ArticleNucleic acids research2006
Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo.
Article in Nucleic acids research, 2006. 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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Who cites it
21 citing papers in PubMed.
- DEAD-box helicase intrinsically disordered domains and structural dynamics of HIV-1 RNA are required to reveal DDX3X catalytic efficiency.Nucleic acids research · 2025Article
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- A Method to Predict the Structure and Stability of RNA/RNA Complexes.Methods in molecular biology (Clifton, N.J.) · 2016Article
- RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications.Nano today · 2015Article
- A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme.RNA (New York, N.Y.) · 2014Article
- Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.RNA (New York, N.Y.) · 2014Article
- The role of salt concentration and magnesium binding in HIV-1 subtype-A and subtype-B kissing loop monomer structures.Journal of biomolecular structure & dynamics · 2013Article
- Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal.RNA (New York, N.Y.) · 2011Article
- Interactions of cations with RNA loop-loop complexes.Biophysical journal · 2011Article
- Importance of diffuse metal ion binding to RNA.Metal ions in life sciences · 2011Review
- Predicting ion binding properties for RNA tertiary structures.Biophysical journal · 2010Article
- Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system.Nucleic acids research · 2010Article
- Mechanical unfolding of two DIS RNA kissing complexes from HIV-1.Journal of molecular biology · 2009Article
- Predicting electrostatic forces in RNA folding.Methods in enzymology · 2009Article
- 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
- Salt dependence of nucleic acid hairpin stability.Biophysical journal · 2008Article
- Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery.Journal of the American Chemical Society · 2007Article
- Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA loop-loop interactions are a prevalent motif in the formation of tertiary structure and are well suited to trigger molecular recognition between RNA molecules. We determined the stabilities of several loop-loop interactions with a constant 6 bp core sequence and varying unpaired flanking nucleotides and found that the flanking bases have a strong influence on the stability and ion dependence of the kissing complex. In general, the stabilities determined in 1 M Na+ are equivalent to those in the presence of near physiological Mg2+ concentrations. Therefore we further tested whether the stabilities determined in vitro and within yeast cells correlate, using a recently developed yeast RNA-hybrid system. For the majority of the loop types analyzed here, the melting temperatures determined in vitro are in good agreement with the relative beta-galactosidase activity in yeast cells, showing that data derived from in vitro measurements reflect in vivo properties. The most stable interactions are the naturally occurring HIV-1 DIS MAL and LAI derived loops with the motif (5' A(A)/(G)N6A 3'), emphasizing the crucial role of stable kissing complexes in HIV genome dimerization.
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