ArticleNucleic acids research2003
Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Harnessing in Silico Design for Electrochemical Aptasensor Optimization: Detection of Okadaic Acid (OA).Biosensors · 2025Article
- Triggering nucleic acid nanostructure assembly by conditional kissing interactions.Nucleic acids research · 2018Article
- On the conformational stability of the smallest RNA kissing complexes maintained through two G·C base pairs.Biochemical and biophysical research communications · 2017Article
- HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway.Nucleic acids research · 2014Article
- Unmasking the information encoded as structural motifs of viral RNA genomes: a potential antiviral target.Reviews in medical virology · 2013Review
- Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop.Journal of nucleic acids · 2012Article
- Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance.Nucleic acids research · 2008Article
- Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Self-association of adenine-dependent hairpin ribozymes.European biophysics journal : EBJ · 2008Article
- Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage.Biophysical journal · 2007Article
- Review
- NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer.Nucleic acids research · 2007Article
- Conformational changes in the expression domain of the Escherichia coli thiM riboswitch.Nucleic acids research · 2007Article
- Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo.Nucleic acids research · 2006Article
- Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.Journal of molecular modeling · 2004Article
- LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1.Nucleic acids research · 2004Article
- Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.Nucleic acids research · 2003Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A RNA aptamer (R06) raised against the trans- activation responsive (TAR) element of HIV-1 was previously shown to generate a loop-loop complex whose stability is strongly dependent on the selected G and A residues closing the aptamer loop. The rationally designed TAR* RNA hairpin with a loop sequence fully complementary to the TAR element, closed by U,A residues, also engages in a loop-loop association with TAR, but with a lower stability compared with the TAR-R06 complex. UV absorption monitored thermal denaturation showed that TAR-TAR*(GA), in which the U,A kissing residues were exchanged for G,A, is as stable as the selected TAR-R06 complex. Consequently, we used the TAR-TAR* structure deduced from NMR studies to model the TAR-R06 complex with either GA, CA or UA loop closing residues. The results of the molecular dynamics trajectories correlate well with the thermal denaturation experiments and show that the increased stability of the GA variant results from an optimized stacking of the bases at the stem-loop junction and from stable interbackbone hydrogen bonds.
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