ArticleRNA (New York, N.Y.)2006
Solution structure of an informationally complex high-affinity RNA aptamer to GTP.
Article in RNA (New York, N.Y.), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
29 citing papers in PubMed, 76 citations in OpenAlex.
- Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.Nucleic acids research · 2025Article
- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli-Pepper aptamer FRET pair.Nucleic acids research · 2023Article
- Biofunctionalization of Multiplexed Silicon Photonic Biosensors.Biosensors · 2022Review
- Single-round deoxyribozyme discovery.Nucleic acids research · 2021Article
- Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.Nucleic acids research · 2020Article
- Inside the Black Box: What Makes SELEX Better?Molecules (Basel, Switzerland) · 2019Review
- Principles for targeting RNA with drug-like small molecules.Nature reviews. Drug discovery · 2018Review
- An intermolecular G-quadruplex as the basis for GTP recognition in the class V-GTP aptamer.RNA (New York, N.Y.) · 2016Article
- Amplification of RNA by an RNA polymerase ribozyme.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Selection and Biosensor Application of Aptamers for Small Molecules.Frontiers in chemistry · 2016Review
- In situ simultaneous monitoring of ATP and GTP using a graphene oxide nanosheet-based sensing platform in living cells.Nature protocols · 2014Article
- Article
- Comprehensive experimental fitness landscape and evolutionary network for small RNA.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX.Chemistry & biology · 2012Article
- Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.Nucleic acids research · 2012Article
- Ribozymes and riboswitches: modulation of RNA function by small molecules.Biochemistry · 2010Review
- Computational approaches toward the design of pools for the in vitro selection of complex aptamers.RNA (New York, N.Y.) · 2010Article
- Computational discovery of folded RNA domains in genomes and in vitro selected libraries.Methods (San Diego, Calif.) · 2010Review
- Convergent donor and acceptor substrate utilization among kinase ribozymes.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown that the additional information needed to improve affinity does not specify more interactions with the ligand. In light of those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP aptamer (K(d) = 75 nM) as determined by NMR. The backbone of the aptamer forms a reverse-S that shapes the binding pocket. The ligand nucleobase stacks between purine platforms and makes hydrogen bonds with the edge of another base. Interestingly, the local modes of interaction for the Class I aptamer and an RNA aptamer that binds ATP with a K(d) of 6 microM are very much alike. The aptamers exhibit nearly identical levels of binding specificity and fraction of ligand sequestered from the solvent (81%-85%). However, the GTP aptamer is more informationally complex (approximately 45 vs. 35 bits) and has a larger recognition bulge (15 vs. 12 nucleotides) with many more stabilizing base-base interactions. Because the aptamers have similar modes of ligand binding, we conclude that the stabilizing structural elements in the Class I aptamer are responsible for much of the difference in K(d). These results are consistent with the hypothesis that increasing the number of intra-RNA interactions, rather than adding specific contacts to the ligand, is the simplest way to improve binding affinity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.