Aptamers selected for higher-affinity binding are not more specific for the target ligand
Open accessAbstract
Previous study of eleven different in vitro-selected RNA aptamers that bind guanosine triphosphate (GTP) with K(d)s ranging from 8 microM to 9 nM showed that more information is required to specify the structures of the higher-affinity aptamers. We are interested in understanding how the more complex aptamers achieve higher affinities for the ligand. In vitro selection produces structural solutions to a functional problem that are are as simple as possible in terms of the information content needed to define them. It has long been assumed that the simplest way to improve the affinity of an aptamer is to increase the shape and functional group complementarity of the RNA binding pocket for the ligand. This argument underlies the hypothesis that selection for higher-affinity aptamers automatically leads to structures that bind more specifically to the target molecule. Here, we examined the binding specificities of the eleven GTP aptamers by carrying out competition binding studies with sixteen different chemical analogues of GTP. The aptamers have distinct patterns of specificity, implying that each RNA is a structurally unique solution to the problem of GTP binding. However, these experiments failed to provide evidence that higher-affinity aptamers bind more specifically to GTP. We suggest that the simplest way to improve aptamer K(d)s may be to increase the stability of the RNA tertiary structure with additional intramolecular RNA-RNA interactions; increasingly specific ligand binding may emerge only in response to direct selection for specificity.
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Greater stability is one of the factors promoting greater functional activity in RNA aptamers.
“Greater stability is one of the factors promoting greater functional activity in RNA aptamers (29,30).”
From Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences (2012) · cites this paper as [29]
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Cites
In vitro selection of RNA molecules that bind specific ligands
Ellington, A. D., & Szostak, J. W. (1990) · Nature · doi:10.1038/346818a0 · Cited by 9,845 · see citing works
Self-citationPrinciples of Nucleic Acid Structure
Saenger, W. (1984) · Springer advanced texts in chemistry · doi:10.1007/978-1-4612-5190-3 · Cited by 4,271 · see citing works
Fast folding and comparison of RNA secondary structures
Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, S., Tacker, M., & Schuster, P. M. (1994) · Monatshefte für Chemie - Chemical Monthly · doi:10.1007/bf00818163 · Cited by 2,314 · see citing works
Adaptive Recognition by Nucleic Acid Aptamers
Hermann, T., & Patel, D. J. (2000) · Science · doi:10.1126/science.287.5454.820 · Cited by 1,665 · see citing works
Fitting Models to Biological Data Using Linear and Nonlinear Regression
Motulsky, H. J., & Christopoulos, A. (2004) · doi:10.1093/oso/9780195171792.001.0001 · Cited by 1,406 · see citing works
In Vitro Selection of Functional Nucleic Acids
Wilson, D. S., & Szostak, J. W. (1999) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.68.1.611 · Cited by 1,209 · see citing works
Self-citationHigh-Resolution Molecular Discrimination by RNA
JENISON, R. D., Gill, S. C., Pardi, A., & Polisky, B. A. (1994) · Science · doi:10.1126/science.7510417 · Cited by 1,192 · see citing works
Information content of binding sites on nucleotide sequences
Schneider, T. D., Stormo, G. D., Gold, L., & Ehrenfeucht, A. (1986) · Journal of Molecular Biology · doi:10.1016/0022-2836(86)90165-8 · Cited by 944 · see citing works
Sassanfar, M., & Szostak, J. W. (1993) · Nature · doi:10.1038/364550a0 · Cited by 593 · see citing works
Self-citationInterlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
Zimmermann, G. R., JENISON, R. D., Wick, C. L., Simorre, J., & Pardi, A. (1997) · Nature Structural Biology · doi:10.1038/nsb0897-644 · Cited by 286 · see citing works
Information theory in molecular biology
Adami, C. (2004) · Physics of Life Reviews · doi:10.1016/j.plrev.2004.01.002 · Cited by 265 · see citing works
Structural basis of RNA folding and recognition in an AMP–RNA aptamer complex
Jiang, F., Kumar, R., Jones, R. A., et al. (1996) · Nature · doi:10.1038/382183a0 · Cited by 255 · see citing works
Informational Complexity and Functional Activity of RNA Structures
Carothers, J. M., Oestreich, S. C., Davis, J. H., & Szostak, J. W. (2004) · Journal of the American Chemical Society · doi:10.1021/ja031504a · Cited by 237 · see citing works
Self-citationMolecular Recognition in the FMN – RNA Aptamer Complex
Fan, P., Suri, A. K., Fiala, R., Live, D. H., & Patel, D. J. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0263 · Cited by 232 · see citing works
Physical Chemistry: with Applications to the Life Sciences
Eisenberg, D. S., & Crothers, D. M. (1979) · Medical Entomology and Zoology · Cited by 222 · see citing works
Isolation of RNA Aptamers for Biological Cofactors by In Vitro Selection
Burgstaller, P., & Famulok, M. (1994) · Angewandte Chemie International Edition in English · doi:10.1002/anie.199410841 · Cited by 221 · see citing works
Let's get specific: the relationship between specificity and affinity
Eaton, B. E., Gold, L., & Zichi, D. A. (1995) · Chemistry & Biology · doi:10.1016/1074-5521(95)90023-3 · Cited by 218 · see citing works
Channel-Like Function of the Na,K Pump Probed at Microsecond Resolution in Giant Membrane Patches
Hilgemann, D. W. (1994) · Science · doi:10.1126/science.8128223 · Cited by 198 · see citing works
Solution structure of an ATP-binding RNA aptamer reveals a novel fold.
Dieckmann, T., Suzuki, E., Nakamura, G. K., & Feigon, J. F. (1996) · Europe PMC (PubMed Central) · Cited by 197 · see citing works
FUNDAMENTALS OF BIOSTATISTICS.
&NA; (1969) · Plastic & Reconstructive Surgery · doi:10.1097/00006534-196908000-00012 · Cited by 193 · see citing works
The Vela glitch of Christmas 1988
McCulloch, P. M., Hamilton, P. A., McConnell, D., et al. (1990) · Nature · doi:10.1038/346822a0 · Cited by 185 · see citing works
In vitro evolution suggests multiple origins for the hammerhead ribozyme
Salehi-Ashtiani, K., & Szostak, J. W. (2001) · Nature · doi:10.1038/35102081 · Cited by 183 · see citing works
Self-citationIsolation of high-affinity GTP aptamers from partially structured RNA libraries
Davis, J. H., & Szostak, J. W. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.182095699 · Cited by 179 · see citing works
Self-citationLancet, D., Sadovsky, E., & Seidemann, E. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.8.3715 · Cited by 160 · see citing works
A Small Aptamer with Strong and Specific Recognition of the Triphosphate of ATP
Sazani, P., Larralde, R., & Szostak, J. W. (2004) · Journal of the American Chemical Society · doi:10.1021/ja049171k · Cited by 159 · see citing works
Self-citationJuneau, K., Podell, E. R., Harrington, D. J., & Cech, T. R. (2001) · Structure · doi:10.1016/s0969-2126(01)00579-2 · Cited by 158 · see citing works
Chance and Necessity in the Selection of Nucleic Acid Catalysts
Lorsch, J. R., & Szostak, J. W. (1996) · Accounts of Chemical Research · doi:10.1021/ar9501378 · Cited by 126 · see citing works
Self-citationThe structural basis for molecular recognition by the vitamin B 12 RNA aptamer.
Sussman, D. R., Wilson, C., & Nix, J. C. (2000) · Nature Structural Biology · doi:10.1038/71253 · Cited by 100 · see citing works
Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena
Christian, E. L., & Yarus, M. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90861-d · Cited by 93 · see citing works
Solution structure of an informationally complex high-affinity RNA aptamer to GTP
CAROTHERS, J. M., DAVIS, J. H., CHOU, J. J., & SZOSTAK, J. W. (2006) · RNA · doi:10.1261/rna.2251306 · Cited by 78 · see citing works
Self-citationMolecular Recognition of cAMP by an RNA Aptamer
Koizumi, M., & Breaker, R. R. (2000) · Biochemistry · doi:10.1021/bi000149n · Cited by 68 · see citing works
Ding, J., Hughes, S. H., & Arnold, E. (1997) · Biopolymers · doi:10.1002/(sici)1097-0282(1997)44:2 · Cited by 64 · see citing works
Isolation of Fast Purine Nucleotide Synthase Ribozymes
Lau, M. W. L., Cadieux, K. E. C., & Unrau, P. J. (2004) · Journal of the American Chemical Society · doi:10.1021/ja045387a · Cited by 63 · see citing works
Use of intrinsic binding energy for catalysis by an RNA enzyme
Hertel, K. J., Peracchi, A., Uhlenbeck, O. C., et al. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.16.8497 · Cited by 55 · see citing works
Evolution of Tetrahymena ribozyme mutants with increased structural stability
Guo, F., & Cech, T. R. (2002) · Nature Structural Biology · doi:10.1038/nsb850 · Cited by 48 · see citing works
Evolutionary Optimization of a Nonbiological ATP Binding Protein for Improved Folding Stability
Chaput, J. C., & Szostak, J. W. (2004) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.04.006 · Cited by 39 · see citing works
Self-citationBeer, E., Feuerer, M., Knorr, A., et al. (1994) · Angewandte Chemie International Edition in English · doi:10.1002/anie.199410871 · Cited by 36 · see citing works
Erratum: correction: Retrotransposition of a bacterial group II intron
Cousineau, B., Lawrence, S., Smith, D., et al. (2001) · Nature · doi:10.1038/35102087 · Cited by 6 · see citing works
Flagged first, then by citations
Research works printed but not linked: 7
- [4]Carothers JM, Szostak JW. In: The aptamer handbook: functional oligonucleotides and their applications. Klussmann S, editor. Berlin: Wiley-VCH; 2006. pp. 3–28. [Google Scholar]
- [12]Adami C, Cerf NJ. Physica D (Amsterdam) 2000;37:62–69. 2000. [Google Scholar]
- [13]Adami C. Physics of Life Reviews. 2004;1:3–22. [Google Scholar]
- [17]Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Monatshefte f. Chemie. 1994;125:167–188. [Google Scholar]
- [18]Sokol RR, Rohlf J. Biometry: The Principals and Practice of Statistics in Biological Research. 3rd ed. New York, NY: W. H. Freeman & Co.; 1995. [Google Scholar]
- [26]Dieckmann T, Suzuki E, Nakamura GK, Feigon J. RNA. 1996;2:628–640. [PMC free article] [PubMed] [Google Scholar]
- [30]Burgstaller P, Famulok M. Angew. Chem. Int. Ed. Engl. 1994;33:1084–1087. [Google Scholar]
Cited by
Sorted by citations
Comprehensive experimental fitness landscape and evolutionary network for small RNA
Jiménez, J. I., Xulvi-Brunet, R., Campbell, G. W., Turk-MacLeod, R., & Chen, I. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307604110 · Cited by 140 · see citing works
Ruff, K. M., Snyder, T. M., & Liu, D. R. (2010) · Journal of the American Chemical Society · doi:10.1021/ja103023m · Cited by 86 · see citing works
Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences
Derr, J., Manapat, M. L., Rajamani, S., Leu, K., Xulvi-Brunet, R., Joseph, I., Nowak, M. A., & Chen, I. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks065 · Cited by 74 · see citing works
Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity
Trevino, S. G., Zhang, N., Elenko, M. P., Lupták, A., & Szostak, J. W. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1107113108 · Cited by 59 · see citing works
Self-citationJo, H., Youn, H., Lee, S., & Ban, C. (2014) · J. Mater. Chem. B · doi:10.1039/c4tb00643g · Cited by 49 · see citing works
- Authors
- Carothers, J. M., Oestreich, S. C., & Szostak, J. W.
- Affiliations
- Massachusetts General Hospital (US)
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-05-27
- Volume
- 128
- Issue
- 24
- Pages
- 7929-7937
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- PMC
- PMC4287982
- OpenAlex
- W1987864397
- Cited by
- 132
- References
- 38
- Citations by year
- 2026: 11 · 2025: 7 · 2024: 4 · 2023: 4 · 2022: 5 · 2021: 6 · 2020: 5 · 2019: 6 · 2018: 4 · 2017: 6 · 2016: 6 · 2015: 5 · 2014: 11 · 2013: 4 · 2012: 3
- FWCI
- 3.67
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of the American Chemical Society (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (GM53936, R01GM053936)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- RNA aptamers, GTP binding, in vitro selection, binding affinity, binding specificity, competitive binding, GTP analogues, RNA tertiary structure
- MeSH terms
- Base Sequence, Binding Sites, Guanosine Triphosphate, Ligands, Nucleic Acid Conformation, RNA, Aptamers, Nucleotide
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