Interaction of HIV-1 Reverse Transcriptase with Modified Oligonucleotide Primers Containing 2'-O-beta-D-Ribofuranosyladenosine

A. S. Golubeva¹, B. S. Ermolinsky¹, E. V. Efimtseva¹, V. L. Tunitskaya¹, A. van Aerschot², P. Herdewijn², S. N. Mikhailov¹, and S. N. Kochetkov^1*

¹Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia; fax: (7-095) 135-1405; E-mail: kochet@eimb.ru

²Rega Institute, Katholieke Univrsiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium

^* To whom correspondence should be addressed.

Received April 21, 2003; Revision received June 26, 2003

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Modified synthetic oligodeoxyribonucleotides containing 2´-O-beta-D-ribofuranosyladenosine were used as primers in the RNA-dependent DNA synthesis catalyzed by HIV-1 reverse transcriptase. The degree of elongation of the primers depends on the position of the additional ribose unit, its presence in the specific position of the primer (-4) (and only in it) completely preventing elongation. Computer-modeled binding of the modified primers to the active site of reverse transcriptase demonstrated that steric hindrances arising from the interaction of the additional ribose residue with the reverse transcriptase region 262-270 interacting with the minor groove of the DNA substrate prevents elongation in the above mentioned case.

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KEY WORDS: HIV-1, reverse transcriptase, 2´-O-beta-D-ribofuranosyladenosine, oligonucleotides, inhibitory analysis, computer modeling

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