Analysis of the ribonuclease H activity of HIV-1 reverse transcriptase using RNA.cntdot.DNA hybrid substrates derived from the gag region of HIV-1

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Abstract
The RNase H activity associated with recombinant p66/p51 HIV-1 reverse transcriptase (RT) has been analyzed in the absence of DNA synthesis by using homogeneous RNA-DNA substrates. The substrates consisted of SP6 runoff transcripts from a portion of the gag region of the HIV-1 genome hybridized to complementary single-stranded DNA from either an M13 subclone or a phagemide transcription vector subclone. The corresponding hybrids either carried a 5''-mismatch of seven nucleotides or were fully base-paired. Analysis of recombinant HIV-1 p66/p51 RT by an activated gel assay employing these substrates suggested that the RNase H activity was exclusively associated with the p66 polypeptide. Denaturing gel electrophoresis was used to analyze the oligonucleotide products generated by hydrolysis of the hybrids by HIV-1 RT, M-MuLV RT, and Escherichia coli RNase H. The significant different in the time-dependent distribution of products of HIV-1 RT vs E. coli RNase H catalyzed cleavage of 5''-mismatched hybrids indicated that the preparation of recombinant HIV-1 RT was free of contaminating bacterial RNase H. Although the HIV-1 RT associated RNase H activity shares many of the general mechanistic features of other retroviral enzymes [Gerard, G. F. (1981) Biochemistry 20, 256-265], the appearance of unique intermediates and end products in the course of hydrolysis of 5''-mismatched and fully base-paired hybrids indicated a significant difference in the sequence dependence of the kinetics of RNase H cleavage by HIV-1 RT and M-MuLV RT.