FAMULOK MICHAEL (DE)
GEIGER ALBERT (DE)
FAMULOK MICHAEL (DE)
WO1992014843A1 | 1992-09-03 |
GEIGER A. ET AL.: "RNA Aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity"
GEIGER, ALBERT ET AL: "RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity", NUCLEIC ACIDS RESEARCH, vol. 24, no. 6, 15 March 1996 (1996-03-15), pages 1029 - 1036, XP002037703
1. | Isolated RNA molecule which has a high affinity for a specific amino acid said affinity being less than about 6.0μm. |
2. | The isolated RNA molecule of claim 1, having an affinity less than about 500 nM. |
3. | The isolated RNA molecule of claim 1, having an affinity less than about 300 nM. |
4. | The isolated RNA molecule of claim 1, wherein said amino acid is arginine. |
5. | The isolated RNA molecule of claim 1, wherein said amino acid is Larginine. |
6. | The isolated RNA molecule of claim 1, having the nucleotide sequence of Ag.06 (SEQ ID NO: 3). |
7. | Method for removing an amino acid from a solution comprising contacting said solution with the isolated RNA molecule of claim 1, bound to a solid phase, wherein said isolated RNA molecule has affinity for said arruno acid, and removing complexes of said amino acid and said RNA bound to a solid phase from said sample. |
8. | Method for separating enantiomers of amino acids from each other, comprising contacting a sample containing said enantiomers with a complex of a solid carrier and the isolated RNA molecule of claim 1, wherein said isolated RNA molecule has affinity for one of said enantiomers, and removing complexes of said enantimoer and sohd carrier bound RNA molecule from said sample. |
9. | The method of claim 8, wherein said enantiomers are L and D arg^Lnine, and said isolated RNA molecule has affinity for Larginine. 7/33 . |
10. | Method for separating a first amino acid from a sample containing at least one additional amino acid, comprising contacting a sample containing at least two amino acids with the isolated RNA molecule of claim 1, bound to a solid carrier, wherein said RNA molecule has affinity tor said first amino acid, and removing complexes of said first amino acid and said complexes of solid phase carrier and said RNA molecule from said sample. |
11. | The method of claim 10, wherein said first amino acid is arginine and said additional amino acid is citrulline. |
12. | A process for purifying an RNA molecule which has affinity of at least about 100 nM for a first amino acid, comprising, in sequence: (a) denaturing an RNA sample; (b) binding said RNA sample to a solid phase; (c) contacting said RNA bound to a solid phase with a solution of a second am o acid which differs from said first arnino acid to elute RNA with low affinity for said second acid; (d) heating said RNA bound to a solid phase; (e) contacting said RNA bound to a solid phase with said solution of a second amino acid for a second time, to elute RNA with high affinity binding for said second amino acid; (f) contacting remaining solid phase bound RNA with a solution of said first amino acid, to elute RNA which has low affinity for said first amino acid; (g) heating any remaining, solid phase bound RNA; and (h) contacting said remaining solid phase bound RNA for a second time with a solution of said first amino acid, to elute RNA with high affinity for said amino acid. |
13. | The process of claim 12, comprising bmding said RNA sample to a sohd phase having said first amino acid immobilized thereon. |
14. | The method of claim 12, further comprising isolating said RNA from eluate formed in step (h). |
15. | The process of claims 12 14, wherein steps (d) and (e) are repeated at least once. |
16. | The process of claims 12 15 , further comprising contacting said solid phase bound RNA with a solution of at least one additional amino acid at least once, to elute RNA having affinity for said amino acids. |
17. | Isolated RNA molecule of claim 1, comprising a nucleotide sequence as set forth in Seq. ID. No: 320. |
FIELD OF THE INVENTION
This invention relates to isolated RNA molecules with high or
strong affinity for amino acids, as well as uses thereof. Also, a part of
the invention are processes lor securing these RNA molecules.
BACKGROUND AND PRIOR ART
Interactions between amino acids and RNA play substantial
roles in a number of biological systems See, e.g., Draper, Ann. Rev.
Biochem 64: 593-620 (1995). For example, arginine inhibits the self-
splicing reaction of the grou jinrron of Tetrahymena by substituting for
two H-donor sites ot the guanosine cofactor which contact the G 2M -C m
base pair in the ribozvme ' s guanosine binding site. Yarus, Science
240:1751-1758 (1988); Michel, et al. Nature 342:391-395 (1989).
Recently, the editing reactions of aminoacyl tRNA synthetases have
been viewed as an example of RNA dependent amino acid recognition.
Schimmel, et al., Trends Biochem. Sci 20:1-2 (1995). These editing
reactions involve RNA dependent steps which eliminate errors of
amino acid activation and aminoacvlation. Jakubowski, et al.,
Microbiol. Rev 56:412-429 (1992). A third example is the interaction of
the HΓV-1 TAT protein with a stem loop structure of TAR RNA, located
at the 5' -end of HIV-1 mRNA. Critical for the recognition of TAT and
TAR is a single arginine within a basic region of TAT. Calnan, et al.,
Science 252:1167-1171 ( 1991). Short oligopeptides resembling the basic
region as well as tree arginine bind specifically to TAR, although
weaker than within the context of the whole protein Weeks, et al.,
Science 249:1281-1285 ( 1990). The TAT-TAR interaction provided the
first example to show that in protein-RNA recognition RNA structures
are involved which interact with individual amino acid side chains in
the protein. It seems likelv that other, yet undiscovered RNA-protein
interactions exist in which single amino acid side chains within a
protein or peptide torm specific contacts to structural elements
provided by RNA to largely determine specificity, functionality, and
strength of binding Draper, supra.
The isolation and characterization of RNA sequences which
specifically recognize individual amino acids might facilitate a better
understanding of biologically relevant protein-RNA or RNA-amino
acid interactions. A powerful tool to obtain amino acid binding RNAs
is in vitro selection as taught by, e.g. Famulok, et al., Agnew. Chem.
Int. Ed. Engl. 31:979-988 (1992). Klug, et al., Mol. Biol. Rep 20:97-107
(1994); Gold, et al. Ann. Rev. Biochem. 64:763-797 (1995); Joyce, Curr.
Opin. Struct. Biol 4:331-336 (1994), all of which are incorporated by
reference. RNA aptamers which specifically recognize amino acids,
such as ύrrimobilized tryptophan, arginine, cirxulline, and valine have
been extracted from pools of up to 10 15 different RNA sequences. See
Connell, et al., Biochemistry 32:5497-5502 (1993); Famulok, J. Am.
Chem. Soc. 116:1698-1706 (1994); Majesfeld, et al., Natur. Struct. Biol.
1:287-292 (1994), all of which are incorporated by reference. The
reported affinities ranged from 60μM (Famulok) to 12mM (Majesfeld)
with a high level of discriinination against other amino acids being
obtained in each case. Among these amino acid binding RNAs, the
arginine specific aptamers might be especially relevant to protein-RNA
recognition because arginine side chains carrying a positive charge at
neutral pH seem to be particularly suited to form specific contacts with
a negatively charged nucleic acid. See Aboul-ela et al., J. Mol. Biol
253:313-332 (1995). For example, the HIV-1 Rev protein contains a
basic region in which ten of seventeen amino acids between positions
34-50 are arginines. A corresponding 17-mer peptide binds to the Rev
responsive element (RRE) RNA IIB hairpin in the same way as within
the context of the lull-length protein with four arginines being
important for specificity. See, respectively, Kjems, et al., EMBO J
11:1119-1129 (1992); Tan, et al. CeU 73:1031-1040 (1993). In the HIV-
TAR/ Tat complex an -irginine and an isoleucine residue were found to
be critical for binding and specificity. Frankel, in Nagai, et al., ed,
RNA-Protein Interactions IRL Press, New York, NY 1994) pp. 221-247.
Furthermore, the Rex-protein of HTLV-I might interact with its natural
RNA binding element XBE through arginine residues. Baskerville et
al., J. Virol 69:7559-7569 ( 1995).
Further work has now been carried out, resulting in the
development of techniques which permit, and have permitted, the
isolation of RNA molecules which have strong or high affinities for
particular amino acid molecules. The present invention is a
development of the work described by Famulok, J. Am. Chem. Soc.
116:1698-1706 (1994), incorporated by reference. Via modifications in
the protocols described therein, it has been possible to isolate RNA
molecules of extremely high affinity, as is shown via the examples
which follow.
BRIEF DESCRIPTION OF THE FIGURES
Figure 1 is a representative elution protocol obtained in
accordance with the invention.
DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
EXAMPLE 1
Two pools of RNA were prepared for screening for high affinity
binding to amino acids. The first pool ("pool 1" hereafter) was
prepared according to Famulok, J. Am Chem. Soc. 116(5) :1698-1706
(1994), incorporated by reference. The Famulok paper teaches the
production of a pool of about 10 l3 RNA molecules which were 111
nucleotides in length. These lllmers were prepared using defined 5'
and 3' sequences, together with a randomized 74mer insert.
-D-
Famulok teaches, inter alia, a particular RNA molecule ("clone
16"), which has high L-citrulline affinity. This clone was used as the
basis for preparing a second, degenerate pool. This pool was prepared,
also following Famulok except that in preparing the 74mer insert, the
reservoirs of phospharamidite were each doped with 10% of each of the
other phospharamidites, to provide reservoirs of, e.g., 70%A, and 10%
of each of G, C and T, and so forth. (The 74mer insert is placed in
between an 18-mer and a 19-mer primer binding site.)
The entirety of pool 2 was then subjected to PCR amplification.
The PCR amplification was carrier out as described by Famulok, supra,
resin the primers described therein, i.e.,
TCTAATACGA CTC ACTA TAG GAG CTC AGC CTT CAC TGC (SEQ ID NO.:l)
and
GTGGATCCGACCGTG GTGCC
(SEQ ID NO: 2),
respectively, as the 5' and 3' primers. Six cycles of amplification were
carried out (94 °C 4min; 42 °C, 7min; 72 °C 7min), and then the
amplification product was extracted with phenol/ CHCL y precipitated
with ethanol, dissolved in 1.3 ml of TE (lOmM Tris-HCl, pH 7.6; ImM
EDTA. pH 80), followed by gel filtration on Sephadex G-50. RNA was
transcribed from the PCR product and used in the s election
protocol s wh ich fo l l ow .
EXAMPLE 2
The RNA produced in Example 1, supra, was selected for high
affinitv amino acid binding. Prior to this, however, it was treated to
purifv it. This procedure is now set forth.
Samples ot the RNA containing solutions of example 1 (10-15 μg,
or 0.4nmoles of RNA), were diluted with water to final volumes of 80
μl. Then, the solutions were heated to 90 °C for 10 minutes, followed
by cooling to 23 °C for 5 additional minutes, after which they were
added to a preselection column. The preselection column consisted of
0.5 ml of agarose which had derivatized glycine bound thereto
(following manufacturer's instructions), and which had been
equilibrated with several column volumes of binding buffer prior to
the addition of the samples.
The RNA containing samples were added to the preselection
column, and then washed with 2-3 volumes of buffer. The effect of this
wash is to start a flow-through from the preselection column, which
was placed directly on top of the selection column (discussed infra).
Positioned direct lv below the preselection column was the
selection column, which was agarose with derivatized arginine bound
thereto, the arginine having been derivatized and attached to the
agarose, in accordance with the manufacturer's instructions. The
selection column had been rinsed, previously, with binding buffer.
Once the RNA had flowed onto the selection column, a selection
scheme was employed to find onlv tightly binding aptamers. First, the
column was washed with five volumes of binding buffer. Then,
counter selection was carrier out, by washing the column with six
column volumes of bmding buffer which contained 20mM of citruJLline.
Next, in order to increase stringency of competition between free
citrulline and bound arginine. the agarose, and hence the RNA bound
to it, was heated to 90°C tor 10 minutes then cooled to 23°C for 15
minutes in the presence of the 20mM citrulline containing solution.
The column was then eluted with another 5 column volumes of
binding buffer containing 20mM citrulline so as to remove any non-
bound RNA.
The column was then washed with 15 column volumes of
binding buffer plus 20mM arginine, and was then heat denatured, in
the presence of this solution, using the parameters set forth supra. This
was done because it was assumed that molecules which have a slow
dissociation rate and hence elute slowly are tight binders when heat
denatured, these tight binding RNA molecules should separate from
the column and renarure in the presence of excess ligand in solution,
thereby avoiding undesired enrichment of those molecules which
require functional groups in the matrix plus the ligand for binding.
The column was then eluted with 5 column volumes of binding
buffer plus 20mM arginine. Eluted RNA was collected by (a) removing
amino acids with phenol (b) precipitating the RNA, and then (c)
amplifying the RNA. This cycle was repeated, twenty times, and was
carried out on both pool 1 and pool 2, as described in Example 1. A
representative elution profile from cycle 20, is shown in Figure 1.
EXAMPLE 3
The RNA aptamers which eluted after cycle 10 and cycle 20 were
subjected to PCR amplification in accordance with Famulok. supra.
and then sequenced. Of 36 clones sequenced following cycle 10, 35%
showed the arginine binding motif taught by Famulok, supra and 65%
did not. When materials obtained after twenty cycles were sequenced,
however, none of those in cycle 10 were found, indicating that the prior
art sequences do not have the same level of affinity for their partner
amino acid as do those left after 20 cycles. The sequences found after
20 cycles are presented in SEQ ID NOS: X through Y. Of the 31 clones
found, one sequence appeared 8 times, four sequences each appeared
twice, and eleven sequences, once only.
When the sequences found in pool 1 and pool 2 were compared,
only one, Le., Ag. 06 (SEQ ID NO: 3 ) was found in both pools. This
molecule was also the most prevalent one.
EXAMPLE 4
Experiments were then carried out to determine the strength of
binding of the isolated aptamers. This is determined by calculating the
dissociation constant, using the well known methods of e.g., Lorsch, et
al. Biochemistry 33:973-982 (1994); Fersht, Enzyme Structure and
Mechanism, 2 nd Ed. (W.H. Freeman and Co., New York, 1985), p 186;
Connors, Binding Constants (Wiley, New York 1987), p. 314,
incorporated by reference. This is an equilibrium dialysis method
using dialvsis chambers of 500 ul volume. The membrane used had a
molecular weight cutoff of 5000 daltons. A sample of RNA, typically
at a concentration of l.O^M was used. Measurements were generally
taken at three different concentrations of L-[2, 3, 4, 5- 3 H] - arginine -
HQ (Le., 250, 25 and 2.5 lvl). Sample volumes of 200 μl were used on
each side of the membrane. The samples were equilibrated at 23 °C
overnight, after which the volume on both sides of the membrane was
determined and adjusted to ensure the amounts were the same.
Aliquots were withdrawn, and subjected to scintillation counting.
Three RNA molecules were used, i.e., Ag. 06 (SEQ ID NO: ), as well
as two other molecules representing point mutations , SEQ ID NOS
4 + 5.
Using the specific activity of arginine, concentrations of bound
ligand [ESJeg, free amino acid [S]eq, and free RNA [E]eg at equiUbrium
were calculated. Kd is defined by the equation:
Kd = ([E]eq X[S]eq) x [ESJeq 1
The value for Ag. 06 was about 330nM, i.e., nearly 200 times greater
than the tightest binders ot Famulok supra. Note that a strong affinity
is represented by a low numerical value, and a weaker affinity by a
higher numerical value. The specific values ranged from 4mM to
330nM, and are on a par with affinity values for other, non-amino acid
substances, such as theophylline (320nM) cyanco balamine (88nM), and
the aminoglycoside antibiotics tobramycin, kanamycin, lividomycin,
and neomycin (20nM - 220nM). See Jenison et al., Science 263:1425-
1429 (1996) Lorch , et al., Biochemistry 33:973-982 (1994); Wang et al.,
Chem & Biol 2:281-290 (1995); Lato, et al., Chem & Biol 2;291-303
(1995); Walks, et al., Chem & Biol 2:543-552 (1995).
EXAMPLE 5
Experiments were carried out to determine if the RNA molecules
could distinguish between L-arginine and D-arginine. Using the
analvtical affinity chroma tography method of Arnold, et al. J.
Chromatog 355:1-2 ( 1986), and when applied to a 4.0mM D-arginine
agarose column, the RNA eluted in the void volume. This leads to the
conclusion that the Kd is 4mM, i.e., the affinity was very weak.
Thus, the mole ules such as Ag. 06 (SEQ ID NO: 3), show great
discrirnination. In this particular case, it is on the order of 12,000 fold
better.
The foregoing examples set forth particular embodiments of the
invention which includes, inter alia, isolated ribonucleic acid (RNA)
molecules which have high affinity for a particular amino acid.
Especially preferred are isolated ribonucleic acid molecules having
affinities of around 300nM, more preferably greater than about 60μM.
These RNA molecules can have the strong affinity for any L- or D-
amino acid. Of particular interest are RNA molecules with high
affinity for L-arginine. and which may permit discrimination between
L- and D-arginine, and /or L-citrulline and L-arginine. Exemplary of
such RNA molecules are those set forth in SEQ ID NOS: 3 through 20 ,
inclusive.
These RNA molecules have various uses, which will be clear to
the skilled artisan. For example, the RNA molecules may be used to
remove particular amino acids from a solution, or determine the
presence or amount ol a particular amino acid, by exploiting this high
affinitv to form complexes of RNA and amino acid which can be
removed from a solution, followed by identification and/ or
quantization of the amino acid via elution, or other standard analytical
techniques. Enantiomers of amino acids may be identified and/ or
separated, such as L and D arginine; different, structurally related
amino acids, such as L-arginine and L-άtrulline may be separated, and
so forth.
Of particular interest as a feature of the invention is a process for
isolating an RNA molecule with high affinity for an amino acid. The
essential steps of this process involve the denaturing of an RNA
molecule or sample, followed by binding the denatured RNA to a solid
phase, using art recognized techniques which need not be repeated
here. Next, the bound RNA is contacted with a solution of an amino
acid which is not the amino acid for which a high affinity binder is
sought. Then, any RNA which remains bound to a solid phase is
heated, followed by contact, a second time, with the amino acid
solution referred to supra. These three steps can be repeated for any
number of cycles, using the same, or different amino acids. For
example, were one looking tor high affinity L-arginine binders, one
might contact the solid phase bound RNA with D-arginine, heat it, and
contact it a second time with D-arginine, followed by a repeat of these
steps using L-citrulline. Preferably, one carries out the cycling for
anywhere from 5 to 20 cycles, most preferably, 10-20 cycles.
Following these steps, any remaining RNA is heated and then
contacted with a solution ot the amino acid for which a strong or high
affinity binder is sought. This serves to elute the desired RNA from
the solid phase.
In these processes, it is preferred that the RNA be bound to the
solid phase by amino acid molecules for which strong affinity binders
are sought.
A strong or high affinity binder, as was noted, supra, is an RNA
molecule which has a low Kd value. For the invention as described
herein, strong affinitv (or high affinity) binders are those with a Kd
value of 60μm or less. More preferably, these molecules have a Kd
value that is an order of magnitude lower, i.e., about 6.0μm or less.
More preferably, this value is about 500 nM or less, and most
preferably, about 300 nM or less.
Other features ot the invention will be clear to the skilled artisan,
and need not be elaborated upon herein.
The terms and expressions which 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, it being
recognized that various modifications are possible within the scope of
the invention.
UAAACCGAUGCUGGGCGAUUCUCCUGAAGUAGGGGAAGAGUUGUCAUGUAUGGG ag 04 r- AUGAUAAACCGAUGCUGGGCGAUUCUCCUGAAGCAGGGGAAGAGUUGUCAUGUAUGGG ag.16 > AUGAUAAACCGAUGCUGGGCGAUUCCCCUGAAGUAGGGGAAGAGUUGUCAUGUAUGGG ag.02* 0 CCAGCCUAUGGACGUGCCUUUACGGCUGUCCGGAAAAGGUGGUGCCGUCCGGCAUGGC
— ag 10*
/ CCAGCCUAUGGACGUGCCUUUACGGCUGUCCGGAAAAGGUAGUGCCGUCCGGCAUGGC a Ol*
23 " GCGGCGGGUGUACUUCGCAAGAGGCCCGUGCGGUGGGAGUGGUAGCCUUGGAAACCAUAG A agll* GGCGGGUGUACUUCGCAAGAGGCCCGUGCGGUGGGAGUGGUAGCCUUGGAAACCAUAGA . ag 13 AGAUCAGGCACGCCGGGUACGAAAUAGCACCAAUGUCAACAUGACUUUUAAAGAGC
M ae 17 AGAUCAGGCACGCCGGGUACGAAAUAGCACCAGUGUCAACAUGACUUUUAAAGAGC
ag 03*
1 2 ACAGCCAACGGUUCGGUCACGGGACUGCUCUUCAUCGUAGGGAGUGGUGGCCUUGGUACG U
GCGGA ag.12
1 3 AAUCUCGAACUCUGCGGUAGUCAAUACCGGCUUUCAGAGAACGGUCGAGGUCGCUUGUCG G
UCUGC ag.05 CGCUGAGAGAGAGUCCUCUGUUUAGGAAGUGUAGCUUAACUUGCGACAGGCAGGCUUCA ag.07
I S " ACAGCAACGCGUGUAAGUCGAUAAACUUCUCUUUAGCAGAAGUGGUAAGCUGUGUGACGU
AAGGC
I <p ag 08 AGCUGCGGUGUGGCGGAAGGAGUGUAGCAUAAGUUAGAGUGAGCCUUCUGCCUGUG
_ ag.09
' / ACGGACUACCAGGUAGGUCGCUGGACGAAUCGGAAGGAGGGUAACCUUGCGGUAGGACUG U G
I $f ag.14 GGAUCAGGGACGGCGGGUAGAAAUAGCACCAAUGUUCAAUCAGUGGGCCCAAAGAGC
I ύ ag.15
1 A ' CAGCAACGCGUGUAAGUCGAUAAACUUCUCUCUAGCAGAAGUGGUAGCUGUGCG ACGUGA
2^0 AG 18* AAUGCUAACCGCAUUGGCCGCGGGACUUCUCGUCUGACCAGUUAGCAUGGCGUGGU
ag.19
AUAGCGCAAAACGGUUCGGCUACGGGCUGCCCGGCGAAGGGUGGUAGCCUUGCUGAU GUUU GGAC
2.2- ag.20 ACGCGUGGUCCUCCUCUCCAUGACUCUCUGGACGGCGUGUAGUCUUGAAACGUCUGAU ag-21 2.? ACACCGAUGCGGGCGAUGGACAUCUCUUCCCUAAUGACUGGAAGGGAUGGUAAGGUGGCU G
UGUGGC
7 <■ ag.24
AACAGGUAGGUCGCUGCACUGUCCUUUGGGACUGUCCGGAAGGAGCGUUGUCAGGUA UCGC