title: Sequence, distance, and accessibility are determinants of 5'-end-directed cleavages by retroviral RNases H.
abstract: The RNase H activity of reverse transcriptase is essential for retroviral replication. RNA 5'-end-directed cleavages represent a form of RNase H activity that is carried out on RNA/DNA hybrids that contain a recessed RNA 5'-end. Previously, the distance from the RNA 5'-end has been considered the primary determinant for the location of these cleavages. Employing model hybrid substrates and the HIV-1 and Moloney murine leukemia virus reverse transcriptases, we demonstrate that cleavage sites correlate with specific sequences and that the distance from the RNA 5'-end determines the extent of cleavage. An alignment of sequences flanking multiple RNA 5'-end-directed cleavage sites reveals that both enzymes strongly prefer A or U at the +1 position and C or G at the -2 position, and additionally for HIV-1, A is disfavored at the -4 position. For both enzymes, 5'-end-directed cleavages occurred when sites were positioned between the 13th and 20th nucleotides from the RNA 5'-end, a distance termed the cleavage window. In examining the importance of accessibility to the RNA 5'-end, it was found that the extent of 5'-end-directed cleavages observed in substrates containing a free recessed RNA 5'-end was most comparable to substrates with a gap of two or three bases between the upstream and downstream RNAs. Together these finding demonstrate that the selection of 5'-end-directed cleavage sites by retroviral RNases H results from a combination of nucleotide sequence, permissible distance, and accessibility to the RNA 5'-end.
authors.affiliation: Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195, USA.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Schultz
authors.forename: Miaohua
authors.initials: M
authors.lastname: Zhang
authors.forename: James J
authors.initials: JJ
authors.lastname: Champoux
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D017931:DNA Primers / Q000737:chemistry; D054303:HIV Reverse Transcriptase / Q000235:genetics; D008969:Molecular Sequence Data; D008979:Moloney murine leukemia virus / Q000201:enzymology; D009841:Oligonucleotides / Q000737:chemistry; D011485:Protein Binding; D012313:RNA / Q000737:chemistry / Q000235:genetics; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D012190:Retroviridae / Q000201:enzymology* / Q000235:genetics; D016914:Ribonuclease H / Q000737:chemistry* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D009841:Oligonucleotides; D012313:RNA; D004247:DNA; D054303:HIV Reverse Transcriptase; D012194:RNA-Directed DNA Polymerase; D016914:Ribonuclease H