ArticleNucleic acids research2008
Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands.
Article in Nucleic acids research, 2008. 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
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- Ion Mobility-Mass Spectrometry Captures the Structural Consequences of Lipid Nanoparticle Encapsulation on Ribonucleic Acid Cargo.Journal of the American Chemical Society · 2024Article
- Multifaceted nucleic acid probing with a rationally upgraded molecular rotor.Chemical science · 2024Article
- Collision-Induced Unfolding Reveals Disease-Associated Stability Shifts in Mitochondrial Transfer Ribonucleic Acids.Journal of the American Chemical Society · 2024Article
- Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder.Current topics in microbiology and immunology · 2015Review
- The essential role of stacking adenines in a two-base-pair RNA kissing complex.Journal of the American Chemical Society · 2013Article
- Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions.International journal of mass spectrometry · 2012Article
- MS analysis of nucleic acids in the post-genomic era.Analytical chemistry · 2011Article
- Functional recognition of the modified human tRNALys3(UUU) anticodon domain by HIV's nucleocapsid protein and a peptide mimic.Journal of molecular biology · 2011Article
- Reverse transcriptase in motion: conformational dynamics of enzyme-substrate interactions.Biochimica et biophysica acta · 2010Review
- A role for the MS analysis of nucleic acids in the post-genomics age.Journal of the American Society for Mass Spectrometry · 2010Article
- Article
- SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids.RNA (New York, N.Y.) · 2009Article
- Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B.Biochemistry · 2009Article
- Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein.Nucleic acids research · 2009Article
- Article
- High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers.Chemistry & biology · 2008Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
The interactions of archetypical nucleic acid ligands with the HIV-1 polypurine tract (PPT) RNA:DNA hybrid, as well as analogous DNA:DNA, RNA:RNA and swapped hybrid substrates, were used to probe structural features of the PPT that contribute to its specific recognition and processing by reverse transcriptase (RT). Results from intercalative and groove-binding ligands indicate that the wild-type PPT hybrid does not contain any strikingly unique groove geometries and/or stacking arrangements that might contribute to the specificity of its interaction with RT. In contrast, neomycin bound preferentially and selectively to the PPT near the 5'(rA)(4):(dT)(4) tract and the 3' PPT-U3 junction. Nuclear magnetic resonance data from a complex between HIV-1 RT and the PPT indicate RT contacts within the same regions highlighted on the PPT by neomycin. These observations, together with the fact that the sites are correctly spaced to allow interaction with residues in the ribonuclease H (RNase H) active site and thumb subdomain of the p66 RT subunit, suggest that despite the long cleft employed by RT to make contact with nucleic acids substrates, these sites provide discrete binding units working in concert to determine not only specific PPT recognition, but also its orientation on the hybrid structure.
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Registered trials
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