ArticleProceedings of the National Academy of Sciences of the United States of America2008
Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 49 citations in OpenAlex.
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.Journal of chemical information and modeling · 2025Article
- Highly conserved s2m element of SARS-CoV-2 dimerizes via a kissing complex and interacts with host miRNA-1307-3p.Nucleic acids research · 2022Article
- Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR.RNA (New York, N.Y.) · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- Triggering nucleic acid nanostructure assembly by conditional kissing interactions.Nucleic acids research · 2018Article
- Aptamers against pathogenic microorganisms.Critical reviews in microbiology · 2016Review
- A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers.Nucleic acids research · 2016Article
- A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme.RNA (New York, N.Y.) · 2014Article
- HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway.Nucleic acids research · 2014Article
- Inhibition of hepatitis C virus production by aptamers against the core protein.Journal of virology · 2014Article
- Article
- Inhibition of hepatitis C virus infection by DNA aptamer against envelope protein.Antimicrobial agents and chemotherapy · 2013Article
- Direct evidence for RNA-RNA interactions at the 3' end of the Hepatitis C virus genome using surface plasmon resonance.RNA (New York, N.Y.) · 2013Article
- Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop.Journal of nucleic acids · 2012Article
- HAPIscreen, a method for high-throughput aptamer identification.Journal of nanobiotechnology · 2011Article
- NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site.Nucleic acids research · 2011Article
- Mechanistic studies of hairpin to duplex conversion for trinucleotide repeat sequences.The Journal of biological chemistry · 2010Article
- Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution.Journal of the American Chemical Society · 2009Article
- Composite RNA aptamers as functional mimics of proteins.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
7 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transactivation-response element (TAR) is a stable stem-loop structure of HIV RNA, which plays a crucial role during the life cycle of the virus. The apical loop of TAR acts as a binding site for essential cellular cofactors required for the replication of HIV. High-affinity aptamers directed against the apical loop of TAR have been identified by the SELEX approach. The RNA aptamers with the highest affinity for TAR fold as hairpins and form kissing complexes with the targeted RNA through loop-loop interactions. The aptamers with the strongest binding properties all possess a GA base pair combination at the loop-closing position. Using liquid-crystal NMR methodology, we have obtained a structural model in solution of a TAR-aptamer kissing complex with an unprecedented accuracy. This high-resolution structure reveals that the GA base pair is unilaterally shifted toward the 5' strand and is stabilized by a network of intersugar hydrogen bonds. This specific conformation of the GA base pair allows for the formation of two supplementary stable base-pair interactions. By systematic permutations of the loop-closing base pair, we establish that the identified atomic interactions, which form the basis for the high stability of the complex, are maintained in several other kissing complexes. This study rationalizes the stabilizing role of the loop-closing GA base pairs in kissing complexes and may help the development or improvement of drugs against RNA loops of viruses or pathogens as well as the conception of biochemical tools targeting RNA hairpins involved in important biological functions.
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