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• W2024996310 abstract "Despite diverging in sequence and size, the polypurine tract (PPT) primers of retroviruses and long terminal repeat-containing retrotransposons are accurately processed from (+) U3 RNA and DNA by their cognate reverse transcriptases (RTs). In this paper, we demonstrate that misalignment of the Ty3 retrotransposon RT on the human immunodeficiency virus-1 PPT induces imprecise removal of adjacent (+)-RNA and failure to release (+)-DNA from the primer. Based on these observations, we explored the structural basis of Ty3 PPT recognition by chemically synthesizing RNA/DNA hybrids whose (–)-DNA template was substituted with the non-hydrogen-bonding thymine isostere 2,4-difluoro-5-methylbenzene (F). We observed a consistent spatial correlation between the site of T → F substitution and enhanced ribonuclease H (RNase H) activity ∼12–13 bp downstream. In the most pronounced case, dual T → F substitution at PPT positions –1/–2 redirects RNase H cleavage almost exclusively to the novel site. The structural features of this unusual base suggest that its insertion into the Ty3 PPT (–)-DNA template weakens the duplex, inducing a destabilization that is recognized by a structural element of Ty3 RT ∼12–13 bp from its RNase H catalytic center. A likely candidate for this interaction is the thumb subdomain, whose minor groove binding tract most likely contacts the duplex. The spatial relationship derived from T → F substitution also infers that Ty3 PPT processing requires recognition of sequences in its immediate 5′ vicinity, thereby locating the RNase H catalytic center over the PPT-U3 junction, a notion strengthened by additional mutagenesis studies of this paper." @default.
• W2024996310 created "2016-06-24" @default.
• W2024996310 creator A5072685090 @default.
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• W2024996310 date "2003-07-01" @default.
• W2024996310 modified "2023-09-30" @default.
• W2024996310 title "Nonpolar Thymine Isosteres in the Ty3 Polypurine Tract DNA Template Modulate Processing and Provide a Model for Its Recognition by Ty3 Reverse Transcriptase" @default.
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• W2024996310 doi "https://doi.org/10.1074/jbc.m302374200" @default.
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