High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers

Author:

Yi-Brunozzi, H. Y.

Brinson, R. G.

Brabazon, D. I.

Lener, D.

Le Grice, S.

Marino, J. P.
Author Address

Yi-Brunozzi, Hye Young, Brinson, Robert G.; Lener, Daniela, Le Grice, Stuart F. J.] NCI, HIV Drug Resistance Program, Frederick Natl Inst Hlth, Frederick, MD 21702 USA. [Brinson, Robert G.; Marino, John P.] Univ Maryland, Inst Biotechnol, Ctr Adv Res Biotechnol, Rockville, MD 20850 USA. [Brinson, Robert G.; Marino, John P.] Univ Maryland, Natl Inst Stand & Technol, Rockville, MD 20850 USA. [Brabazon, Danielle Im.] Loyola Coll Maryland, Dept Chem, Baltimore, MD 21210 USA.

Abstract:

A purine-rich region of the plus-strand RNA genome of retroviruses and long terminal repeat (LTR)-containing retrotransposons, known as the polypurine tract (PPT), is resistant to hydrolysis by the RNase H domain of reverse transcriptase (RT) and ultimately serves as a primer for plus-strand DNA synthesis. The mechanisms underlying PPT resistance and selective processing remain largely unknown. Here, two RNA/DNA hybrids derived from the PPTs of HIV-1 and Ty3 were probed using high-resolution NMR for preexisting structural distortions in the absence of RT. The PPTs were selectively modified through base-pair changes or by incorporation of the thymine isostere, 2,4-difluoro-5-methylbenzene (dF), into the DNA strand. Although both wild-type (WT) and mutated hybrids adopted global A-form-like helical geometries, observed structural perturbations in the base-pair and dF-modified hybrids suggested that the PPT hybrids may function as structurally coupled domains.

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