Journal
EMBO JOURNAL
Volume 20, Issue 6, Pages 1449-1461Publisher
WILEY
DOI: 10.1093/emboj/20.6.1449
Keywords
HIV-1; polypurine tract; reverse transcriptase; RNase H; RNA : DNA
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Funding
- NIAID NIH HHS [R01 AI027690, R37 AI027690, AI 27690, F32 AI009578, AI 09578] Funding Source: Medline
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We have determined the 3.0 Angstrom resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis. The 'RNase H primer grip', consisting of amino acids that interact with the DNA primer strand, may contribute to PNase H catalysis and cleavage specificity. Cleavage specificity is also controlled by the width of the minor groove and the trajectory of the RNA:DNA, both of which are sequence dependent, An unusual 'unzipping' of 7 bp occurs in the adenine stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register and then, following two offset base pairs, an unpaired base on the primer strand re-establishes the normal register. The structural aberration extends to the RNase H active site and may play a role in the resistance of PPT to RNase H cleavage.
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