Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands

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 tra...

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Bibliographic Details
Published in:Nucleic acids research 2008-05, Vol.36 (8), p.2799-2810
Main Authors: Turner, Kevin B, Brinson, Robert G, Yi-Brunozzi, Hye Young, Rausch, Jason W, Miller, Jennifer T, Le Grice, Stuart F.J, Marino, John P, Fabris, Daniele
Format: Article
Language:English
Subjects:
Aminoglycosides - chemistry
Binding Sites
DNA, Viral - chemistry
Framycetin - chemistry
HIV-1 - genetics
Human immunodeficiency virus 1
Ligands
Mass Spectrometry
Nuclear Magnetic Resonance, Biomolecular
Nucleic Acid Probes
Purines - chemistry
RNA, Viral - chemistry
Structural Biology
Thermodynamics
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkn129