Crystal structure and conformation of a DNA–RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)–r(GAAGAAGAA)

AbstractBackground: DNA–RNA hybrids are substrates for RNase H. This enzyme catalyzes the hydrolysis of the RNA strand in the hybrid form. The polypurine tract (PPT) in human immunodeficiency virus 1 (HIV-1) is a short stretch of purines (∼ 15 bases) located at the 3′-end of the U3 region of the RNA genome. The PPT has the unique ability to resist digestion by RNase H and serves as a primer for plus-strand DNA synthesis.Results: The crystal structure of a DNA–RNA hybrid duplex containing a polypurine RNA strand, d(TTCTTBr5CTTC)–r(GAAGAAGAA), has been determined at 1.8 å resolution. The structure was solved by molecular replacement methods and refined to a final R factor of 20.1% (R free 23.7%). The hybrid duplex adopts a standard A-form conformation. All of the sugar rings and glycosidic torsion angles are found in the standard C3′-endo/anti conformation, as seen in A-RNA or A-DNA. The crystal packing is dominated by the DNA strand, where the terminal base pairs of the hybrid abut the neighboring A-DNA sugar–phosphate backbone on the minor groove side.Conclusions: The present DNA–RNA hybrid duplex containing a polypurine RNA strand exhibits standard A-form geometry. This observation might suggest that the RNA PPT resists the RNase H activity of HIV reverse transcriptase as a result of its A-form conformation. In addition, there appears to be a correlation between the percentage purine content of the RNA and the DNA backbone conformation