uptake of SYTO 21 with the same propensity as untreated cells (FIG. 1A); however, the uptake of PI has increased tenfold, demonstrating that PEs induce moderate membrane damage to the extent that 73% of cells are killed in the absence of light. FIG. 1 C shows that B. atrophaeus vegetative cells are somewhat vulnerable to UVA irradiation, with 3% of bacilli killed in an hour. Significan t killing ofB. atrophaeus vegetative cells was only achieved upon exposure to light-activated PE; an exposure duration of 1 hour causes 99% cell death (FIG. ID). It is important to note that membrane damage to vegetative bacilli rarely results in non-specific uptake of both stains; that is, the uptake of one stain appears to occur independently of the other.

[0015

EO-PE (Th,C2)

[ΘΘ157] Having defined regions of fluorescence characteristic of viable and non- viable B. atrophaeus vegetative cells, flow cytometry was then utilized to determine the extent by which EO-PE (Th,C2) inflicts damage on B.

atrophaeus spores. Spores were treated under the same conditions as the aforementioned vegetative cells (depicted in FIGS. 1 A-D); however, spores were stained with SYTO 21 and PI for 45 minutes, whereas vegetative cells needed just 15 minutes to stain.

[ΘΘΪ 58] FIGS. 2A-D illustrate flow cytometry-reported germination of

10,000 B. atrophaeus spores determined by changes in PI (X-axis) and SYTO 21 (Y-axis) fluorescence; the S gate represents spores, the L Gate represents viable germinating spores, and the D gate represents cells that have died during germination; B, atrophaeus spores were suspended in physiological saline solution for 1 lir; A: negative control (0 ^ig/mL PE) in the dark; B: 20 μg/mL PE in the dark; C: negative control (0 ,ug/mL PE) in UVA light; D: 20 .ug/mL PE in UVA light. Despite a prolonged staining period, the untreated B. atrophaeus spores depicted in FIG, 2A exhibit decreased uptake of both stains relative to the untreated vegetative cells shown in FIG. 1A. Decreased nucleic acid staining in Bacillus spores is attributed to their low water content, relatively small volume, and limited access of stains to centralized supercoiled DMA resulting from an intact inner spore membrane. The S gate is therefore included in FIGS. 2A-D to indicate regions of fluorescence characteristic of untreated B. atrophaeus spores. As can be seen in FIG. 2B, the addition of EO-PE (Th,C2) affects spores' stain uptake in a different manner than was observed with B. atrophaeus vegetative cells in FIG. IB. While exposure to PEs in the dark selectively enhanced uptake of Pi in vegetative cells, the uptake of SYTO 21 is also significantly enhanced in spores following PE exposure in the dark. This non-specific fluorescent enhancement is characteristic of Bacillus spore germination: within 10 minutes of induced germination, spore coat porosity rapidly increases, leading to a water influx event, and thus, increased cell volume and increased uptake of stains.

[00159] This method of interrogation suggests thai the water influx event sufficiently progressed in 39% of spores to the point where the magnitude of stain uptake matched that ofB. atrophaeus vegetative cells. FIG. 2B shows that 61% of spores still fluoresce in a manner characteristic of that of untreated spores (the S gate), which suggests these spores either underwent delayed germination or were not induced to germinate at all. In the absence of light, PE- exposed spores were found to germinate into viable vegetative cells meaning they were capable of forming colonies on TSA, while also exhibiting fluorescence characteristic of late-fog-phase vegetative cells.

100160] Irradiating B. atrophaeus spores with UVA light, alone, does not affect stain uptake, as is shown in FIG. 2C. FIG, 2D shows that exposing spores to light-activated PE also results in non-specific stain uptake; however, in this case, the uptake ratio of membrane impermeable stain (PI) to membrane permeable stain (SYTO 21 ) is increased, resulting in failed germination and inability to form colonies. Therefore, light-activated PE promptly kills most germinating spores— not surprising, given the susceptibility of Bacillus vegetative cells to light-activated PE (FIG. ID). Increasing the PE concentration to 50 or 100 |ig/mL was found to have no increased effect on the death or germination of B. atrophaeus spores, presumably to the inner filter effect.

[00161] The presence of UVA light is significant in achieving significant biocidal activity with cationic PEs, as light-induced inactivation of B. anthracis Sterne is believed to involve three steps. First, the PE is excited from the ground state, So, to its excited singlet state, Si . Second, via intersystem crossing, Si decays to a longer- lived, albeit lower energy, triplet state, S ₃ ; in turn, S ₃ transfers its energy to molecular triplet oxygen, subsequently generating singlet oxygen (Ό ₂ ) and ROS via a type I and type II photoreactions, respectively. Thirdly, ROS and Ό ₂ can locally oxidize lipids, proteins, and nucleic acids. It is evident that the additional level of PE-inflicted damage conferred by the presence of UVA light plays a major role in viability of germinating B, atrophaeus spores. The additional damage inflicted by light activation of PE (as opposed to PE in the dark) may stunt germination by limiting the progression of one or both water influx events, as both fluorescence magnitudes (FIG. 2D) and forward scatter values are mitigated in this scenario.

[00162] The ability of PEs to induce germination of B. atrophaeus spores was confirmed with scanning electron microscopy (SEM). FIGS. 3A-E illustrate scanning electron microscope images of B. atrophaeus spores (with vegetative cells that arose from PE-induced spore germination also visible); A: spores suspended in physiological saline solution for 5 hrs in the dark; B: spores exposed to 20 μg/mL PE for 5 hrs in the dark; C: spores suspended in physiological saline solution for 5 hrs in UVA light; D and E: spores exposed to 20 }ig/mL PE for 5 hrs in UVA light. Scale bars spanning 3 μηι are included. Arrows indicate spore coat remnants. As shown in FIGS. 3A-E, SEM imaging illustrates an increased quantity of germinating cells following their exposure to PE in the dark, as evidenced by their increased volume, rod-like morphology, and spore coat remnants. Vegetative cells were present in the negative control, although they were far outnumbered by spores (the gating scheme used in FIG. 2 A indicates that spores represent 3% of all bacteria, in this instance). The observed dimensions of the rod-like vegetative cells (diameter: 0.8 μιη; length: 2-3 μηι) and spores (width: 0.7 μπι; length: 1.8 μτη) both match previously reported records. Arrows are included (FIGS. 3B and 3D) to highlight the presence of spore coat remnants— the presence of which generally coincides with one of the last stages of spore germination. In the case of many bacilli, however, there is no sign of a spore coat remnant, signifying that there is a large degree of disparity concerning germination progress across the sample population— corroborating the heterogeneous fluorescence exhibited by germinating 8, atrophaeus spores seen via flow cytometry. While germination is still observed in the presence of light -activated PE, the majority of cells exhibit significant morphoiogical damage that is too severe for the bacterium to overcome (FIGS. 3D and 3E).

[00163] In order to accurately determine the viability of Bacillus spores and subsequently germinated vegetative cells with accuracy, Bacillus anthracis Sterne was evaluated by standard plating techniques. FIG. 4 illustrates B.

anthracis Sterne vegetative cell viability following exposure to 10 μ^'ηαΕ PE. C denotes Negative Controls, where PE was not used. FIG. 5 illustrates B. anthracis Sterne spore and germinated vegetative cell viability as a function of starting concentration. PE exposed to varying spore concentrations for 90-min durations in the absence (A) and presence (B) of UVA light. Viability was inferred based on the spore's capacity to gro colonies on TSA before and after heat treatment, as described by Equations 1.1-1.3. FIG. 4 illustrates the profound killing of B. anthracis Sterne vegetative cells in the presence of light- activated PE, thereby corroborating the rapid death of germinating spores observed in FIG. 5. Once again, standard plating techniques are implemented, with colony growth being used as the determining factor in viability. Nearly 4 log reduction of B. anthracis Sterne vegetative cells is observed within 30 minutes; within 90 minutes, 5 log reduction is observed.

[00164] FIG. 5 illustrates that, within 90 minutes, 81% of spores were induced to germinate, even though the large majority (72% of all spores) are not killed and thus achieve successful germination into a viable, colony-forming vegetative cell. The percentage of spores able to germinate into viable vegetative cells actually decreased when the starting concentration of spores was lessened. Germination still occurs in the presence of UVA light: however, the resulting viability of germinated vegetative cells is severely compromised in this case. 90 minutes is a sufficient amount of time for light-activated PEs to induce germination in B. anthracis Sterne spores and subsequently damage resulting vegetative cells to the point where they are incapable of colony growth.

Exposing B. anthracis Sterne spores at a relatively high PE-to-spore ratio (20 ng PE/spore) resulted in 99% killing within just 90 minutes.

[00165] FCS Express (De No vo Software) was used to quantify the fraction of all spores that germinate upon exposure to UVA light and/or oligomer, according to the florescence gates defined in FIGS. 1A-D and 2A-D. Even though exposure of B. atrophaeus spores to PE in the dark facilitates germination within 30 minutes, longer exposure times only marginally increased the percentage of spores that are induced to germinate. Increasing the exposure time beyond 90 minutes did not increase the percentage of spores that were induced to germinate presumably due to PE photodegradation and loss of biocidal efficacy. In the presence of light-activated PE, j ust 15% of spores will successfully germinate. Furthermore, in the case of both B. atrophaeus and B. anthracis Sterne spores, 20 ,g/mL PE was insufficient to induce complete germination. In an effort to induce complete spore germination, the starting concentration of spores was diminished, with the PE concentration held constant at 20 ,u.g/mL.

Example 2.

Example 2.1.

[00166] Materials, -1C was synthesized as previously described. ÷2C was synthesized as previously reported. Both PEs are light yellow solids, and readily dissolve in aqueous solution. Lauroyl choline chloride (Tokyo Chemical Industry Co.; Tokyo, Japan) was obtained as a. solid powder and the container was stored under vacuum over dessicant. l,2-dilauroyl-sn-glycero-3-phospho- (1 -rac-glycerol) (DLPG) (Avanti Polar Lipids, Alabaster, AL) was obtained as a lyophilized solid powder, and was dissolved in methanol and stored at -21°C prior to use. Phosphoiipase A} (PLA1) from Thermomyces lanuginosus was obtained (Sigma- Aldrich, St. Louis, MO) as a liquid solution with a

concentration of 10,000 Units/g. Phosphoiipase A2 (PLA2) from Croialus adamanteus venom was obtained as a lyophilized power with buffer salts at an activity of 320 U/mg (Worihingion Biochemical, Lakewood, NJ).

Acetylcholinesterase (AChE) from human erythrocytes was obtained as a pH 8.0 buffered solution with an activity of >500 U/mg (Sigma-Aldrieh, St. Louis, MO). A "unit (U) of PLA2 activity," as referred to herein, is measured as the amount of enzyme needed to release one raicromole of titratable fatty acid per minute at pH 8.9 and 25°C from lecithin emulsion. A "unit of activity for PLAl," as referred to herein, is defined the same, except at a pH of 7.5 AChE activity units are defined similarly, with one micromole of acetylthiocholine iodide hydro lyzed per minute at pH 7.4 and 37°C.The AChE inhibitors

Meptazino 1 HC1 (3-(3 -ethylhexahydro- 1 -methyl- 1 H-azepin-3 -y!)-pheno 1 hydrochloride) , Itopride HC3 ΓΝ-[[4-[2- (Dimetiiyiamino)ethoxy]pheny4]meiiiyi]-3,4-dimethoxy

benzamidehydrochloride), and TAE-1 (2,2',2'-[l ,3,5-Triazme-2,4,6-t.riyItris(oxy- 4, 1 -plienylenecarbonyloxy)]tris[ ,N,N-trimethyl-ethanaminium tri- iodide ) were obtained as solids (Sigma- Aldrich, St. Louis, MO). Ail solutions were prepared using filtered water with a resistivity of >! 8.2 MQ*cm (EMD Millipore, Billerica, MA), with a pH of 7.5. The PEs tested were as shown below in Scheme 2.

[001 7] Scheme 2.

-nC series (-1C, n = 1)

Example 2.2.

[00168] Sample preparation . A typical preparation of a - 1 C/lauroyl choline("LaCh") sensor is given. In a quartz cuvette with stirring, 20 uL of 500 mM -1C is added to 1970 iiL of water. After 15-30 seconds of mixing, 10 μΐ, of a 2 mg/mL solution of LaCh is added and allowed to mix for se veral minutes. A similar procedure is followed for the preparation of the +2C/DLPG sensor.

Typical sensors used in experiments with +2C/DLPG had concentrations of 1.4 μΜ PE and DLPG concentrations of 16 μΜ. For the AChE sensor, 5 μΜ of -1C was used, and LaCh used for enzyme studies was 32 μ.Μ. Enzyme

concentrations in the range of 50 to 0.5 mU were tested for PLA1 and PLA2, and the range for AChE was 0.1 to 0.8 U,

Example 2.3

[00169] Ahsorhance and Fluorescence Spectroscopy. UV -visible absorption spectra were obtained using a. Lambda-35 UV-VIS Spectrometer fitted with a temperature-controlled ceil with magnetic stirring (Perkin Elmer, Waltham, MA). Fluorescence spectra were obtained using a Photon Technology International fluorescence spectrometer equipped with a 75 W xenon arc lamp housed in an elliptical reflector (Photon Technology International,

Birmingham,NJ). Fluorescence quantum yields were calculated using the comparative method relative to the previously reported value for +2C . Least- squares linear regressions for substrate concentration calibration and fluorescence quantum yield determinations were performed using the software Origin 9.

Example 2.4

[001 70 Detection of Enzyme Activity. The monitoring of the sensor was performed using the absorbance wavelength of 430 nm and the fluorescence wavelength of 440 nm (excitation of 370 nm for -1C, 375 nm for +2C). For both absorbance and fluorescence measurements of the sensor upon addition of enzyme, the sensor was prepared as described above in a quartz cuvette with constant stirring at room temperature (25°C). The lid of the instrument was quickly lifted and enzyme injected, resulting in a -0.5 second delay in the initial change registered. Enzyme kinetics were determined for PLA1 and PLA2 by converting the intensity of fluorescence or absorbance of the aggregate to substrate (DLPG) concentration, as given in equation (2.1 ), below.

(2.1)

Where: [S] ₍ denotes substrate concentration at time t, [S]o is initial substrate concentration, I _t is fluorescence intensity at time t, Io is initial fluorescence intensity, is background fluorescence intensity. Once the fluorescence at 440 nm or absorbance at 430 nm is converted to substrate concentration, standard Michaelis-Menten kinetics can be used. Non-linear fitting to a velocity vs substrate concentration plot was performed using the Hill equation using Origin 9, with the formula given in equation (2.2). The Michaelis-Menten equation serves as a special example of the Hill equation, and when n=l the Hill equation is equivalent to the Michaelis-Menten equation commonly used for enzyme kinetics.

max

y

(k _m ⁿ + x ^« )

(2.2)

Where n = cooperativity, V _ma x is the max velocity in _i uMol/min*mg or μΜ/min, and k _m , which is the substrate concentration at half of V„, _ax ,

Example 2.5 [00171] Computational Methods. PEs were parametrized to the generalized Amber forcefield (GAFF) framework using the antechamber program in AmberTools 12. The Lipidl4 parameters for Amber were used for the lipid l ,2-dioleoyl-5«-glycero-3-phospho-r-rac-glycerol (DOPG). The Gauss ian09 software package was used for all quantum- level calculations for residue parameirization, with geometry optimized at the B3LYP/6-31g** level and electrostatic potentials used for residue parameirization derived with Hartree-Fock and a 6-3 lg** basis set. GAFF atomtypes were used to assign Van der Waals parameters and bonding force constants. The assigned partial charges of the PE from the quantum-level calculations were fitted using the RESP charge fitting method. The initial system configurations were prepared using the program Packmol. Systems were solvaied with water and neutralized with sodium and chloride ions, and the TIP3 water model was used. Simulations used full PME electrostatics and cubic periodic boundary conditions. The system was first minimized using the steepest descent method for 2500 steps, followed by a 250 step gradient minimization. Heating was carried out from 0 K to 100 K in 500 ps, and then from 100 K to 303.15 K in 500 ps using the NVT ensemble. Simulations were performed for 100-250 ns using the NPT ensemble with the Langevin barostat and thermostat with a time constant of 1/ps. The Amber 12-GPU software package was used with SPFP precision. Radial distribution functions were measured over the simulation trajectory using the center of masses of the individual PEs using the cpptraj program in AmberTools. In order to sort out the most likely aggregated form of an PE dimer, cpptraj was used to cluster interacting pairs of PEs with the hierarchical agglomerative approach. The distance between frames was calculated using best-fit RMSD of the coordinates, and clustering analysis was carried out for PEs within 5 A apart. UCSF Chimera version 1.10 was used for rendering snapshots of the trajectories and further clustering of the trajectories of the top clustered results from cpptraj, based on pairwise best-fit root-mean-square deviations between separate PEs, to distinguish common aggregate structures and provide a graphical representation of the clusters over time.

Example 2.6

|00172] Photophysical Effects of Complex Formation. The

fluorescence detection of enzyme activity on lipids or lauroyl choline was enabled by the strong photophysical changes which occurred upon aggregation of the PEs. The changes in absorbance and fluorescence spectra of +2C with DLPG and -1 C with LaCh are shown in FIGS. 6A-D. FIGS. 6A-D illustrate absorbance and fluorescence Spectra of (A) absorbance and (B) fluorescence (Ex: 375 nm) of 1.4 μ.Μ +2C with DLPG; (C) absorbance and (D) fluorescence (Ex: 370 nm) of 5 μΜ -1C with LaCh; all spectra indicate the varying

DLPG/LaCh concentration or ratio of substrate to PE.

[00173] As can be seen in FIGS. 6A-D, there are significant changes in the fluorescence and absorbance of aggregates of both anionic and cationic PEs. Interestingly, the changes resulting from aggregation are very similar for the

+2C/DLPG and -lC/LaCh complexes. The absorbance spectrum is strongly red- shifted, with the major transition moving trom 375 to 440 nm. The minor band at -320 nm forms a bimodal shape with a second peak at 330 nm for -1C and 340 nm for +2C upon aggregation. In a solution of 0.5 OD or higher, the aggregates give a transparent yellow solution with a slight bluish haze. In addition to the strong changes to absorbance, the fluorescence is significantly altered upon aggregation with the substrate molecules. The most significant effect which can be utilized for sensing is a strong enhancement of fluorescence from a broadened, weak fluorescence to a very strong, structured emission centered at 450 nm for +2C and 442 nm for -1C,

[00174] The spectra in FIGS. 6A-D also show that the aggregates result in structured bands in both the absorbance and fluorescence spectra which are within 10 nm apart. This suggests that a very highly-efficient fluorescence is occurring, resulting in very little energy loss and a very active sensor. This contrasts significantly with the non- fluorescent, uncolored compound before complexation. The red-shifted absorbance and enhanced fluorescence is typical of a "J-aggregate", which leads to the prediction that the molecular structure that results in these enhanced electronic properties allows these rigid molecules to align. Comparing FIG. 6B with FIG. 6D, it is clear that the -IC/LaCh aggregate has a more dominant structured band at -440 nm than the +2C/DLPG aggregate. This suggests that the structure of the -IC/LaCh aggregate is that of a well- defined J-dimer, where the +2C/DLPG aggregate likely is also a J-dimer but with more conformational freedom. This result of fluorescence enhancement suggests that the fluorescence quantum yields would be useful for describing the enhancement by the aggregation.

[00175] FIGS. 7A-B illustrates integrated fluorescence versus absorbance for (A) 5 uM -1C (squares) and 5 uM -1C with 32 uM LaCl (diamonds), and (B) 1.4 uM +2C (squares) and 1.4 uM +2C with 16 uM DLPG (diamonds). This data was used to calculate the fluorescence quantum yields by the comparative method, and the new values for the quantum yields that were corrected from a previous study are given next to the line. Excitation was 370 nm for A and 375 no! for B, with fluorescence excitation wavelengths from 390 to 600 nm.

Fluorescence quantum yields were determined using the comparative method as discussed above, and the least-squares linear regressions of the results are given in FIGS. 7A-B. FIGS. 7A-B demonstrate that the quantum yields of the PEs are greatly enhanced by the aggregation induced by the substrates DLPG or LaCh. Calculation of the fluorescence yield by the comparative method using the reported value of 0.039 for +2C leads to vastly overstated quantum yields of fluorescence of both AChE and PLA sensors in excess of unity. While it is understandable that the previous value of +2C was difficult to pinpoint due to the very low fluorescence of +2C in water, the results of fluorescence quantum yield measurements performed in this study suggest that the quantum yield for +2C is no larger than 0.016 rather than 0.039, This value would assume a quantum yield for the -I C/LaCh complex of near unity, and while the aggregation-induced fluorescence is extremely efficient, the quantum yield is more likely between 90 and 100 percent. The aggregation of +2C with DLPG results in a fluorescence enhancement 39 times at 440 nm, which correlates to an increase of fluorescence quantum yield from 0.016 to 0.63. The aggregation of - 1C with LaCh results in a considerable enhancement of fluorescence quantum yield, which is 66 times higher for the -IC/LaCh complex than -1 C alone. This correlates with an enhancement from 0.015 to 0.991, following the correction of the quantum yield of fluorescence of ÷2C from 0.039 to 0.016.

[00176] In addition to the strong changes in absorbance and fluorescence of the PEs, the formation of a complex can be confirmed through circular dichi'oism (CD) spectroscopy. Circular dichroism spectra of 1.4 uM +2C with and without 16 uM DLPG added were acquired, and illusirated that +2C strongly absorbs circularly polarized light with a strong negative band at 445 nm. Since DLPG is chiral, it is reasonable that an aggregate formed on a DLPG template would be optically active. The photophysical changes observed upon complexation allow for a variety of strategies for indication of the presence of a substrate. While the magnitude of the fluorescence enhancement is much greater than that of the absorbance change, the ability to use colorimetric means for determinations allows for cheaper and more flexible detection strategies than are accessible by fluorescence measurements. The aggregation with surfactants and substrates is useful, and the introduction of substrates which are degradable by enzymes allows use of PEs as fluorescence-quenching enzyme sensors. The use of PEs for sensing of enzyme activity is powerful, as their strong fluorescence quenching and dequenching allows for highly sensitive detection.

100177] The aggregate formed between -1C and lauroyl choline gives rise to evidence of a structured aggregate with "J-type" character. In order to further investigate the structure of the aggregate that is formed, a set of large-scale molecular simulations was carried out.

Example 2.7

[00178] Molecular Aggregates for Monitoring Enzyme Activity -

Phospholipases AJ , A2 and C. The use of lipids such as DLPG to induce aggregation allows for the creation of a. sensor which can be affected by phospholipases. Phospho lipases are a class of phosphodiesterases that can cleave the acyl chains or phosphate groups of the lipids, depending on the class. Phospholipases Al and A2 ("PLAl," "PLA2") cleave the SN-1 and SN-2 acyl chains respectively, while Phospholipase C ("PLC") cleaves before the phosphate, forming diacylglycerol and a phosphate-containing headgroup.

Observation of the effects of these three different enzymes on the photophysical properties of the +2C/DLPG complex allow for assessment of the ability of the enzymatic products to maintain aggregation of the PEs. The changes in absorbance and fluorescence of the +2C/DLPG complexes were monitored after addition of either PLAl , PLA2, or PLC to the solution as described in the methods section, in addition to varying enzyme concentration, a study varying the concentration of DLPG was also carried out to determine changes in the response rate of the sensor when excess lipid is present.

|00179] The effects of enzymatic activity on the +-2C/DLPG sensor are shown for PLAl and PLA2 in FIGS. 8A-D. FIGS. 8A-D illustrate fluorescence ersus time for PE with various concentrations of DLPG and PLAl or PLA2; (A) fluorescence of the +2C/DLPG aggregates over the course of PL Al acti vity with 1.4 μΜ PE and a DLPG concentration of 7.27 μΜ, with enzyme added ranging from 0.5 to 5 mU of PLA l ; (B) 1.4 μΜ of +2C with DLPG at a series of concentrations from 10.6 to 35.6 μΜ (7,5 - 25.4 DLPG: PE ratio), followed by addition of 4 mU of PLAl ; (C) fluorescence of the +2C/DLPG aggregates over the course of PLA2 activity with 1 .4 μΜ PE and a DLPG concentration of 7.27 μΜ, with enzyme added ranging from 0.5 to 5 mU of PLA2; (D) 1.4 μΜ of +2C with DLPG at a series of concentrations from 2.37 to 17.8 μΜ (1.7 - 12.7 DLPGiPE ratio), followed by addition of 40 mU of PLAl . t=-l s is the time of enzyme addition.

100180] As can be seen in FIGS 8A-D, decomposition of the DLPG lipids by PL Al and PLA2 results in swift quenching of the fluorescence and increased transmittance at 440 nrn. While monitoring either absorbance or fluorescence can allow one to determine enzyme activity, enhanced fluorescence quenching and dequenching allows for a more sensitive sensor to be achieved through fluorescence monitoring. In FIGS. 8B and D, the effects of varying lipid concentration on the rate of enzymatic degradation was tested. In samples which had a lipid concentration higher than the saturation point of -1 : 16 PE:lipid ratio, a lag period was observed after the addition of the enzyme. This lag period is tied to the amount of excess, "free" lipid in solution, as it increases with increasing lipid and constant PE concentration. It is likely that there is a population of lipids which are circulating in solution without being involved in an aggregate with a PE, and these lipids can act as a sort of "reserve," which can become involved in an aggregate, if needed. The enzymes will also be acting on these free lipids, halting the degradation of the PE-Lipid sensor. Once this population of excess lipids is enzymatically cleaved by PLAl or PLA2, the lipids making up the sensor are then disassembled and the fluorescence quenching occurs. FIGS. 8A and C demonstrate the high sensitivity of the phospho lipase sensor, as enzymatic cleavage is observed with both PLAl and PLA2 at enzyme concentrations below 5 mU/mL. Since the weight of PLAl from T. lanuginosus is not known, and the enzyme is obtained with

concentration listed in terms of units of activity, it is difficult to compare PLAl limits of detection on a molar basis. The concentration of PLA2 that corresponds with 0.5 mU/mL at 320 U/mg protein is 500 fM, marking at least a 10-fold increase in sensitivity over the previously reported PLC sensor.

[00181] Interestingly, the activity of PLC does not result in a strong change to the sensors aggregated state. The changes resulting from addition of PLC were studied, and it was clear that not only is there no rapid fluorescence quenching or absorbance change observed with PLC as was seen with PLA1 and PLA2, but there is even a slight fluorescence enhancement. This behavior suggests that one or both of the products of PLC degradation, diacyl glycerol and l-lauroyl-s«-glycerol 3-phosphate, also result in aggregation of the PE which allows retention of the enhanced fluorescence.

Example 2.8

|00182] Monitoring Enzyme Kinetics— PLA Sensing. The difference between the aggregation of PL A and AChE sensors is further shown by examining the kinetics of complex formation at different concentrations. The ability to quantify substrate concentration is afforded by these sensors when substrate concentration can be effectively calculated from the fluorescence or absorbance of the aggregate. It is visible when comparing FIGS. 6A and B with FIGS. 6C and D that the increase of the absorbance (430 nm) or fluorescence peaks (440 nm) representing the aggregate changes with a different

concentration dependence for the two sensors. This is better shown via calibration curves to fit fluorescence or absorbance to substrate (DLPG or LaCh) concentration,

[00183] The linear correlation between fluorescence at 440 nm and substrate concentration is given for both PLA and AChE sensors in FIGS. 9A-C, showing linear regression of (A) absorbance of 10 μΜ PE-2+; (B) fluorescence of 1.4 μΜ PE-2+ (Ex: 375 nm, Em: 440 nm), with increasing DLPG

concentration; (C) fluorescence of PE-1- with increasing LaCh concentration (Ex:370 nm, Em: 440 nm). The curves shown in FIGS. 9A-C illustrate a difference in the concentration dependence for formation of the PLA and AChE sensor. +-2C shows a linear increase in fluorescence with increasing DLPG concentration, but -1 C shows a sharp change with a typical sinusoidal shape between 20 and 30 μΜ of LaCh. The linear response of the PLA sensor is ideal for quantification of kinetic parameters, as the concentration of lipid can be calculated from the linear regression. The sinusoidal response of the AChE sensor does provide a linear fluorescence signal to LaCh concentration. This suggests that despite the similarities between the aggregates, the formation of the aggregates follows different kinetics. The kinetics of the degradation of the +2C/DLPG sensor by PLAl and PLA2 were followed by conversion of the fluorescence or absorbance to concentration, as discussed above. An example of the result is given in FIGS. 10A-B, where the loss of fluorescence over time is converted into velocity vs substrate concentration for calculating enzyme kinetics. FIGS. 10A-B illustrate (A) fluorescence of PLA sensor (Ex. 375 nm; Em. 440 nm) composed of 1.4 μΜ +2C and 16 μΜ DLPG following addition of 0.04U of PLAl ; (B) velocity versus substrate plot after conversion of data in (A) to velocity and substrate following the equations given in the methods section. |00184] The activity of PLAl and PLA2 were determined by nonlinear fitting of fluorescence or absorbance of the aggregated PEs in the sensor by the Hill fit. PLAl from T. lanuginosus was found to have a V _max of 141.7 +/- 6,8 μΜ/min, and a k _m of 5.41 +/- 0.28. PLA2 from C. adamanteus venom had a Vmax of 37.4 +/- 1.84 μΜ/min and a k _m of 6.39 +/-0.29. The specific activity of PLA2 was calculated using 0.05 U/mL of 320 U/mg PLA2 to be 1295

Mol-m n ^' Sng ^"1 , nearly 1000-fold greater than the 14 μΜο1^ίη ^"1 η¾ ^"1 obtained from a previous study of PLA2 from C. atrox venom. For these sensors the km is tied to the PE concentration, and in cases with PLAl where the PE

concentration is 10 μΜ instead of 1.4 μΜ, the kM is 97 μΜ rather than 5.4. A strong correlation is observed between increased substrate concentration and enzyme activity due to a cooperative effect. This is expressed as n in equation 2, which was fit to the results to determine kinetic parameters. In a case of no cooperativity, n is equal to one, but for both PLAl and PLA2 it is fit to be 3.

The cooperative effect is visible in FIG, 10B, where there is a decreased slope of v/[S] in regions of lo substrate. This is reasonable, as PLAl and PLA2 have been previously shown to be membrane-associated proteins which have activity that is highly dependent on the local lipid environment.

Example 2.9

[00185] Monitoring Enzyme Activit— Acetylcholinesterase.

Acetylcholinesterase ("AChE") is an important enzyme which is responsible for terminating synaptic transmission by hydrolyzing the neurotransmitter acetylcholine. In addition to the absorbance and fluorescence spectra in FIGS 6A-D, the quantum yields were calculated to be near unity upon formation of aggregates between -IC and iauroyi choline. This highly-sensitive fluorescence response in particular makes this an ideal sensor for detection of AChE. The detection of AChE by fluorescence and absorbance using the -I C/LaCh sensor is shown in FIGS. 11A-B, showing (A) absorbance at 430 nm and (B) fluorescence (Ex:370 nm, Em:440 nm) of -IC and LaCh at 0.2, 0.4, and 0.6 U of AChE.

[00186] As shown in FIGS. I IA-B, there is clear detection of AChE activity through the loss of the characteristic absorbance at 430 nm and fluorescence at 440 nm over time. There was a clear difference in the rate of enzymatic degradation of the complex which correlated with amount of enzyme added. There is a slightly different profile to the change in absorbance versus fluorescence over time. In the absorbance spectrum, there is a quick drop from 0.16 OD, and for the 0.4 and 0.2 Unit additions of AChE this rate progressively decreases, leading to a curve with a more gradual slope. The slope of the 430 nm absorbance loss after adding 0.6 Units of enzyme is fairly constant until 0.1 OD approaches, indicating that the aggregate has been dissociated. Monitoring the enzyme activity through fluorescence gives similar results as absorbance, except that the magnitude of change is greater. In FIG. 1 IB, the fluorescence drops an order of magnitude from IE6 to 1E5 photons/second, compared with a change from 0.16 to 0.1 OD for the change in absorbance at the same concentration. The fluorescence spectra in FIG. 1 IB are similar to the absorbance spectra in FIG. 1 1A, and the changes occur on the same timeframe. These results show that the - IC/LaCh sensor is effective at detection of AChE. activity both through colorimetric means (absorbance) and through fluorescence assays.

[00187] As stated above, AChE is responsible for termination of nerve signals. This causes many inhibitors of AChE to be highly neurotoxic, and many pesticides and nerve agents are strong AChE inhibitors. In order to determine whether the AChE sensor based on the -IC/LaCh complex could be used for detection of AChE inhibitors such as nerve agents and pesticides, the sensor was added to a solution of one of three different AChE inhibitors prior to addition of AChE. While the compounds; TAE- 1, Itopride, and Meptazinoi, all have been shown to be AChE inhibitors, these compounds are less volatile and toxic than the nerve agents and pesticides that are of primary interest for AChE inhibition detection. The inhibition of AChE by these three inhibitors using the - IC/LaCh sensor was carried out as described above, and the fluorescence of the sensor over time with and without inhibitor is given in FIGS. 12A-C, illustrating a - IC/LaCh complex (5 μΜ PE, 32 μΜ LaCh) showing fluorescence change after addition of 0.6 U of AChE in the presence of AChE inhibitor (A) itopride HQ; (B) meptazinol HC1; and (C) TAE-1 ; traces with inhibitor are denoted with +1 and the inhibitor concentration, and -I indicates no inhibitor.

[00188] As shown in FIGS, 12A-C, it is clear that inhibition of AChE by se veral different inhibitors is apparent in the attenuated loss of fluorescence compared with the reference solution, with no inhibitor. In order to confirm that this result is not due to aggregation between the PE and the inhibitors, the absorbance and fluorescence spectra of the PE and inhibitor without LaCh were obtained. FIGS. 13A-B illustrate (A) absorbance and (B) fluorescence (Ex: 370 nm) of 5 uM -1 C with 5 ug/mL of either LaCh or one of the three AChE

Inhibitors used in this study. As shown in FIGS. 13A-B, there is no significant aggregation induced by itopride or Meptazinol. TAE-1 however, does result in a red-shifted absorbance and a strongly red-shifted and broadened green fluorescence. Further, there is little overlap between the fluorescence of the TAE-l/PE complex and that of the PE/LaCh complex.

Example 2.10.

[00189] Prediction of Aggregate Structure by Molecular Simulations.

To study the structure of the aggregate formed between cationic PEs and anionic phospholipids, simulations with +1C and DOPG near the experimentally- observed ratio of lipidiPE were performed using all-atom molecular dynamics. While +2C was used primarily in this study, +1C was shown to form an aggregate resulting in similar photophysieal changes (FIGS. 14A-B, illustrating (A) absorbance and (B) fluorescence of 4.3 uM +1C with various concentrations ofDLPG). In order to reduce computational time, +1 C was used in the simulations rather than +2C. It should be noted that the simulations where only 2 PEs were used did not result in the formation of an aggregate within the 150 ns simulation time, as the two PEs in the simulation never came close enough to interact with one another in this time. This was observed at both simulation box sizes used (8 nm or 10 nm side length), and with a PE lipid ratio of 1 :3 and 1 : 10. Timelines of the three simulations in which a Example 3.

Example 3.1 : Overview

[00190] Four PEs (Scheme 3) were synthesized for evaluation against native hen egg white lysozyme (HEWL) amyloids. The PEs used, designated for brevity PEn+ and PE1-, all have ethyl ester terminal moieties on the PE backbone and side-pendant charged groups; the caiionic compounds have n === 1, 2 and 3 repeat units and the anionic compound has one repeat unit. The compounds are amphiphiiic and water soluble due to the hydrophobic backbone and charged side groups. These ester-terminated compounds were selected for the effective sensing modality of fluorescence yield increase from reduced quenching by water when bound to a hydrophobic surface.

100191] Scheme 3.

/

PEn+ series (PER, n - 1 ; PE! -h, n = 2; PER, n

PEn- series (PE- 1 , n = 1 )

Example 3.2

[00192] Formation and Characterization of HEWL Amyloids. Hen egg white lysozyme (HEWL) was used to form fibrillary amyloid aggregates for use in this study. Lysozyme has been suggested as a useful model protein for amyloid studies, due to its low ^r cost and the relative ease with which it can be induced to form amyloid aggregates. Lysozyme amyloid oligomers and fibrils have also been shown to exhibit cytotoxicity towards human neuroblastoma cells, indicating that the amyloid-aggregate contormer of lysozyme recapitulates most of the relevant properties of known disease-associated proteins. For these experiments, HEWL (Sigma- Aldrich) was incubated at 70°C and a concentration of 350 μΜ in pH 3 sodium citrate buffer ( 10 mM) with 100 mM aCL Visible precipitates of aggregated lysozyme were observed to accumulate over the time of incubation, and the formation of amyloid fibrils was determined by Thio flavin T (ThT) fluorescence assay (FIG, 15, illustrating a plot of PE and Thio flavin T (10 μΜ) fluorescence enhancement with variously incubated HEWL- ( 10 μΜ monomer basis, 0.5 mg/mL), with unbound dye fluorescence normalized to 0 and maximum dye fluorescence normalized to 1), far-UV circular dichroism (CD) spectroscopy (FIG. 16, illustrating far-UV circular dichroism spectra of Oh, 2h and 4h incubated HEW... (0, 14 mg/mL) in pH 3 citrate buffer (10 mM)), and atomic force microscopy (AFM) and transmission electron microscopy (TEM) (FIG. 17, illustrating TEM (top) and AFM (bottom) images of Oh, lh, 1.5h and 4h incubated HEWL; scale bars = 200 nm; 4h, inset: view of a single isolated fibril, showing twisted morphology; AFM image Z-height: Oh, 25 nm; lh, 25 nm; 1 .5b, 15 nm; 4b, 100 nm).

[00193] ThT -positive aggregates were detected by the second hour of incubation (FIG. 15), and the profile of ThT fluorescence enhancement over incubation time had the sigmoidal shape consistent with the nucleation- dependent mechanism that is well accepted for amyloid formation, Far-UV circular dichroism measurements (FIG. 16) showed conversion of primarily a- helix structure of monomeric lysozyme (Oh), as indicated by the negative bands at 222 and 208 nm, into primarily β-sheet structure in the mature aggregates (2h and 4h), as indicated by the single negative band at 218 nm and the positive band just, visible at the 200 nm edge of the spectrum.

[ΘΘ194] Fibrillar morphology of HEWL aggregates was confirmed by direct visualization by AFM and TEM, AFM on dry mica and TEM (FIG. 17) on non-glow discharged carbon grids showed thai unmcubated HEWL formed a homogeneous film without large features. One hour of incubation caused the HEWL to form distinguishable bumps, hypothesized to be pre -thio flavinophilic oligomers. By 1.5 hours of incubation when amyloid formation was just reaching plateau phase as indicated by ThT fluorescence, small linear aggregates were observed, which lengthened by the fourth hour into short, bundled fibrils 20-30 nm wide and 60-200 nm long. No fibrils significantly longer than these were observed, even for longer incubated samples. These fibrillary, β-sheet

6.3 enriched, ThT -positive HEWL amyloid aggregates were then used to evaluate the binding activity and phoiophysical changes of PEs against amyloid.

Example 3.3.

[ΘΘ195] Spectrophotometry of PE-HEWL Interactions. Excitation and emission spectra of PEs in phosphate buffer alone, with monomelic HEWL and with HEWL amyloids (8h incubated) are shown in FIGS. 18A-H, and relevant photophysical properties are summarized in Table 1. FIGS. 1 8A-H illustrate excitation (A, B, C, D) and emission (right; E, F, G, H) spectra of PEs (A, E: PE1+; B, F: PE1-; C, G: PE2+; D, H: PE3+) in phosphate buffer (PB, pH 7.4, 10 mM) alone (long dashed line) with HEWX monomers (short dashed line) and with HEWL amyloids (solid line); PE concentration; 500 nM, protein concentration: 5 μ,Μ monomer basis / 0.25 mg/mL; emission and excitation wavelengths, respectively, were chosen as shown in Table 1 for each sample. A 10: 1 molar ratio of protein to PE was used for these experiments. Absorbance spectra were taken, but background light scattering from insoluble amyloid aggregates made them difficult to interpret, so "fluorescence detected absorbance" in the form of excitation spectra was used instead. Normalized excitation and emission spectra, in which peak shifts and lineshape changes of spectra were somewhat easier to visualize, were used. Ail four PEs exhibited significant fluorescence enhancement in solution with HEWL amyloids (FIGS. 18E, F, G, H), and no fluorescence change with HEWL monomers except for PE1-. The fluorescence enhancement over baseline was most significant for the longer PE2+ and PE3+ (FIGS. 18G and FI), which also had notably sharpened fluorescence spectra with small (~10 nm) bfueshifting of the maximum. PE1- had a similarly sharpened and blueshifted emission spectrum (FIG. 18F) with both HEWL monomers and amyloid, with the addition of a shoulder at 465 nm with amyloid. PE1+ (FIG. 18E) had no change in wavelength or lineshape of emission spectrum, just a large increase in intensity when mixed with amyloids. The excitation spectra (FIGS. 18A, B, C, D) show a notable bathochromic shift for each PE in solution mixed with amyloid, of 23, 27, 35 and 29 nm for PE1+, PE2-'-, PE3+ and PE!-, respectively, observing only the low-energy band. The high- energy band, less relevant for imaging purposes, was also bathocnromicaliy shitted. The cationic PEs, as before, did not appear to interact with HEWL monomer in such a way as to produce a fluorescence change. PE I- had similar excitation spectrum (FIG. 18B) with monomer and amyloid, except for a large intensity difference.

[00196] A plot of normalized fluorescence enhancement for all four PEs and Thio flavin T with HEWL fibrils incubated for different lengths of time is shown in FIG. 15. PE1+ and PE2+ track amyloid formation in roughly the same way as ThT, showing a sigmoidal curve with onset of a logarithmic growth phase occurring at the same time, around ! hour of incubation. The plateau phase, as monitored by fluorescence of any of those three PEs or ThT, appeared at 2 hours incubation. PE3+ fluorescence enhancement shows a similar length lag phase but a slower growth phase, taking up to 3.5 hours to reach its plateau phase. PEl - has greater fluorescence enhancement when mixed with monomeric species than with amyloid at the equimolar concentrations used for this assay. Example 3.4

[00197] Determination of PE/Amyloid Binding Constants, Next, binding saturation assays were conducted to quantify the affinity of PE-amyloid binding; data and fitted curves were produced and the fitted parameters are summarized in the last two columns of Table 1. Since the linear fibril binding sites could fit many PEs, fits to binding curves were performed to the Hill equation to capture possible binding cooperativity:

p _max A v"

y—

K ⁿ + x ⁿ

where x is PE concentration (with protein concentration fixed), y is PE fluorescence intensity, F _max is PE fluorescence intensity at saturation, k is the equilibrium dissociation constant and the exponential term n is the Hill parameter which describes cooperativity of binding. n=l indicates non- cooperative, independent binding, n> l indicates that binding of one ligand increases affinity of the binding of a second, and n<l indicated that binding of one ligand decreases affinity of the binding of a second. Fits to the data for the three cationic PEs produced Fmax values close to the observed saturation value, and the other two parameters are reported as calculated. The fits indicated that PEl-;-, PE2+ and QPE3+ bound to HEVVL amyloid with low micro molar affinity dependent on PE length, with the calculated dissociation constant decreasing from 2.6 μΜ for PER to 1.15 μΜ for Pl- 7 . and still further to 858 nM for PE3+. Furthermore, the cooperativity of PE binding increased from almost no cooperativity for PE1+, to some positive cooperativity for PE2+, to still more positive cooperati vity for PE3+. The quantitative physical meaning of the Hill parameter is not quite clear except in special cases, but in a general way it is possible to conclude that for the cationic PEs, the shortest PE has non- cooperative binding to HEWL amyloid (Michaelis-Menten binding), and the two longer PEs have increasingly positively cooperative binding. The binding of PEl - to HEWL monomers appeared to be linear and non-saturabie at reasonable concentrations (see, FIG. 19, illustrating linear (non-saturabie) binding of PEl- to HEWL monomers (5 μΜ / 0.25 mg/niL); linear fit shown for clarity; this experiment was performed once), indicating a low-affinity binding to a very large number of sites. The effect ofPEl- non-specific binding to HEWL monomers precluded accurate determination of a binding constant for PE1 - /amyloid interactions s uch that a quantitative comparison of binding between the cationic and anionic compounds could not be made.

[00198] Table 1. Relevant ph.otophysi.ca3 properties of PEs alone and bound to HEWL amyloid, and apparent binding constants and Hill coefficients of PE binding to HEWL amy3oid.

Example 3.5

[00199] induced Circular Dichroism of PE-Amyloid Complexes.

Circular dichroism measurements were performed to determine if the intrinsic chira3ity of the HEWL fibrils was transferred to the PE chromophore by a chira3 backbone twist, or an "excitonic" chiral supramolecular aggregate. CD spectroscopy (CPEs in PB with HEWL monomer and with HEWL amyloid; performed for (a): PER; (b): PE1 -; (c): PE2+; (d): PE3+; PEs 10 μΜ, HEWL 10 μΜ monomer basis / 0.5 mg/mL) indicated induced circular dichroism of PEs when bound to HEWL amyloids. As expected, no PE had optical activity by itself in phosphate buffer solution and none of the PEs had any CD with HEWL monomer, including PE1-. PE1+ did not have optical activity with HEWL amyloid, but the other three PEs did. PE1-, PE2+ and PE3+ all had strong induced CD with a negative Cotton effect when bound to HEWL amyloid fibrils. PE2+ and PE3+ gave rise to similar CD spectra, with more intense bands in the spectrum for PE3+. The induced CD spectrum for PE1- had a pronounced two- band structure, reflecting the more intense high-energy band for the anionic PE when bound to HEWL amyloid.

Example 3.6

[00200] Proieift-^PE Energy Transfer in PE-Amyloid Complexes.

Since lysozvme is an intrinsically fluorescent protein whose emission spectmm overlaps significantly with the excitation spectra of PEs, we chose to investigate the possibility of Forster resonance energy transfer (FRET) from the protein chromophore to PEs by a simple spectroscopic method. Emission spectra of solutions containing PEs and HEWL, amyloids or monomers were obtained using the excitation wavelength of HEWL (280 ma) and PE emission was observed only from PE/amyloid samples, indicating that HEWL~> PE energy transfer was occurring only with PEs bound to amyloid fibrils. The results are summarized as FRET efficiencies in FIG, 20, illustrating HEWL~> PE FRET efficiencies calculated from spectral data by the equation E = FA / (FD+FA) where FD is the integrated area under the donor emission peak, and FA is the integrated area under the acceptor emission peak. This simple expression is valid for this case since the PEs are nonfluorescent when excited at the donor excitation wavelength, eliminating crosstalk. Thus, FA is the total number of energy transfer events, and (FA+F D) is the total number of excitation events.

Theoretically, the efficiencies should be convertible into distances by E — but PEs and HEWL amyloids are not a well-characterized FRET pair with a defined Forster radius Ro. Qualitatively, some determinations based on the relative measured efficiencies for the different PEs can be made. The measured FRET efficiency will be affected by multiple independent factors averaged over all the PE-HEWL pairs in solution, such as the number of bound PE molecules, the bound PE-HEWL chromophore distance, and the spectral overlap integral 1(λ), all of which will vary by PE. The highest efficiency observed for PE2+ is probably the result of its higher binding constant than PE1- or PE1+ combined with its greater overlap integral than \' i ^: 7 ^■ .

Example 3.7

[00201] Explicating the Mode of PE-Amyloid Binding. The results of these experiments indicate modes of interaction between PEs and HEWL monomers and amyloids, as summarized in cartoon form in FIG. 21. All four PEs tested were observed to bind to HEWL amyloid, with good affinity, but with different properties depending on chain length and charge. Generally, the PEs either do not interact with protein, bind as single molecules, or bind as J dimers which are either raeemic or chirally biased. Overall, it has become clear that J- type aggregation is a naturally favorable mode of PE-PE interaction for PEs with side chain charged groups when the Coulombic repulsion between the charged groups is reduced.

[00202] The spectral changes of PE2+, PE3+, and PEl - in complex with

HEWL amyloids, and of PEl- in complex with HE WL monomers, are highly indicative of J aggregation: redshifted absorbance, sharpening of fluorescence band, and narrowed Stokes shift. The enhancement of fluorescence intensity is attributable all or in part to the reduced quenching of the PE by water when bound to the hydrophobic surface of the protein; this solvent-access effect is in play for all four PEs. The current study indicates that the longer cationic PEs, PE2+ and PE3+, form J dimers (or possibly larger aggregates) on the HEWL amyloid fibril surface, and PE l - forms J dimers on both HEWL monomers and HEWL amyloid fibrils. The aggregates formed on amyloid have a chiral bias to the PE-PE offset angle, producing a chiral supramoiecular chromophore, or an excitonic optical activity, responsible for the circular dichroism seen

experimentally. The exact source of this bias is hard to pin down; it could be a result of the helically twisted fibril axis or more specific to a binding site.

Notably, the aggregates formed by PEl - must be raeemic, indicating that the PEs are not interacting with a specific site but simply sticking to oppositely charged areas of the lysozyme surface. PE1+ has some small redshifting of excitation spectrum, but its emission spectrum does not shift at all and it acquires no optical activity, indicating that this compound binds to HEWL fibrils as single molecules rather than as a structured aggregate. The small excitation redshift could be due to minor backbone planarization, and the increase of fluorescence intensity to reduced solvent access.

[00203] The results of binding saturation assays support these conclusions for the cationic PEs. PE2+ and PE3+ show positive cooperativity, meaning that the binding of one PE increases the affinity of the next binding event. The formation of J aggregates on the fibril surface satisfies this condition: a single PE might bind to a favorable site, and a second finds it and forms an even more favorable J aggregate due to π-π and hydrophobic interactions. It is also possible that PEs could form J dimers in solution that subsequently find the fibril surface, but this seems unlikely due to charge repulsion. Furthermore, the curve for PE3+ shows a larger cooperative effect than that for PE2+, and the induced CD bands for PE3+ are also more intense; the increased length ofPE3+ increases the available area for aggregate formation, forming more or larger chiral aggregates. The PE1+/HEWL amyloid binding assay indicated no cooperative binding effect, which is consistent with independent, single-molecule binding.

[00204] One notable result of this study is the large differences between

PE1+ and PE1 - in their interactions with HEWL monomers and amyloid. The two single-repeat PEs tested differ by the charge on the side-pendant soiubilizing groups, and their interactions with HEWL monomer and amyloids were highly different. PE1+ exhibited non-cooperative and saturable binding to amyloid without induced optical activity or large shifts in absorption or emission bands, and when bound, its emission was the least enhanced over free PE. Its anionic counterpart, PF.1-, proved quite different both in its nonspecific binding to

HEWL monomer and in its interaction with HEWL amyloid. This interaction was seen to be fairly weak, as indicated by the non-saturable binding, but it overwhelms the PEl-/amyloid interaction at high PE concentrations, after all the amyloid binding sites are occupied. In vitro, without interfering effects from other cellular/tissue components, such an effect could prove useful for monitoring the disappearance of similarly charged monomers. The differences in the PE1+ and PE1- binding to amyloid— E1+ binds singly and PE1- as chiral

J aggregates could be due to charge or H-bonding interactions specific to sites on the lysozyme fibril surface. The specificity of these possible charge effects is notable, since the arrangement of charged residues on the fibril surface is controlled by the protein ^' s primary, secondary and tertiary structure. This effect may provide useful means of differentiating amyloids formed from different monomers.

100205] The absence of FRET in any monomer/PE solution reconfirms the weak and non-specific nature of PE 1 -/monomer binding, since the PE is not held within range of the fluorescing residues. Aromatic residues may also only be surface exposed, and within range of transfer to PEs, in the amyloid state; HEWL intrinsic fluorescence is found to decrease over the course of incubation, which implies that fluorescing residues are increasingly exposed to solvent as more amyloid forms. The large differences between PE1 + and PEl-'s interactions with monomeric and amyloid HEWL, likely influenced by specific charged residues in the HEWL primary sequence, may be employed for differentiation of amyloids with different monomers, a useful effect, for example, in the study of the intermediate disorder called dementia with Lewy bodies, in which Lewy bodies (formed of alpha-synuclein and normally characteristic of Parkinson's disease) and amyloid plaques are comorbid.

[00206] The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that, various modifications are possible within the scope of the embodiments of the present invention. Thus, it should be understood that although the present invention has been specifically disclosed by specific embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those of ordinary skill in the art, and that such modifications and variations are considered to be within the scope of embodiments of the present invention. Example 3.8

[00207] PE Synthesis and Chemical Reagents. Except PEs, all reagents were obtained commercially and used without further purification. Synthesis of PEs has been reported previously, except for PE1-, which was synthesized analogously to PE1+. Hen egg white lysozyme and Thio flavin T were obtained from Sigma-Aldrich Chemical Company (St. Louis, MO). Suspensions of protein aggregates were gently vortexed to distribute aggregates before use in experiments.

[00208] Preparation of Lysozyme Amyloid Fibrils. Lyophilized HEWL was dissolved at 10 mg mL in 10 mM pH 3 sodium citrate buffer with 0.1 M aCl. The solution was incubated in a 70C oil bath and magnetically stirred at 250 rpm for 12h, and aliquots were withdrawn at half-hour intervals. The initially clear solution was observed to form cloudy aggregates by Ih incubation. Half of each aliquot was immediately diluted into pH 7.4 phosphate buffer to prevent further influence of acidic conditions and stored at 4C. The samples were observed to undergo no noticeable degradation over the co urse of one month, and these neutralized aliquots were used for all following experiments except for measurements of protein circ ular dichroism.

[00209] Spectrophotometry of PE/ThT-protein Complexes. For studies of fluorescence enhancement vs. protein incubation time, dyes were mixed with protein sample in phosphate buffer (10 mM, pH 7.4) at equal monomer concentration of 10 μΜ in the wells of a standard 96-well plate.

Emission spectra were obtained using top read with a SpectraMax M2e plate- reading spectrophotometer (Molecular Devices, Sunnyvale, CA). Experiments were performed in duplicate and errors are reported as standard deviation. For analysis of bound PE excitation and emission spectra and protein-PE energy transfer, PEs (500 nM) were mixed with protein sample (5 μΜ, monomer basis) in phosphate buffer and the solution transferred to a. quartz fluorometry cuvette. Spectra were obtained on a PTI QuantaMaster 40 steady state spectrofluorometer (HORJBA Scientific, Edison, NJ).

[ΘΘ210] Circular Dichroism Spectroscopy. PEs and protein samples were diluted in phosphate buffer, gently vortexed, and read in a 1mm pathiength quartz CD cuvette using an Aviv 410 CD spectrometer (Aviv Biomedical, Lakewood, NJ), 15s averaging time. A blank spectmm (PB only) was subtracted from each sample to remove background activity. Error bars are standard deviation over multiple reads of a single sample as reported by the instrument. [Θθ21ί ] Determination of Binding Constant. For determination of binding constant of PEs to amyloid aggregates, PEs were mixed with HEWL amyloid in phosphate buffer at a final concentration of 100 nM - 5 μΜ for PEs and 5 μΜ (monomer basis) for protein. The solutions were then transferred to a quartz fiuorometry cuvette and emission measured at the pertinent wavelength. Experiments were performed in duplicate and errors reported as standard deviation. Hill function fits to PE binding curves were calculated in OriginPro 9.

[002J 2] AFM Imaging. For AFM, a droplet of each protein sample at 5 mg/niL was pipetted onto freshly cleaved mica, substrate and allowed to physisorb for 20 min, followed by a single rinse with HPLC-grade water and gentle drying under a stream of N ₂ . Imaging was performed with a Nanoscope Ilia AFM (Veeco, Plainview, NY) in tapping mode under a constant stream of dry _? . gas using a rectangular silicon cantilever with a spring constant of 40 N/m (Veeco model TESPA-W). Veeco Nanoscope software was used to capture and analyze the images. Oh and 111 images are cropped from 1 μηι width images subjected to a first-order x,y plane fit and flattened. 1.5h image is cropped from a 5 μηι width image subjected to a third-order x,y plane fit and flattened. 4h image is cropped from a 5 μιη width image subjected to a first - order x,y plane fit.

[00213] TEM Imaging. For TEM imaging, incubated HEWL solutions at a concentration of 350 μΜ were diluted 1 :5 in water and aliquoted onto carbon- coated grids, allowed to adsorb, washed with deionized water and stained with 2% uranyl acetate solution. Excess liquid was removed and the samples allowed to dry in air. Samples were imaged on a Hitatchi H7500 transmission electron microscope (Hitachi High Technologies Corp., Tokyo, Japan) with tungsten filament illumination, operating with an AMT X60 bottom mount CCD camera detector. Additional Embodiments.

100214] The following exemplary embodiments are provided, the numbering of which is not to be construed as designating levels of importance:

[00215] Embodiment 1 provides a method of inducing germination of microbial spores comprising contacting the microbial spores with a p-phenylene ethynyiene compound.

[00216] Embodiment 2 provides the method of Embodiment I, wherein the microbial spore is at least one of a Bacillus anthracis, & Bacillus atrophaeus, a Bacillus cereus, and a Bacillus suhtilis. Embodiment 3 provides the method of any one of Embodiments 1 -2, wherein the p-phenylene ethynvlene compound comprises a repeating unit having the structure:

wherein

R ^! has the structure:

_Z_L ² -R ²

wherein

at each occurrence Z is independently chosen from --a ! .- . · ()·, ··:>·. and -NH-;

at each occurrence L ² is independently chosen from (Ci -C5o)hydrocarbyiene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence R ² is independently chosen from -H, (Ci -C ₅ )alkyl, -S0 ₃ ^" , -C0 ₂ ^' , -Η ₂ Ρ0 ₄ ^' , HP0 ₄ ^2" , P0 ₄ ^3" , phenolate, (C _} - Cio)alkyl-(l ,4-substituted l,4-diazabicyclo[2.2.2]octaiie-l,4-diium)-, and 3- methylimidazolium, and - ⁺ ( ^A )3 wherein at each occurrence R ^A is independently (C \ -C ₅ )allcyl;

at each occu ently chosen from a bond and

j is about 0 to about 4.

[00218] Embodiment 4 provides the method of any one of Embodiments

1 -3, wherein the p-phenylene ethynvlene compound comprising a repeating unit having the structure:

wherein

at each occurrence R ³ is independently chosen from ~N ((¾) n is about 2 to about 4.

[ΘΘ219] Embodiment 5 provides the method of any one of Embodiments 1-4, wherein the p-phenylene ethynylene compound has the structure:

wherein

R has the structure:

-Z— ·!.. p2 wherein

at each occurrence Z is independently chosen from

^• t ! ! >··. ··()·. -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci-Csojhydrocarbylene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence R ² is independently chosen from -H, (Ci-C ₅ )alkyl, -S0 ₃ ^" , -C0 ₂ ^" , -H ₂ P0 ₄ ^" , HP0 ₄ ² \ P0 ₄ ^3" , phenolate, (Ci- C io)alkyl-( 1 ,4-substit uted 1 ,4-diazabicyclo [2.2.2,]octane- 1 ,4-diium)-, and 3 - methylimidazolium, and -N ^T (R ^A ) ₃ wherein at each occurrence R ^A is independently (C i -C 5 )alkyl;

j is about 0 to about 4;

at each occurrence L ^! is independently chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(0)0-(Ci-Cio)hydrocarbyl, -C(0)NH-(Ci- Cjojhydrocarbyl, and ( ^' ! () )( ⁾ i i: and

m is about 1 to about 1,000. Embodiment 6 provides the method of Embodiment 5, the p-phenylene et

wherein

at en from -N i i U _; n

, and / n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alkyl; and

q is about 1 to about 50.

[00221 ] Embodiment 7 provides the method of Embodiment 6, wherein A is -C(0)OCH ₂ CH ₃ .

[00222] Embodiment 8 provides the method of any one of Embodiments 1-7, wherein the ρ-phenylene ethynylene compound has the structure: wherein

R ^! has the structure:

— Z— L ² — R ²

wherein

at each occurrence Z is independently chosen from

^» C¾-, -0-, -S~, and -NH-:

at each occurrence L ² is independently (Ci-

Csojhydrocarby!ene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from --0-, -S-, and -NH-;

at each occurrence R ² is independently chosen from -H, (Ci-Cs)alkyL -S0 ₃ ^" , -C0 ₂ ^' , -Η ₂ Ρ0 ₄ ^' , HP0 ₄ ^2" , P0 ₄ ^3" , phenolate, (Ci- C j o)alkyi-( 1 ,4-substituted 1 ,4-diazabicyclo [2.2.2]octane- 1 ,4-diium)-, and 3 ^■■ methylimidazolium, and -N ^T (R ^A )3 wherein at each occurrence R ^A is

independently (Ci-Cs )alkyl; and

p s about 1 to about 10.

[ΘΘ223] Embodiment 9 provides the method of Embodiment 8, wherein at each occurrence Z is -0-;

at each occurrence L ² is independently (Ci-C ₅ )alkyl;

at each occurrence R ² is independently chosen from -N ^T (CH ³ )3 ,

p is about 1 to about 5.

[00224] Embodiment 10 provides the method of any one of Embodiments

8-9, wherein the -phenylene ethynylene compound has the structure:

wherein p is about 2.

[00225] Embodiment 11 provides a method for detecting an enzyme, the method comprising (i) introducing an enzyme to a composition comprising a p- phenylene ethynylene compound and an enzyme substrate; and (ii) analyzing the change in fluorescence of the p-phenylene ethynylene compound following introduction of the enzyme.

[00226] Embodiment 12 provides the method of Embodiment 11 , wherein the p-phenylene ethynylene compound and the enzyme substrate form a complex.

[00227] Embodiment 13 provides the method of any one of Embodiments

1 1-12, wherein the introduction step (i) and the analyzing step (ii) occur in an aqueous environment.

[00228] Embodiment 14 provides the method of Embodiment 12, wherein the fluorescence of the p-phenylene ethynylene compound decreases following the introduction of the enzyme.

[ΘΘ229] Embodiment 15 provides the method of Embodiment 14, wherein the fluorescence decreases due to a molecular transformation of the enzyme substrate to an entity or entities that do not complex with the p-phenylene ethynylene compound.

[00230] Embodiment 16 provides the method of any one of Embodiments

1 1 - 15, wherein the p-phenylene ethynylene compound is a cationic p-phenylene ethynylene compound.

|0023l] Embodiment 17 provides the method of Embodiment 16, wherein the cationic p-phenylene ethynylene compound has the structure:

wherein

R ^l has the structure:

— Z— —

wherein

at each occurrence Z is independently chosen from

-€¾-, ·() ·. -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci -Cso)hydrocarbylene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence IV is independently chosen from -H, { ( ^' , -( ia ikyi. -S0 ₃ ^" , -·( ^' < > > . -H ₂ P0 ₄ ^" , HP0 ₄ ² \ PO i ^; . phenolate, (Cj - C io)alkyl-( 1 ,4-substituted 1 ,4-diazabicyclo[2.2.2]octane-l ,4-diium)-, and 3- methylimidazolium, and -N ^T (R ^A >3 wherein at each occurrence R ^A is independently (C i -C 5 )alkyl;

j is about 0 to about 4;

at each occurre ly chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubsiiiuied -C(0)0-(Ci -C io)hydrocarbyl, and -C(0)NH-(C _} C 10 )hy drocarby 1 ; and

m is about 1 to about 10. Embodiment 18 provides the method of any one of Embodiments 16-17, wherein the cationic p-phenylene ethynylene compound has the structure:

R JrirP

wherein

at eac f C ^' i i . n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(C _s -C ₅ )alkyl; and

q about 1 to about 5.

100233] Embodiment 19 provides the method of any one of Embodiments

16-18, wherein the cationic p-phenylene ethynylene compound has the structure:

—

wherein t is about 1 to about 3.

[00234] Embodiment 20 provides the method of any one of Embodiments

16-19, wherein the enzyme subsirate is an anionic enzyme substrate.

[ΘΘ235] Embodiment 21 provides the me thod of Embodiment 20, wherein the anionic enzyme substrate is 1 ,2-dilauroyl-sn-glycero-phospho-(l '-rac- glycerol).

[00236] Embodiment 22 provides the method of any one of Embodiments

1 1-21, wherein the p-phenylene ethynylene compound is an anionic p-pheny3ene ethynylene compound.

[ΘΘ237] Embodiment 23 provides the me thod of Embodiment 22, wherein the anionic p-pheny1ene ethynylene compound has the structure:

wherein

R ^l has the structure:

|.... Z-- L ² --R ²

5 wherein

at each occurrence Z is independently chosen from

-CH ··. -0-, -S-, and -NH-;

at each occurrence L ^" is independently chosen from (C i -C--o)hydrocarbylene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 10 groups independently chosen from -0-, -S-, and -Mi-;

at each occurrence R ^"' is independently chosen from -H, i( r-C a ik v !. -S0 ₃ \ -CO . . -H ₂ P0 ₄ ^" , HPQ ₄ ^2~ , P0 ₄ ^3" , and henoiate;

j is about 0 to about 4:

at each occurrence L ¹ is independently chosen from a bond and I s ¹ (...) ^{^}

at each occurrence A is independently chosen from -H, substituted or unsubsiituied -C(0)0-(Ci -Cio)hydrocarbyl, and -C(0)MI-(C _} - Ciojhydrocarb l,

m is about 1 to about 10.

[00238] Embodiment 24 provides the method of any one of Embodiments

22-23, wherein the anionic p-pheny!ene ethynyiene compound has the structure:

wherein

at each occurrence R ³ is independently chosen from -SO3 ^" , -CO2 ^" -H2PO4 ^" , HPO4 ² P0 ₄ ^3' , and phenoiate;

n is about 2 to about 4; at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alkyl; and

q is about 1 to about 5.

[00239] Embodiment 25 provides the method of any one of Embodiments

22-24, wherein the anionic p-phenylene ethynyiene compound has the structure:

wherein t is about 1 to about 3.

|00240] Embodiment 26 pro vides the method of any one of Embodiments

22-25, wherein the enzyme substrate is a cationic enzyme substrate.

[00241] Embodiment 27 provides the method of Embodiment 26, wherein the cationic enzyme substrate is a substituted or unsubstituted (Ci - C25)hydrocarbyl-C(0)0-(Ci -Cio)alkyl-N ^" ((Ci -Cs)alkyl) ₃ .

[00242] Embodiment 28 provides the method of any one of Embodiments

26-27, wherein the cationic enzyme substrate is a substituted or unsubstituted (C _} -C ₂ 5)alkyl-C(0)0-(C i -C ₄ )alkyl-r>r (CH 3 ) 3.

[00243] Embodiment 29 provides the method of any one of Embodiments

26-28, wherein the cationic enzyme substrate is chosen from lauroyl choline and acetylcholine.

[00244] Embodiment 30 provides the method of any one of Embodiments 26-29, wherein the cationic enzyme substrate is lauroyl choline.

[00245] Embodiment 31 provides the method of any one of Embodiments

1 1-30, wherein the enzyme is chosen from phosphohpase Al, phosphohpase A2, phosphohpase C, and acetyl cholinesterase.

[00246] Embodiment 32 provides a method for detecting an enzyme, the method comprising (i) introducing an enzyme to a composition comprising a p- phenylene ethynyiene compound and an enzyme substrate; and (ii) analyzing the change in fluorescence of the p-phenylene ethynyiene compound following introduction of the enzyme;

wherein

the p-phenylene ethynyiene compound has the structure:

wherein s is about 1 to about 3 ;

the enzyme substrate is l,2-diiauroyl-sn-glycero-phospho-(l '-rac- glycerol); and

the enzyme is at least one of phospholipase Al , phosphollpase A2, and phospholipase C.

[ΘΘ247] Embodiment 33 provides a method for detecting an enzyme, the method comprising (i) introducing an enzyme to a composition comprising a p- phenylene ethynylene compound and an enzyme substrate; and (ii) analyzing the change in fluorescence of the p-phenylene ethynylene compound following introduction of the enzyme;

wherein

the p-phenylene ethynylene compound has the stmcture:

so

wherein t is about 1 to about 3

the enzyme substrate is lauroyl cholin

the enzyme is acetylcholinesterase.

[00248] Embodiment 34 provides a sensor, the sensor comprising a p- phenylene ethynylene compound and an enzyme substrate,

[00249] Embodiment 35 provides the sensor of Embodiment 34, wherein the p-phenylene ethynylene compound is a charged p-phenylene ethynylene compound and the enzyme substrate is an oppositely charged enzyme substrate.

[00250] Embodiment 36 provides the sensor of any one of Embodiments 34-35, wherein the p-phenylene ethynylene compound is a cationic p-phenylene ethynylene compound. [00251] Embodiment 37 provides the sensor of Embodiment 36, wherein the cationic p-phenylene ethvnylene compound has the structure: wherein

R ¹ has the structure:

— Z— L ² — R ²

wherein

at each occurrence Z is independently chosen from

-OH .-. -0-, -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci -Cso)hydrocarbyiene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence " is independently chosen from -H, (C _l -C ₅ )alkyl _! -SQ ₃ ^" , -C0 ₂ ^" , -H ₂ P0 ₄ ^" , HP0 ₄ ^2" , P0 ₄ ³ \ phenolate, (C _s - C io)alkyl-( 1 ,4-substituted l,4-diazabicyclo[2.2.2]octane- l ,4-diium)-, and 3- methylimidazolium, and -N ⁺ (R ^A )3 wherein at each occurrence R ^A is

independently (C i -C 5 )a3kyl;

j is about 0 to about 4:

at each occurre ly chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(0)0-(C i -C io)hydrocarbyl, and -C(0) H-(Ci- Cio)hydrocarbyl; and

m is about 1 to about 10.

[00252] Embodiment 38 provides the sensor of any one of Embodiments

36-37, wherein the cationic p-phenylene ethvnylene compoimd has the structure: wherein

at each en from -N ^÷ (CH ₃ ) ₃ , n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alky1; and

q is about 1 to about 5.

[ΘΘ253] Embodiment 39 provides the sensor of any one of Embodiments

36-38, wherein the cationic p-phenylene ethynylene compound has the structure

wherein s is about 1 to about 3.

[00254] Embodiment 40 provides the sensor of any one of Embodiments

36-39, wherein the enzyme substrate is an anionic enzyme substrate.

[ΘΘ255] Embodiment 41 provides the sensor of Embodiment 40, wherein the anionic enzyme substrate is l,2-dilauroyl-sn-glyeero-phospho-( -rac- glycerol).

[ΘΘ256] Embodiment 42 provides the sensor of any one of Embodiments

34-41, wherein the p-phenylene ethynylene compound is an anionic p-phenylene ethynylene compound.

[ΘΘ257] Embodiment 43 provides the sensor of Embodiment 42, wherein the anionic p-phenylene ethynylene compound has the structure:

wherein

R ¹ has the structure: wherein

at each occurrence Z is independently chosen from

-CI S .-. -0-, -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci -Cso)hydrocarbylene interrupted by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence R ^" is independently chosen from -H, { ( ^' , - ⁽ : ia !kyi. -S0 ₃ ^" , -C0 ₂ ^" , -H ₂ P0 ₄ ^" , HP0 ₄ ^2" , PO.i ¹ . and phenolate;

j is about 0 to abo ut 4:

at each occurre ly chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(Q)0-(Ci-Cio)hydrocarbyl, and -C(0)NH-(Cj - Cio)hydrocarbyl,

m is about 1 to about 10.

|00258] Embodiment 44 pro vides the sensor of any one of Embodiments

42-43, wherein the anionic p-phenylene ethynylene compound has the structure: wherein

at each occurrence R' is independently chosen from -SO ₃ ^" , -CO? ^" -H ₂ P0 ₄ ^" , HPO4 ^2" , P0 ₄ ^3" , and phenolate;

n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci -C ₅ )alkyl; and

q is about 1 to about 5.

[00259] Embodiment 45 provides the sensor of any one of Embodiments

42-44, wherein the anionic p-phenylene ethynylene compound has the structure:

wherein t is about 1 to about 3.

Embodiment 46 provides the sensor of any one of Embodiments 42-45, wherein the enzyme substrate is a cationic enzyme substrate.

[00261] Embodiment 47 provides the sensor of Embodiment 46, wherein the cationic enzyme substrate is a substituted or unsubstituted (Ci- C ₂ s)hydrocarbyl-C(0)0-(C -C ₁ o)alkyi-N ⁺ ((C _i -C5)alkyi) ₃ .

|00262] Embodiment 48 pro vides the sensor of any one of Embodiments

46-47, wherein the cationic enzyme substrate is a substituted or unsubstituted (Cs -C ₂ 5)aikyl-C(0)0-(Ci-C4)alkyl- ⁺ (CH ₃ ) .

[ΘΘ263] Embodiment 49 provides the sensor of any one of Embodiments

46-48, wherein the cationic enzyme substrate is chosen from laurovl choline and acetylcholine.

[ΘΘ264] Embodiment 50 provides the sensor of any one of Embodiments 46-49, wherein the cationic enzyme substrate is lauroyl choline.

[00265] Embodiment 51 provides the sensor of any one of Embodiments 34-50, wherein the enzyme is chosen from phospholipase Al, phospholipase A2, phospholipase C, and acetyl cholinesterase.

[ΘΘ266] Embodiment 52 provides a sensor, the sensor comprising a cationic p-phenylene ethynylene compound and an anionic enzyme substrate; wherein

the p-phenylene ethynylene compound has the structure:

wherein s is about 1 to about 3; and the anionic enzyme substrate is 1 ,2-dilauroyl-sn-glycero- phospho-( 1 '-rac-glycerol). [00267] Embodiment 53 provides a sensor, the sensor comprising a p- phenylene ethynylene compound and an enzyme substrate;

wherein

the p-phenylene ethynylene compound has the stracture:

wherein t is about 1 to about 3 ; and the enzyme substrate is lauroyi choline.

00268] Embodiment 54 pro vides a method for protein analysis, the method comprising (i) introducing a p-phenylene ethynylene compound to a biological sample comprising at least one protein and (ii) analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample comprising the at least one protein.

[ΘΘ269 Embodiment 55 provides the me thod of Embodimen t 54, wherein the fluorescence of the p-phenylene ethynylene compound is analyzed prior to being introduced to the biological sample comprising the at least one protein.

[00270 Embodiment 56 provides the method of any one of Embodiments

54-55, wherein analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample comprising the at least one protein comprises analyzing the spectral changes between the fluorescence of the p-phenylene ethynylene compound of step (i) and the fluorescence of the p- phenylene ethynylene compound in the presence of the biological sample comprising the at least one protein of step (ii).

[00271] Embodiment 57 provides the method of any one of Embodiments

54-56, wherein the morphology of the protein in the biological sample is determined by analyzing spectral changes between the fluorescence of the p- phenylene ethynylene compound of step (i) and the fluorescence of the p- phenylene ethynylene compound in the presence of the biological sample comprising the at least one protein of step (ii).

[00272] Embodiment 58 provides the method of Embodiment 57, wherein the spectral changes in the fluorescence of the p-phenylene ethynylene compound between step (i) and step (ii) are induced by changes in the conformational freedom of the p-phenylene etliynylene compound between step (i) and step (ii).

[00273] Embodiment 59 provides the method of any one of Embodiments

54-58, wherein the p-phenyiene etliynylene compound has the stracture:

wherein

R ^l has the structure:

— Z— L ² — R ²

wherein

at each occurrence Z is independently chosen from

-€¾-, -0-, -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci-Csojhydrocarbylene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence R ^7' is independently chosen from -H, (Ci-C ₅ )alk l, -S0 ^" , -C0 ₂ ^" , -H ₂ P0 ₄ ^" , HP0 ₄ ^2" , P0 ₄ ³ , phenolate, (Ci- C s ojalkyi- ^■ ( 1 ,4-substituted 1 ,4-diazabicyclo [2.2.2]octane- 1 ,4-diium)-, and 3 ^■■ methylimidazolium, and -N ^T (R ^A )3 wherein at each occurrence R ^A is independently (C i -Cs )alk l ;

j is about 0 to about 4;

at each occurre ly chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(0)0-(C i -C i o)hydn>carbyl, and -C(0)NH-(Ci- Cjojhydrocarbyl; and

m is about 1 to about 10.

[00274] Embodiment 60 provides the method of any one of Embodiments

54-59, wherein the p-phenylene etliynylene compound has the stracture:

wherein

at each occurrence R ³ is independently chosen from -N ^" (CH ₃ ; ,

, and n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alky1; and

q is about 1 to about 5.

[00275] Embodiment 61 provides the method of any one of Embodiment

54-60, wherein the p-phenylene ethvnylene compound has the structure:

wherein s is about 1 to about 3.

[00276] Embodiment 62 provides the method of any one of Embodiments

54-61 , wherein the protein is at least one of an amyloid beta protein, Αβ-40, Αβ- 42, tau, and a-synuclein, islet amyloid precursor protein, Huntingtin, prion, lysozyme, TDP-43 (iransactive response DNA -binding protein 43 ), FUS (fused in sarcoma) and insulin,

[00277] Embodiment 63 provides a method for protein analysis, the method comprising (i) analyzing the fluorescence of a p-phenylene ethvnylene compound; (ii) introducing the p-phenylene ethynylene compound to a biological sample comprising at least one protein; (iii) analyzing the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample comprising the at least one protein; and (iv) determining the moiphology of the at least one protein in the biological sample by analyzing spectral changes between the fluorescence of the p-phenyiene ethynylene compound of step (i) and the fluorescence of the p-phenylene ethynylene compound in the presence of the biological sample comprising the at least one protein of step (iii);

wherein

-phenylene ethynylene compound has the structure:

wherein s is 1 ; and

the protein is at least one of an amyloid beta protein, Αβ-40, Αβ-42, tau, and a-synuclein, islet amyloid precursor protein, Huntingtin, prion, lysozyme, TDP-43 (transactive response DNA-binding protein 43), FUS (fused in sarcoma) and insulin.

[00278] Embodiment 64 provides a method for detecting a chemical agent, the method comprising (i) exposing a sensor composition comprising a complex comprising a. p-phenyiene ethynylene compound and an enzyme substrate to a sample; (ii) introducing an enzyme to the sensor composition of step (i); and (iii) analyzing the change in fluorescence of the p-phenyiene ethynylene compound between the exposing step (i) and the introducing an enzyme step (ii).

[ΘΘ279] Embodiment 65 provides the me thod of Embodiment 64, wherein a change in fluorescence between the exposing step (i) and the introducing an enzyme step (ii) indicates the presence of a chemical agent that does interact with the enzyme.

[00280] Embodiment 66 provides the method of any one of Embodiments

64-65, wherein a minimal change in fluorescence between the exposing step (i) and the introducing an enzyme step (ii) indicates the presence of a chemical agent that does interact with the enzyme. II] Embodiment 67 provides the method of any one of Embodiments 64-66, wherein the p-phenyiene ethynylene compound is a cationic p-phenylene ethynylene compound.

[00282] Embodiment 68 provides the method of Embodiment 67, wherein the cationic p-phenyiene ethynylene compound has the structure:

wherein

R ^l has the structure:

— Z— L ² — R ²

wherein

at each occurrence Z is independently chosen from

-€¾-, -0-, -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci-Csojhydrocarbylene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence R ^7' is independently chosen from -H, (Ci-C ₅ )alk l, -S0 ₃ ^" , -C0 ₂ ^" , -H ₂ P0 ₄ ^" , HP0 ₄ ^2" , P0 ₄ ³ , phenolate, (Ci- C s ojalkyi- ^■ ( 1 ,4~substituted 1 ,4-diazabicyclo [2.2.2]octane- 1 ,4-diium)-, and 3 - meihylimidazolium, and -N ^r (R ^A )3 wherein at each occurrence R ^A is

independently (Ci-Cs)alkyl;

j is about 0 to about 4;

at each occurre ly chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(0)0-(C i -C io)h.ydrocarbyl, and -C(0)NH-(Ci- Cjojhydrocarbyl; and

m is about 1 to about 10.

[00283] Embodiment 69 provides the method of any one of Embodiments

67-68, wherein the cationic p-phenylene ethynylene compound has the structure:

wherein

at each occurrence R ³ is inde endentl chosen from - ^" (CH ₃ ) ,

n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alky1; and

q is about 1 to about 5.

[00284] Embodiment 70 provides the method of any one of Embodiments

67-69, wherein the cationic p-phenylene ethynylene compound has the structure

wherein s is about 1 to about 3.

[00285] Embodiment 71 provides the method of any one of Embodiments

67-70, wherein the enzyme is chosen from phospholipase A1 , phospho lipase A2, and phospholipase C.

[ΘΘ286] Embodiment 72 provides the method of any one of Embodiments

67-71, wherein the enzyme substrate is an anionic enzyme substrate.

[00287] Embodiment 73 provides the method of Embodiment 72, wherein the anionic enzyme substrate is 1 ,2-dilauroyl-sn-glycero-phospho-(l '-rae- glycerol).

[ΘΘ288] Embodiment 74 provides the method of any one of Embodiments

64-73, wherein the p-phenylene ethynylene compound is an anionic p-phenylene ethynylene compound. )] Embodiment 75 provides the method of Embodiment 74, anionic p-phenylene ethynyiene compound has the structure: wherein

R ¹ has the structure:

— Z— L ² — R ²

wherein

at each occurrence Z is independently chosen from

-OH .-. -0-, -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci -Cso)hydrocarbyiene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence R" is independently chosen from -H, (C _l -C ₅ )alkyl _! -S0 ₃ ^" , -C0 ₂ ^" , -H ₂ P0 ₄ ^" , HP0 ₄ ^2" , P0 ₄ ³ \ and phenolate;

j is about 0 to about 4;

at each occurrence L ¹ is independently chosen from a bond and

\

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(0)0-(C i -C i o)hydrocarbyl, and -C(0)NH-(Cj - Cjojhydrocarbyl,

m is about 1 to about 10.

[00290] Embodiment 76 provides the method of any one of Embodiments

74-75, wherein the anionic p-phenylene ethynyiene compound has the structure:

wherein

at each occurrence R ^J is independently selected from ~S€ ^~ C0 ₂ ^" , -H2PO4 ^" , HPO4 ^2" , PO.i ^: . and phenolate; n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alkyl; and

q s about 1 to about 5.

[ΘΘ291] Embodiment 77 provides the method of any one of Embodiments

74-76, wherein the anionic p-phenylene ethynylene compound has the structure:

wherein t is about 1 to about 3.

[00292] Embodiment 78 provides the method of any one of Embodiments 74-77, wherein the enzyme substrate is a cationic enzyme substrate.

[00293] Embodiment 79 provides the method of Embodiment 78, wherein the cationic enzyme substrate is a substituted or unsubstituted (Ci~

C25 )hydrocarby 1-C(0)0-(C 1 -C s ₀ )alk l-N ⁺ ( ( C . -C ₅ )alkyi) 3.

[00294] Embodiment 80 provides the method of any one of Embodiments 78-79, wherein the cationic enzyme substrate is a substituted or unsubstituted

(C ! -C25 )alkyl-C(0)0-(C _x -C ₄ )alkyl-N"(CH 3)3.

[00295] Embodiment 81 provides the method of any one of Embodiments

78-80, wherein the cationic enzyme substrate is chosen from lauroyl choline and acetylcholine.

[00296] Embodiment 82 provides the method of any one of Embodiments

78-81, wherein the cationic enzyme substrate is lauroyl choline.

[00297] Embodiment 83 provides the method of any one of Embodiments

78-82, wherein the enzyme is acetylcholinesterase.

[ΘΘ298] Embodiment 84 provides a method for detecting a chemical agent, the method comprising (i) exposing a sensor composition comprising a complex comprising a p-phenylene ethynylene compound and an enzyme substrate to a sample; (ii) introducing an enzyme to the sensor composition of step (i); and (iii) analyzing the change in fluorescence of the p-phenylene ethynylene compound between the exposing step (i) and the introducing an enzyme step (ii); wherein

the p-phenylene ethynyiene compound has the structure:

wherein t is about I to about 3; and the enzyme substrate is lauroyl choline; and

a change in fluorescence between the exposing step (i) and the introducing an enzyme step (ii) indicates the presence of a chemical agent thai does interact with the enzyme.

[00299] Embodiment 85 provides a sensor for detecting the presence of a chemical agent, the sensor comprising a sensor composition comprising a complex comprising a p-phenylene ethynyiene compound and an enzyme substrate.

[00300] Embodiment 86 provides the sensor of Embodiment 85, wherein the p-phenylene ethynyiene compound is a cationic p-phenylene ethynyiene compound.

[00301] Embodiment 87 provides the sensor of Embodiment 86, wherein the cationic p-phenylene ethynyiene compound has the structure:

wherein

R ^! has the structure:

|_ Z— L ² -R ²

wherein

at each occurrence Z is independently chosen from

--CH2-, -0-, -S~, and -NH-;

at each occurrence L ² is independently chosen from (C i -C--o)hydrocarbyiene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-; at each occurrence R ^" is independently chosen froffi -H, (Ci -C ₅ )alkyL -S0 ₃ ^" , ·( ^' () · . -H ₂ P0 ₄ ^" , HP0 ₄ ^2" , P0 ₄ \ phenolaie, (Ci- Cio)alkyl-(l,4-substituted l,4-diazabicyclo[2.2.2]octane-l,4-diium)-, and 3- methylimidazolium, and -N ⁺ ( ^A ) ₃ wherein at each occurrence R ^A is

independently (C 1 -C5)alkyl;

j is about 0 to abo t 4:

at each occ ly chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(0)0-(C i - C i o)hydrocarbyl, and -C(0) ^' NH-(Ci - Cio)hydrocarbyl; and

m is about 1 to about 10.

[00302] Embodiment 88 provides the sensor of any one of Embodiments

86-87, wherein the cationic p-phenylene ethynylene compound has the structure: wherein

at each en from -N (CilY , n is about 2 to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alky1; and

q is about 1 to about 5.

[00303] Embodiment 89 provides the sensor of any one of Embodiments

86-88, wherem the cationic p-phenylene ethynylene compound has the structure

wherein s is about 1 to about 3.

[00304] Embodiment 90 provides the sensor of any one of Embodiments

86-89, whereirs the enzyme substrate is an anionic enzyme substrate.

[00305] Embodiment 91 provides the sensor of Embodiment 90, wherein the anionic enzyme substrate is l ,2-dilauroyl-sn-glycero-phospho-(r-rac- glycerol).

[00306] Embodiment 92 provides the sensor of any one of Embodiments

85-91, wherein the p-phenyiene etliynylene compound is an anionic p-phenylene etliynylene compound.

[00307] Embodiment 93 provides the sensor of Embodiment 92, wherein the anionic p-phenylene etliynylene compound has the structure:

wherein

R ^l has the structure:

}_Z_L ² -R ²

wherein

at each occurrence Z is independently chosen from

-CH ·· . -0-, -S-, and -NH-;

at each occurrence L ² is independently chosen from (Ci-C5o)hydrocarbyiene interrupted by 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 groups independently chosen from -0-, -S-, and -NH-;

at each occurrence R ^"' is independently chosen froffi -H, (Ci -C ₅ )alkyL -Si) . . -CO . . -I h PO, . HP0 ₄ ^2" , P0 ₄ ^3" , and phenolate;

j is about 0 to about 4:

at each occurrence L ^! is independently chosen from a bond and

at each occurrence A is independently chosen from -H, substituted or unsubstituted -C(Q)0-(C i -Cio)hydrocarbyl, and -C(0)NH-(Ci - C io)hydrocarbyl,

m is about 1 to about 10.

[00308] Embodiment 94 provides the sensor of any one of Embodiments

92-93, wherein the anionic p-phenylene ethynylene compound has the structure: wherein

at each occurrence R ^J is independently chosen from -SO ₃ ^" , -CO? ^" ,

-H2PO4 ^' , ITPO4 ^2" , PCXf , and phenolate;

n i about 2, to about 4;

at each occurrence A is independently chosen from -H and - C(0)0-(Ci-C ₅ )alky1; and

q is about 1 to about 5.

[00309] Embodiment 95 provides the sensor of any one of Embodiments

92-94, wherein the anionic ρ-phenylene ethynylene compound has the structure:

■SO,

wherein t is about 1 to about 3.

[ΘΘ310] Embodiment 96 provides the sensor of any one of Embodiments

92-95, wherein the enzyme substrate is a cationic enzyme substrate.

[00311] Embodiment 97 provides the sensor of any one of Embodiments

92-96, wherein the cationic enzyme substrate is a substituted or unsubstituted (C 1 -C ₂₅ )hydroearbyl-C(0)0-(C 1 -Cio)alkyl-N ⁺ ((C -C ₅ )aikyl) ₃ . [00312] Embodiment 98 provides the sensor of any one of Embodiments

92-97, wherein the cationic enzyme substrate is a substituted or unsubstituted (Ci -C _2S )alkyl-C(0)0-(C , · ⁽ ., )alkyl-N ^{1 "} (CH ₃ ) ₃ .

[00313] Embodiment 99 provides the sensor of any one of Embodiments 92-98, wherein the cationic enzyme substrate is chosen from lauroyl choline and acetylcholine.

[00314] Embodiment 100 provides the sensor of any one of Embodiments

92-99, wherein the cationic enzyme substrate is iauroyi choline.

[00315] Embodiment 101 provides a sensor for detecting the presence of a chemical agent, the sensor comprising a sensor composition comprising a complex comprising a p-phenylene ethynylene compound and an enzyme substrate;

wherein

-phenylene ethynylene compound has the structure:

wherein t is about 1 to about 3 ; and enzyme substrate is lauroyl choline.

[00316] Embodiment 102 provides the method or sensor of any one or any combination of Embodiments 1-101 optionally configured such that all elements or options recited are available to use or select from.