ArticleNucleic acids research2009
Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Polymorphic potential of SRF binding site ofRSC advances · 2024Article
- Retroviral nucleocapsid proteins and DNA strand transfers.Biochimie open · 2018Review
- Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR.Nucleic acids research · 2017Article
- Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.Angewandte Chemie (International ed. in English) · 2016Article
- Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA.Biophysical journal · 2015Article
- Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer.Nucleic acids research · 2013Article
- The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge.Biochemistry · 2012Article
- Intrinsic nucleic acid dynamics modulates HIV-1 nucleocapsid protein binding to its targets.PloS one · 2012Article
- Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein.Nucleic acids research · 2011Article
- Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC.Nucleic acids research · 2011Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop-loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR). We show that the upper stem located between the apical and the internal loops is stable, but that the lower stem of mini-cTAR is unstable. The residues of the internal loop undergo slow motions at the NMR time-scale that are consistent with conformational exchange phenomena. In contrast, residues of the apical loop undergo fast motions. The lower stem is destabilized by the slow interconversion processes in the internal loop, and thus the internal loop is responsible for asymmetric destabilization of mini-cTAR. These findings are consistent with the functions of cTAR in first strand transfer: its apical loop is suitably exposed to interact with the apical loop of TAR RNA and its lower stem is significantly destabilized to facilitate the subsequent action of the nucleocapsid protein which promotes the annealing reaction.
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