WANG YAJUN (US)
SPITALE ROBERT (US)
NGUYEN KIM (US)
WO2000009672A1 | 2000-02-24 |
WANG ET AL.: "Evolution of a general RNA-cleaving FANA enzyme", NATURE COMMUNICATIONS, vol. 9, no. 1, 2018, XP055954514
WANG ET AL.: "Evaluating the Catalytic Potential of a General RNA-Cleaving FANA Enzyme", CHEMBIOCHEM, vol. 21, no. 7, 1 April 2020 (2020-04-01), pages 1001 - 1006, XP055954516
CULBERTSON ET AL.: "Evaluating TNA stability under simulated physiological conditions", BIOORG MED CHEM LETT, vol. 26, no. 10, 2016, pages 2418 - 2421, XP029659124, DOI: 10.1016/j.bmcl.2016.03.118
NGUYEN ET AL.: "Allele-Specific RNA Knockdown with a Biologically Stable and Catalytically Efficient XNAzyme", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 143, no. 12, 31 March 2021 (2021-03-31), pages 4519 - 4523, XP055954518
WHAT IS CLAIMED IS: 1. A composition for gene silencing, the composition comprising: a) a 15-nucleotide catalytic domain according to SEQ ID NO: 1, wherein one or more nucleic acids of the catalytic domain is replaced by xeno-nucleic acids (XNA); b) a first substrate recognition domain 5’ to the catalytic domain; c) a second substrate recognition domain 3’ to the catalytic domain; d) a 5' terminal threose nucleic acid (TNA) residue; and e) a 3' terminal TNA residue; wherein one or more nucleic acids of the first substrate recognition domain or the second recognition domain is replaced by XNA; and wherein the composition has enhanced stability and enhanced catalytic activity compared to a control molecule comprising wild type SEQ ID NO: 1 as its catalytic domain. 2. The composition of claim 1, wherein the XNA is 2'-fluoroarabino nucleic acid (FANA). 3. The composition of claim 1, wherein the XNA is TNA. 4. The composition of claim 1, wherein the composition is for knocking down a target RNA. 5. The composition of claim 4, wherein the target RNA is KRAS. 6. The composition of claim 1, wherein the first substrate recognition domain and second substrate recognition domain are at least 5 nucleotides long. 7. A method of treating a disease or condition or a symptom thereof, the method comprising administering an effective amount of a 10-23 analogue composition to a subject in need thereof, wherein the composition comprises: a) a 15-nucleotide catalytic domain according to SEQ ID NO: 1, wherein one or more nucleic acids of the catalytic domain is replaced by xeno-nucleic acids (XNA); b) a first substrate recognition domain 5’ to the catalytic domain; c) a second substrate recognition domain 3’ to the catalytic domain; and d) a 5' terminal threose nucleic acid (TNA) residue; and e) a 3' terminal TNA residue; wherein one or more nucleic acids of the first substrate recognition domain or the second recognition domain is replaced by XNA 8. The method of claim 7, wherein the XNA is 2'-fluoroarabino nucleic acid (FANA). 9. The method of claim 7, wherein the XNA is TNA. 10. The method of claim 7, wherein the composition is for knocking down a target RNA. 11. The method of claim 10, wherein the target RNA is KRAS. 12. The method of claim 7, wherein the first substrate recognition domain and second substrate recognition domain are at least 5 nucleotides long. 13. The method of claim 7, wherein the disease or condition is caused by a common or rare genetic disease, viral or bacterial pathogen, cancer, inflammation, cardiovascular disease, immune deficiency or a neurological disorder. 14. A method of validating gene mutations associated with a disease or condition, the method comprising: a) administering a 10-23 analogue composition to a cell line or animal model, wherein the composition comprises: i) a 15-nucleotide catalytic domain according to SEQ ID NO: 1, wherein one or more nucleic acids of the catalytic domain is replaced by xeno-nucleic acids (XNA); ii) a first substrate recognition domain 5’ to the catalytic domain; iii) a second substrate recognition domain 3’ to the catalytic domain; iv) a 5' terminal threose nucleic acid (TNA) residue; and v) a 3' terminal TNA residue; wherein one or more nucleic acids of the first substrate recognition domain or the second recognition domain is replaced by XNA; and b) analyzing the cell line for characteristics associated with the disease or condition. 15. The method of claim 14, wherein the XNA is 2'-fluoroarabino nucleic acid (FANA). 16. The method of claim 14, wherein the XNA is TNA. 17. The method of claim 14, wherein the composition mutates a target RNA. 18. The method of claim 14, wherein the target RNA is KRAS. 19. The method of claim 14, wherein the first substrate recognition domain and second substrate recognition domain are at least 5 nucleotides long. 20. The method of claim 14, wherein the disease or condition is caused by a common or rare genetic disease, viral or bacterial pathogen, cancer, inflammation, cardiovascular disease, immune deficiency or a neurological disorder. |
[0065] The present invention may further feature a method of validating gene mutations associated with a disease or condition. In some embodiments, the method comprises administering a 10-23 analogue composition to a cell line or animal model, and analyzing the cell line or animal model for characteristics associated with the disease or condition. In some embodiments, the composition comprises a 15-nucleotide catalytic domain according to SEQ ID NO: 1 with one or more nucleic acids of the catalytic domain are replaced by xeno-nucleic acids (XNA), a first substrate recognition domain 5’ to the catalytic domain, a second substrate recognition domain 3’ to the catalytic domain, a 5' terminal threose nucleic acid (TNA) residue, and a 3' terminal TNA residue. In some embodiments, one or more nucleic acids of the first substrate recognition domain or the second recognition domain are replaced by XNA. [0066] As used herein, an appropriate cell line refers to a cell line that is biologically relevant to the disease or the condition being studied. In some embodiments, cell lines may include, but are not limited to, HEK-293, HeLa, or Chinese hamster ovary cells (CHO). As used herein, “characteristics associated with a disease or condition” may refer to measurable molecular changes in a cell line. [0067] EXAMPLE [0068] The following is a non-limiting example of the present invention. It is to be understood that said example is not intended to limit the present invention in any way. Equivalents or substitutes are within the scope of the present invention. [0069] Optimizing the substrate recognition domain. [0070] XNA containing oligonucleotide synthesis and preparation: TNA phosphoramidites were synthesized using known methods. Standard β-cyanoethyl phosphoramidite chemistry and an Applied Biosystems 3400 DNA Synthesizer were used to synthesize TNA oligonucleotides on Universal Support II CPG columns in 1 μmole scale. Standard DNA coupling procedures were modified for FANA and/or TNA containing oligonucleotides such that coupling time for FANA and TNA amidites was increased to 360 s and 1200 s, respectively. Detritylation was performed in two cycles for TNA amidites, 60 s each. Oligonucleotides used for biostability studies were coupled with a 5'-hexynyl phosphoramidite for later IR-680 fluorophore tagging via click chemistry. Cleavage from the solid support and final deprotection of oligonucleotides synthesized were achieved simultaneously in NH 4 OH (33%) for 18 h at 55°C. Oligonucleotides were purified on denaturing (8 M urea) PAGE, recovered by electro-elution, and subsequently desalted by buffer exchange using microcentrifugal concentrators, and quantified by nano-drop. All oligonucleotides synthesized in-house were subjected to Quadrupole time-of-flight mass spectrometry (Q-TOF) for identity confirmation. [0071] Recognizing that XNAs harbor physicochemical properties that are distinct from those found in natural DNA and RNA, whether XNA residues could be used to enhance the RNA- cleavage activity of 10-23 under physiological conditions needed to first be determined. First, all of the DNA residues were replaced in the binding arms of the substrate recognition domain with 2'-fluoroarabino nucleic acids (FANA, FIG. 1B). FANA is a close structural analog of DNA that contains a fluorine atom at the 2' position of a 2'-deoxyarabinose sugar. [0072] Apart from thymidine, which was substituted for uridine, each DNA nucleotide was replaced with the corresponding FANA nucleotide. LNA was also considered as a possible XNA modification due to its high thermal stability with RNA (~2-3 °C per base pair), but concerns over its cellular toxicity led to focusing the efforts on FANA. This version of 10-23, termed F10-23, functions with a pseudo first-order rate constant (k obs ) of 0.57 min -1 under single-turnover conditions in the buffer containing 10 mM MgCl 2 and 150 mM NaCl (pH 7.5, 24ºC), which is nearly 2-fold faster than the unmodified parent enzyme (FIG. 1C, FIG. 1E). The enhanced activity of F10-23 over 10-23 is maintained under physiological conditions in which the Mg 2+ concentration is reduced to 1 mM (k obs of 0.015 min -1 versus 0.009 min -1 , respectively) (FIG.1D, FIG.1F) [0073] Cleavage of long RNA substrates: [0074] Generation of RIMKLA mRNA transcript for in vitro cleavage assay by 10-23 and F10-23: Homo sapiens ribosomal modification protein rimK like family member A (RIMKLA) was reversed transcribed from HeLa total RNA using SuperScript RT III (Invitrogen-Life Technologies, CA) according to manual instruction. RIMKLA cDNA was subjected to 2-round nested PCR using KOD polymerase (Fisher Scientific, Cat# 710863) to introduce T7 promoter upstream of the coding sequence of RIMKLA for subsequent in vitro transcription. mRNA was then transcribed in 1x RNAPol reaction buffer, supplemented with 0.5 mM each ATP, UTP, GTP, CTP, 5 mM dithiothreitol (DTT), 1 U/μL RNase inhibitor using 4 μg/μL of the purified DNA amplicon and 25 U/μL of T7 RNA polymerase at 37ºC for 16 h. Transcription was terminated by the addition of 10 U/mL of RNase-free DNase I and incubation at 37ºC for 15 min. The transcription reaction was resolved by 10% denaturing purification PAGE (8 M urea), and the gel was visualized by UV-shadowing. The RNA transcript was excised, electroeluted, exchanged into H2O using EMD Millipore YM-3 micro centrifugal device, and UV quantified by Nanodrop before in vitro kinetic cleavage assays by 10-23 and F10-23. [0075] To provide further evidence of RNA cleavage activity, F10-23 was challenged to cut a much longer RNA substrate that was more reminiscent of a biological RNA molecule found in nature. For this example, a 103 nt segment of the ribosomal modification protein rimK, was chosen, and an unlabeled RNA transcript was generated by in vitro transcription with T7 RNA polymerase. The catalytic activity of F10-23 was compared to standard 10-23 under single-turnover, steady-state, and multiple-turnover conditions in a physiological buffer containing 1 mM MgCl2 and 150 mM NaCl (pH 7.5, 24ºC). Here steady-state kinetic measurements are viewed as a more rigorous test of catalytic activity than the more common single-turnover reaction. Analysis of the reaction products by denaturing polyacrylamide gel electrophoresis (PAGE) (FIG. 3A and 3B) with ethidium bromide staining reveals the appearance of upstream (37 nt) and downstream (66 nt) cleavage fragments produced by sequence-specific cleavage of a central G-U dinucleotide junction. F10-23 is faster on the shorter RNA substrate than the parent 10-23 enzyme in all cases tested, suggesting that F10-23 has the potential to invade folded RNA structures found in cellular systems. [0076] Optimizing the catalytic core: [0077] To determine if the activity of 10-23 could be further enhanced by introducing chemical modifications into the catalytic domain. Although this region of the sequence represents an evolutionary optimum in which almost any nucleotide change leads to a mutant enzyme with reduced catalytic activity, substantially less is known about the tolerance of the catalytic core toward chemical modifications that alter the sugar moiety. Each DNA residue was systematically replaced in the catalytic core with the corresponding FANA nucleotide (e.g., dA was replaced with fanaA (i.e, fA); Table 1). The complete set of 15 single-point mutant enzymes were assayed for RNA cleavage activity under single-turnover conditions in a physiological buffer containing 1 mM MgCl2 and 150 mM NaCl (pH 7.5, 24ºC). The catalytic profile (FIG. 2A, FIG. 4A) indicates that residues G2 and T8 are highly tolerant to substitution with the FANA residues, maintaining ~80% activity relative to the parent enzyme. This result shows that G2 and T8 accept conformational distortions caused by 2'-5' phosphodiester linkages. Of the remaining positions, substitutions made to the T4 and A9 positions show moderate activity (50- 60%), while the C9, G14, and A15 positions have low activity (20-30%). The remaining 8 positions are each inactive when the wild-type DNA residue is replaced with FANA. Surprisingly, a designed version of 10-23 carrying both the G2 and U8 FANA mutations is nearly 50% more active than the parental enzyme FIG.4B), suggesting that these two substitutions function with synergistic activity. [0078] Designing the X10-23 enzyme: [0079] Encouraged by the structural mutagenesis study, a new version of the enzyme was synthesized in which the catalytic core of F10-23 was modified to contain both G2 and U8 FANA substitutions (SEQ ID NO: 17) and non-complementary ɑ-L-threofuranosyl thymidine (tT) residues were added to the 5' and 3' terminal positions to protect the oligonucleotide against nuclease digestion (FIG. 2B). ɑ-L-threofuranosyl nucleic acid (TNA) is an artificial genetic polymer in which the natural five-carbon ribose sugar found in RNA has been replaced with an unnatural four-carbon threose sugar. TNA is an ideal choice for stabilizing the backbone structure against nuclease digestion as TNA is completely recalcitrant to DNA and RNA degrading enzymes This new version of the enzyme, termed X10-23, contains three different classes of nucleic acids (DNA, FANA, and TNA) and functions with a pseudo first-order rate constants of 0.68 min -1 and 0.018 min -1 in reaction buffer [150 mM NaCl (pH 7.5, 24ºC)] containing 10 mM and 1 mM MgCl2 , respectively (FIG.2C, 2D, 2E, and 2F). These rates are at least 2-fold faster than the parent enzyme. [0080] Next, whether the enhanced chemical diversity of X10-23 enabled higher multiple- turnover activity in vitro was determined. First 10-23, F10-23, and X10-23 were evaluated under steady-state conditions with equimolar concentrations of substrate and enzyme. Kinetic measurements reveal that F10-23 and X10-23 (FIG. 5A) are ~3-fold faster than 10-23, which is consistent with their activity under pre-steady-state conditions. However, striking differences were observed under multiple turnover conditions when the RNA substrate is present in 10-fold molar excess over the enzyme. Under these conditions, F10-23 and X10-23 are ~50-fold more active than the parent enzyme, suggesting that important structural differences exist between the pre- and post-catalytic state of X10-23 versus the parent 10-23 DNAzyme. No significant difference in catalytic activity was observed when the binding arms of the parent enzyme were extended by 1 nt (7+7 rather than 6+6) (FIG. 5A). Furthermore, product inhibition was not observed when the analogous 7+7 construct was tested for F10-23 (FIG. 6A-6D), indicating that FANA provides a balanced solution to the problem of how to enhance substrate binding kinetics while avoiding the harmful effects of product inhibition. [0081] Evaluating the biostability of X10-23 [0082] Biostability measurements: All biostability assays were performed in DMEM containing 1 μM of tested construct with the presence of 2 mg/mL of human liver microsome, or 50% human serum (v/v), or 10 mU/mL of snake venom phosphodiesterase at 37°C. Multiple time points were collected for each condition by quenching 1.5 μL of reactions using 15 μL (10 equivalents, v/v) of formamide containing 25 mM EDTA. Samples were denatured for 15 min at 95ºC and analyzed by 15% denaturing PAGE. Gels were visualized using a LI-COR Odyssey CLx. [0083] Along with efficient catalytic activity, biostability is a critical parameter for achieving improved efficacy in cellular systems that contain strong DNA and RNA degrading enzymes. For this assay, the stability of the 10-23, F10-23, and X10-23 scaffolds was analyzed in concentrated human liver microsomes (HLM) and 50% human serum (HS) in Dulbecco's Modified Eagle Medium (DMEM). Both assays provide a rigorous test of oligonucleotide stability due to the abundance and diversity of nucleases present in the media. In addition, each scaffold was also evaluated against snake venom phosphodiesterase (SVPDE), an aggressive enzyme with strong 3'-exonuclease activity commonly employed to evaluate the stability of oligonucleotide therapeutics. The results (FIG. 5B, FIG. 7) clearly show that X10-23 displays markedly enhanced biostability under all conditions tested, with almost no degradation observed after either 21 hours of incubation in HLM and HS or 90 minutes of incubation in SVPDE. By comparison, 10-23 and F10-23 show significant degradation with F10-23 being slightly less stable than 10-23. This result validates the utility of TNA as a capping agent for protecting the 5' and 3' termini against nuclease digestion. [0084] Comparing X23-10 to 2’-O-methyl RNA and LNA version of 10-23: [0085] Kinetic cleavage reaction of 10-23, F10-23, X10-23, OME10-23, and LNA10-23: Single-turnover kinetic cleavage reactions were conducted in 50 mM Tris buffer (pH 7.5) containing 150 mM NaCl, 1 mM MgCl2, 0.5 μM of substrate, and 2.5 μM of enzyme at 24ºC. Purified enzymes and substrates were annealed in a 50 mM Tris buffer (pH 7.5) by heating for 5 min at 90ºC and cooling for 5 min on ice. Reactions were initiated by the addition of NaCl and MgCl2 to the reaction. For determination of pseudo first-order rate constant, multiple time points were collected by quenching 1.5 μL of reaction using 15 μL (10 equivalents, v/v) of formamide stop buffer (99% deionized formamide, 25 mM EDTA) and cooling on ice. Samples were denatured for 15 min at 95ºC and analyzed by 15% denaturing PAGE. Gels were visualized and quantified using a LI-COR Odyssey CLx. Values of k obs were calculated by fitting the percentage of substrate cleaved and reaction time (min) to the first-order decay equation (1) using Prism 6 (GraphPad, USA): where P t is the percentage of cleaved substrate at time t, P ∞ is the apparent reaction plateau and k obs is the observed first-order rate constant. For kinetic cleavage reactions under stoichiometric and multiple-turnover conditions, substrate concentrations were poised at 0.5 μM, and enzyme concentrations were adjusted to 0.5 μM and 50 nM, respectively. [0086] How X10-23 compared to other chemically enhanced versions of 10-23 that have been previously evaluated as gene silencing reagents was determined next. Among the various combinations, 2'-O-methyl ribonucleotides and LNA have received significant attention as chemical modifications that function with enhanced activity and biostability which is consistent with their broad deployment in other classes of therapeutic oligonucleotides. OME10-23 (UCAUGAGGCTAGCUACAACGAGGUUAG; SEQ ID NO: 52) and LNA10-23 (TCATGAGGCTAGCTACAACGAGGTTAG; SEQ ID NO: 53), two 10-23 analogs with substrate binding arms that are complementary to the RNA substrate (FIG.8A and 8B), were synthesized. OME10-23 is an analog of 10-23 in which 16 DNA residues are replaced with 2'-O-methyl ribonucleotides (bolded -10 in the substrate binding arms and 6 in the catalytic core (underlined)), while LNA10-23 is a 10-23 analog in which three terminal DNA residues in each binding arm are replaced with LNA (replaced residues are bolded and the catalytic core is underlines in the aforementioned sequences). [0087] Kinetic measurements indicate that LNA10-23 is significantly faster than OME10-23 under all conditions tested. Under single turnover conditions, LNA10-23 functions with a rate of 0.26 min -1 in the presence of 10 mM MgCl 2 and 0.03 min -1 when the concentration of Mg 2+ is reduced to 1 mM (FIG. 9A, 9B, 9C, and 9D). These values compare favorably against OME10-23, which achieves rates of only 0.011 and 0.001 min -1 under identical conditions of high and low Mg 2+ ions, respectively. The superior activity of LNA10-23 over OME10-23 is maintained under steady-state conditions where substrate and enzyme are present in equimolar concentrations (FIG. 8C). However, the kinetic profile changes dramatically under multiple turnover conditions where LNA10-23 shows clear signs of product inhibition (FIG. 8C). Thus, even though LNA10-23 is a faster enzyme than X10-23 under single turnover conditions, X10-23 is a better candidate for cellular applications (FIG.8D) due to its robust multiple turnover activity in vitro. [0088] Intracellular reduction of GFP: [0089] Next, the activity of X10-23 in cultured mammalian cells was determined using the green fluorescent protein (GFP) as an optical reporter for gene silencing activity. GFP expression was measured in the presence and absence of two X10-23 reagents that were designed to target G-U dinucleotides in the coding (internal) and 3' untranslated region (3'UTR) of the GFP mRNA transcript (FIG. 10A). Both reagents were independently validated in vitro using synthetic RNA oligonucleotides that matched the GFP segments targeted in the cellular assays (FIG. 11A and 11B). Cellular assays were performed in multiple formats using HEK293T cells that were transfected with a GFP expression plasmid driven by a CMV promoter. Fluorescent images collected after 24 hours of incubation post-transfection reveal a significant loss of GFP signal for cells that were co-transfected with the GFP plasmid and an X10-23 reagent targeting either the internal site or 3'UTR site, or both sites simultaneously, as compared to cells transfected with the GFP plasmid only (FIG. 10B). qRT-PCR measurements confirm that loss of the GFP signal is due to a drop in mRNA template copy number for GFP (FIG.10C), demonstrating a reduction of both protein and mRNA levels in the cell. [0090] Without wishing to limit the present invention to any theory or mechanism it was thought that given the strength of the CMV promoter, each X10-23 reagent must be engaging multiple mRNA templates in the cytoplasm in order to maintain strong gene silencing activity under constitutive GFP expression conditions. [0091] Recognizing that constitutive gene expression from a CMV promoter produces larger quantities of RNA than endogenous gene expression, a dose-dependent treatment of actinomycin D for 4 hours was administered after 20 hours of incubation post-transfection to inhibit RNA transcription. Actinomycin D is a transcriptional inhibitor that prevents continued expression of GFP in the cell, allowing X10-23 to engage only those GFP transcripts that are present when the antibiotic is administered to the cells. qRT-PCR analysis of cellular GFP transcripts shows a 3-fold reduction in template copy number by X10-23 when the cells are treated with 40 μM of actinomycin D, as compared to cells that are co- transfected with the GFP plasmid and X10-23 but not treated with the antibiotic (FIG.12). These results compare favorably against the parent 10-23 DNA enzyme synthesized with an 3' inverted dT cap (FIG. 7) as well as the inactive X10-23 variant and a fully complementary FANA antisense strand capped at the 5' and 3' ends by unmatched terminal tT residues (FIG. 13A and 13B). Of the controls, the inactive X10-23 enzyme shows no reduction in GFP protein and mRNA template copy number, while the parent DNAzyme and antisense strand yield slightly elevated values of GFP mRNA and protein (FIG.13A and 13B). [0092] Intracellular reduction of endogenous KRAS [0093] Having demonstrated that X10-23 is capable of knocking down the expression of transiently transfected genes in cultured cells, whether similar effects could be achieved for endogenous mRNA transcripts was determined next. KRAS was chosen as a cellular target due to its implication in lung, pancreatic, and colorectal adenocarcinomas. KRAS has been the focus of many drug targeting campaigns and is often viewed as an “undruggable” target due to the inherent difficulty of altering its cellular expression profile. Two X10-23 reagents were designed, synthesized, and tested for targeting the 1st exon and 3'UTR (FIG. 14A) of endogenous KRAS in cervical cancer (HeLa) and breast cancer (MDA-MB-231) cell lines. HeLa and MDA-MB-231cells were either transfected with or without 4 μg of X10-23 and KRAS mRNA levels were quantified by qRT-PCR after 48 hours of incubation post-transfection (FIG. 14B). Relative to the transfection control, both cell lines show a >65% reduction of mRNA copy number for the X10-23 reagent targeting the 1st exon (FIG. 14C and 14D). The X10-23 reagent targeting 3'UTR was slightly less effective, yielding a ~35- 45% reduction in KRAS mRNA copy number. Differences in the RNA cleavage activity between the two X10-23 reagents is congruent with their in vitro activity observed with synthetic oligonucleotides (FIG. 15A and 15B), and likely reflects sequence-specific differences in the binding energetics of the two reagents. Overall, these data clearly demonstrate that X10-23 can be used to knockdown the expression of disease-causing proteins in human cells. [0094] Mechanistic insights into cellular cleavage: [0095] In vitro RNAse H activity assay with X10-23, unmatched X10-23, and inactive X10-23: All RNase H activity assays were performed under simulated physiological buffer conditions in 50 mM Tris-HCl (pH 7.5) containing 0.5 mM MgCl2, 150 mM NaCl, and 0.1 unit/μL of RNase H at 37°C. 1 μM of RNA substrate was mixed with 1 μM of the tested constructs of X10-23, unmatched X10-23, and inactive X10-23 in Tris-HCl (pH 7.5) buffer, respectively, to anneal by heating for 5 min at 90ºC and cooling for 5 min on ice. Reactions were initiated by the addition of MgCl2, NaCl, and RNase H to the final concentration. Reactions were sampled by quenching 1.5 μL of reactions using 15 μL (10 equivalents, v/v) of formamide containing 25 mM EDTA at time points of 0, 1, 5, and 20 hours. Samples were denatured for 15 min at 95ºC and analyzed by 15% denaturing PAGE. Gels were visualized using a LI-COR Odyssey CLx. [0096] RNase H has been implicated as a contributor to RNA-based degradation by 10-23 variants due to the presence of complementary substrate binding arms that mimic antisense oligonucleotides. Recognizing the substantial difference in multiple turnover activity between 10-23 and X10-23, it was hypothesized that the newly engineered X10-23 reagent was sufficiently fast that it would be less susceptible to the effects of an RNase H induced cleavage pathway. To investigate this possibility, the catalytic activity of X10-23 was evaluated under simulated physiological conditions in buffered solutions that either contain or lack RNase H. X10-23 variants were designed to cleave segments of GFP and KRAS transcripts that were prepared as synthetic oligonucleotides. Inactive versions of X10-23 and active versions that were non-complementary to the mRNA targets were used as negative controls. The X10-23 reagents show strong site-specific RNA cleavage activity in the presence and absence of RNase H (FIG. 16A and 16D), implicating Mg 2+ -dependent XNAzyme catalyzed RNA cleavage as the predominant mechanism of RNA degradation. Among the negative control sequences, the inactive X10-23 variant targeting GFP yields a banding pattern consistent with limited RNase H activity, while the equivalent KRAS targeting reagent shows no activity in the presence or absence of RNase H (FIG. 16B and 16E). This observation may be attributed to differences in the hybridization efficiency of the two X10-23 reagents, or possibly, some unknown sequence specificity preference of RNase H. As expected, the second X10-23 control with non-complementary binding arms but an active catalytic core fails to cut the RNA GFP and KRAS RNA substrates (FIG. 16C and 16F). Similar results were obtained for in vivo GFP and KRAS gene silencing experiments performed in mammalian cells comparing the active X10-23 reagent to the inactive or unpaired control reagents. [0097] Table 3: Note: Catalytic domain = underlined; FANA = bolded; TNA = t ; LNA = italicized [0098] The present invention aims to narrow the gap between DNAzymes and protein-based gene silencing tools by expanding the chemical space of nucleic acid analogs used to construct nucleic acid enzymes. Efforts were focused on xeno-nucleic acids, which are artificial genetic polymers with novel sugar-phosphate backbones that harbor unique physicochemical properties relative to natural DNA and RNA. [0099] Without wishing to limit the present invention to any particular theory or mechanism it is thought that appropriate positioning of XNA residues in the nucleic acid backbone structure of a highly evolved DNAzyme will lead to enhanced RNA cleavage activity under physiological conditions, while simultaneously protecting the molecule from the harmful effects of nuclease digestion. This hypothesis is supported by limited structural data showing subtle yet important differences in the helical geometry of XNA duplexes. [00100] Critical to the design of the present invention was the need to identify XNA residues that would (i) increase substrate binding kinetics without sacrificing multiple turnover activity, (ii) improve cofactor binding, and (iii) minimize the exolytic activity of biological enzymes. Using a medicinal chemistry approach that systematically probed the substrate binding arms and catalytic domain of the classic DNAzyme 10-23, a highly efficient and biologically stable variant that comprises three different classes of nucleic acid molecules (DNA, FANA, and TNA) was discovered. Relative to the parent enzyme, X10-23 achieves a ~50-fold increase in multiple turnover activity under simulated physiological conditions and enhances the biological stability of the backbone structure >100-fold under stringent nuclease conditions. In cultured mammalian cells, X10-23 imbues a >60% reduction in mRNA and protein abundance under conditions of constitutive expression, which is further enhanced upon treatment with a transcriptional inhibitor. Similar activity profiles were observed for X10-23 reagents targeting endogenous KRAS expression in human cancer cell lines, implying that X10-23 has the potential to alter the expression profiles of proteins that are thought to be “undruggable”. Finally, compelling evidence was provided showing that X10-23 does not rely on RNase H as a mechanism for RNA degradation. [00101] In summary, the present invention establishes X10-23 as a new tool in the ever expanding toolbox of gene silencing reagents. The ability for X10-23 to function with high activity and biological stability in vitro and in cultured mammalian cells suggests that even highly evolved nucleic acid enzymes can be optimized for improved activity. Based on these findings, the exploration of new molecular chemotypes provide a powerful approach for creating highly active nucleic acid enzymes with potential value as future therapeutic agents. [00102] Intracellular GFP and KRAS reduction test: [00103]Cell lines and mammalian cell cultures and conditions: HEK293T (HEK) and HeLa cells were cultured in DMEM (Corning, Cat#: 10-017-CM) supplemented with 10% FBS, 1% (1 mg/mL) penicillin and streptomycin and grown at 37°C, 5% CO2. MDA-MB-231 cells were cultured in the same medium as HEK and HeLa cells but supplemented with additional components of 1 mM sodium pyruvate. [00104]Transfection: For titrating amount of single or multivalent X10-23 experiments: After 48 h seeding of 2.5x10 5 cells/well, HEK293T in 6-well plates were transfected with 1 μg of pCDNA3.3-EGFP only (Negative control) or with 1 μg of pCDNA3.3-EGFP and 4, 6, or 8 μg of either internal or 3’UTR GFP X10-23 in single experiments or 2/2 μg, 3/3 μg or 4/4 μg of both internal/3’UTR GFP X10-23 in multivalent (dual X10-23) experiments by using JetPrime Transfection reagent (Polyplus Transfection, France) according to manual instruction except adding 5x higher than the manual recommended volume of JetPrime Reagent. For negative controls, the volume of JetPrime Reagent used for each well was the same as those with X10-23 to ensure the same transfection condition in the control and experimental samples [00105]For comparison of active, inactive core and active unpaired X10-23: After 48h seeding at 2.5x10 5 cells/well (6-well plate), HeLa cells were transfected with 5.9 μg X10-23 variants targeting the 3’UTR region of KRAS transcript (active vs. inactive core) or GFP transcript (active core but unpaired binding arms) using JetPrime Transfection reagent. At 96h post transfection, cells were harvested and subjected to total RNA extraction and subsequently underwent DNAse treatment as described in the RNA isolation section. DNA-free RNA was subjected to RT-qPCR as described in the reverse transcription and SYBR Green qPCR analysis section. [00106]For multivalent benchmark experiments: After 48 h seeding at 2.5x10 5 cells/well, HEK293T in 6-well plates were transfected with 1 μg of pCDNA3.3-EGFP only (Negative control) or with 1 μg of pCDNA3.3-EGFP and 4/4 μg of both internal/3’UTR GFP X10-23 (dual X10-23), DNA10-23 (dual DNA10-23), antisense (dual antisense oligos), inactive X10-23 (dual Inactive X10-23) or inactive DNA10-23 (dual inactive DNA10-23). Parameters used in subsequent imaging and RNA isolation at 48 h post-transfection are the same as described in RNA isolation section. [00107]For single or multivalent KRAS X10-23 experiments in HeLa or MDA-MB-231 cells: After 48 h, 76 h seeding of 2.5x10 5 cells/well of HeLa or MDA-MB-231 cells in 6-well plates, respectively, the cells were transfected with transfection carrier only (Negative control) or with 4/4 μg of both internal/3’UTR KRAS X10-23 in multivalent (dual X10-23) or 8 μg of either Internal or 3’UTR KRAS X10-23 experiments using JetPrime Transfection reagent (Polyplus Transfection, France). Parameters used in RNA isolation at 48 h post-transfection are the same as described in the RNA isolation section. [00108]Cell imaging: At 24 h or 48 h post-transfection, cells were subjected to live imaging using 200M Axiovert Zeiss fluorescent microscope with 10x objective and GFP filter. Following imaging, the cells were subjected to RNA extraction. [00109]Reverse transcription (RT): Two micrograms (2 μg) of DNA-free RNA were subjected to cDNA synthesis using SuperScript III First-strand Synthesis System (Invitrogen-Life Technologies, CA) with random hexamer primers in a 20 μL reaction according to the manufacturer instructions. cDNA was subsequently purified using DNA Clean & Concentration columns from Zymo Research (Cat# D4003) according to the manufacturer instructions and eluted 2x with 100 μL water/each. [00110] SYBR Green semi-quantitative PCR (qPCR) analysis. To quantify copy number of GFP transcript in the presence or absence of GFP-X10-23, cDNA was subjected to qPCR analysis using iQ(tm) SYBR(R) Green Supermix (BioRad, Cat# 1708880) on BioRad CFX real time PCR system. In each qPCR run, known concentration of DNA standards at 5 serial dilutions was used to establish standard curve and calculation of starting quantity (SQ) of target transcripts. Specific primers for interrogating EGFP, KRAS, GAPDH (loading control) transcripts as well as for qPCR Standards are listed in Table 4. For each experimental sample, three replicates were performed, and each serial diluted Standard was assayed in duplicates. Relative mRNA copy number of target transcripts was calculated by multiplying individual starting quantity (SQ) to a corresponding scaling factor derived from loading control GAPDH SQ. By dividing the median of GAPDH SQ in a qPCR run to individual GAPDH SQ, a scaling factor for that particular sample was generated. Fold reduction was calculated using 1/2 ΔΔCt . [00111] Table 4: Table of Primers used for qRT-PCR [00112]RNA Polymerase inhibitor (Actinomycin D, ActD) treatment. In titration of ActD concentration experiment, cultures of HEK293T cells in 6-well plates transfected with either 1 μg of pCDNA3.3- EGFP only (Negative control) or with 1 μg of pCDNA3.3-EGFP and 4 μg of Internal GFP X10-23 were treated with ActD at final concentration of 0, 10, 20, 40 μM at 20 h post transfection and harvested at 4 h later (at 24 h post transfection). Treated cells were harvested and subjected to total RNA isolation and subsequent analyses. In benchmark experiment, 40 μM ActD was added to HEK293T cells transfected with dual 4 μg Internal and 4 μg 3’UTR of X10-23, 10-23, Inactive X10- 23 or antisense at 44 h post transfection and incubated at 37°C for additional 4 h prior harvesting time at 48 h post transfection. Treated cells were imaged and subjected to total RNA isolation and subsequent analyses. [00113]RNA isolation. To each well of the 6-well plate of cells (HEK293T, HeLa or MDA-MB-231), total RNA isolation was performed using 1 mL/well Trizol Reagent (Invitrogen) according to the manufacturer instructions. Total RNA was treated with Turbo DNAse (20 U/reaction) at 37°C for 30 min on shaker, and followed by purification using equal volume of Phenol-Chloroform, pH 4.5 (Thermal Fisher, Ambion Cat#:AM9720). Aqueous layer was transferred to a new tube and precipitated with one tenth volume of 5 M NaCl and one volume of isopropanol at -20°C overnight. Precipitated RNA was pelleted at 4°C and 15000 rpm using bench-top centrifuge and followed by two washes with cold (-20°C) 70% ethanol [00114]General Information: 2’F-araNTPs (faATP, faCTP, faGTP, faUTP) were obtained from Metkinen Chemistry (Kuusisto, Finland). DNA, FANA, and 5’-hexynyl phosphoramidites, as well as Universal Support II CPG columns were purchased from Glen Research (Sterling, Virginia). TNA phosphoramidites were synthesized in-house following procedures reported previously in the art. Oligonucleotides containing FANA and TNA were synthesized on an ABI3400 DNA synthesizer using chemical synthesis reagents purchased from Glen Research (Sterling, Virginia). DNA and RNA oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA). All oligonucleotides were purified by denaturing polyacrylamide gel electrophoresis and quantified by UV absorbance. YM-3 microcentrifugal concentrators were purchased from EMD Millipore (Billerica, MA). Dulbecco's Modified Eagle Medium (DMEM) was purchased from ThermoFisher Scientific (Waltham, MA). Human serum and snake venom phosphodiesterase were purchased from Sigma Aldrich (St. Louis, MO). Human liver microsome was purchased from Sekisui XenoTech, LLC. [00115] As used herein, the term “about” refers to plus or minus 10% of the referenced number. [00116] Although there has been shown and described the preferred embodiment of the present invention, it will be readily apparent to those skilled in the art that modifications may be made thereto which do not exceed the scope of the appended claims. Therefore, the scope of the invention is only to be limited by the following claims. In some embodiments, the figures presented in this patent application are drawn to scale, including the angles, ratios of dimensions, etc. In some embodiments, the figures are representative only and the claims are not limited by the dimensions of the figures. In some embodiments, descriptions of the inventions described herein using the phrase “comprising” includes embodiments that could be described as “consisting essentially of” or “consisting of”, and as such the written description requirement for claiming one or more embodiments of the present invention using the phrase “consisting essentially of” or “consisting of” is met.
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