STRUCTURE OF A DNA ANALOG OF THE PRIMER FOR HIV-1 RT 2ND-STRAND SYNTHESIS

The non-self-complementary DNA decamer C-A-A-A-G-A-A-A-A-G/C-T-T-T-T-C -T-T-T-G is a DNA/DNA analogue of a portion of the polypurine tract or PPT, which is a RNA/DNA hybrid that serves as a primer for synthesis of the (+) DNA strand by HIV reverse transcriptase (RT), and which is not digested by the RNase H domain of reverse transcriptase following (-) strand synthesis. The same unusual conformation that eludes RNase H, thought to be a change In width of minor groove, may also be respon sible for the inhibition of HIV RT by minor groove binding drugs such as distamycin and their bis-linked derivatives. The present X-ray crys tal structure of this DNA decamer exhibits the usual properties of A-t ract B-DNA under biologically relevant conditions: large propeller twi st of base-pairs, narrowed minor groove, and a straight helix axis. Gr oove narrowing is fully developed in the A-A-A-A region, but not in th e A-A-A region, which previous investigators have proposed as being to o short to exhibit typical A-tract properties. The RNA;DNA hybrid prod uced by HIV reverse transcriptase during (-) strand synthesis presumab ly forms a ''heteromerous'' or H-helix with narrower minor groove than an A-helical RNA/RNA duplex. if the narrowing of minor groove in A-tr act H-helices is comparable to that seen in A-tract B-helices, then th e narrowed minor groove of the polypurine tract could make the second primer site both (1) impervious to RNase H digestion, and (2) suscepti ble to inhibition by minor groove binding drugs. (C) 1997 Academic Pre ss Limited.