ArticleNucleic acids research2007
Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 58 citations in OpenAlex.
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- Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?Frontiers in chemistry · 2020Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- Retroviral RNA Dimerization: From Structure to Functions.Frontiers in microbiology · 2018Review
- Mechanistic insights into type I toxin antitoxin systems in Helicobacter pylori: the importance of mRNA folding in controlling toxin expression.Nucleic acids research · 2017Article
- Translational readthrough-promoting drugs enhance pseudoknot-mediated suppression of the stop codon at the Moloney murine leukemia virus gag–pol junction.The Journal of general virology · 2015Article
- Charge reduction and thermodynamic stabilization of substrate RNAs inhibit RNA editing.PloS one · 2015Article
- Retrospective on the all-in-one retroviral nucleocapsid protein.Virus research · 2014Review
- HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway.Nucleic acids research · 2014Article
- Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.Nucleic acids research · 2013Article
- A proposal for a new HIV-1 DLS structural model.Nucleic acids research · 2012Article
- Recognition of HIV TAR RNA by triazole linked neomycin dimers.Bioorganic & medicinal chemistry letters · 2011Article
- Mechanistic insights into an engineered riboswitch: a switching element which confers riboswitch activity.Nucleic acids research · 2011Article
- Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.Nucleic acids research · 2010Article
- A fast selenium derivatization strategy for crystallization and phasing of RNA structures.RNA (New York, N.Y.) · 2009Article
- Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry.Methods in enzymology · 2009Article
- Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging.Nucleic acids research · 2008Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Owing to a striking, and most likely fortuitous, structural and sequence similarity with the bacterial 16 S ribosomal A site, the RNA kissing-loop complex formed by the HIV-1 genomic RNA dimerization initiation site (DIS) specifically binds 4,5-disubstituted 2-deoxystreptamine (2-DOS) aminoglycoside antibiotics. We used chemical probing, molecular modeling, isothermal titration calorimetry (ITC) and UV melting to investigate aminoglycoside binding to the DIS loop-loop complex. We showed that apramycin, an aminoglycoside containing a bicyclic moiety, also binds the DIS, but in a different way than 4,5-disubstituted 2-DOS aminoglycosides. The determination of thermodynamic parameters for various aminoglycosides revealed the role of the different rings in the drug-RNA interaction. Surprisingly, we found that the affinity of lividomycin and neomycin for the DIS (K(d) approximately 30 nM) is significantly higher than that obtained in the same experimental conditions for their natural target, the bacterial A site (K(d) approximately 1.6 microM). In good agreement with their respective affinity, aminoglycoside increase the melting temperature of the loop-loop interaction and also block the conversion from kissing-loop complex to extended duplex. Taken together, our data might be useful for selecting new molecules with improved specificity and affinity toward the HIV-1 DIS RNA.
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