3.1.13.2 12 bp RNA/DNA hybrid + H2O 5'-(6-carboxyfluorescein)-labeled 12 base RNA (5'-cggagaugacgg-3') is hybridized with with a 1.5 M equivalent of the complementary DNA Halobacterium sp. ? - ? 429130 3.1.13.2 12 bp RNA/DNA hybrid + H2O 5'-(6-carboxyfluorescein)-labeled 12 base RNA (5'-cggagaugacgg-3') is hybridized with with a 1.5 M equivalent of the complementary DNA Halobacterium sp. NRC-1 ? - ? 429130 3.1.13.2 18mer DNA-RNA hybrid + H2O the RNA is labeled with 6-carboxytetramethyl rhodamine at the 3' end and annealed to complementary nonlabeled DNA Human immunodeficiency virus 1 ? - ? 380872 3.1.13.2 3' end-labeled 41-nt RNA annealed to a 77-nt DNA template - Human immunodeficiency virus 1 DNA + RNA fragments the most RNA fragments are cleaved by a combination of primary, secondary primary, and 5-nt cuts ? 364125 3.1.13.2 5' end-labeled 41-nt RNA annealed to a 77-nt DNA template - Human immunodeficiency virus 1 DNA + RNA fragments The first product observed is the primary cut. The primary cut occurs faster than the secondary cut ? 364123 3.1.13.2 5' end-labeled 50-nt RNA annealed to a 77-nt DNA template - Human immunodeficiency virus 1 DNA + RNA fragments The first product observed is the primary cut. The primary cut occurs faster than the secondary cut ? 364124 3.1.13.2 5' end-labeled RNA cleavage of 267 nt RNA substrate to produce a 47 nt long product, the second cleavage produces RNA fragments that are 38 nt long Human immunodeficiency virus 1 RNA fragments - ? 364096 3.1.13.2 5' RNA-DNA duplex + H2O - Human immunodeficiency virus 1 oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 364111 3.1.13.2 5'-end-labeled RNA cleavage of 267nt RNA substrate to produce a 47nt long product, the second cleavage produces RNA fragments that are 38nt long. Human immunodeficiency virus 2 RNA fragments - ? 364110 3.1.13.2 5'-end-labeled RNA cleavage of 267nt RNA substrate to produce a 47nt long product, the second cleavage produces RNA fragments that are 38nt long. Human immunodeficiency virus 2 D-194 RNA fragments - ? 364110 3.1.13.2 5'-end-labeled RNA cleavage of 267nt RNA substrate to produce a 47nt long product, the second cleavage produces RNA fragments that are 38nt long. Human immunodeficiency virus 2 ROD RNA fragments - ? 364110 3.1.13.2 5'-fluorescein-labeled RNA/DNA hybrid + H2O - Halobacterium sp. ? - ? 429812 3.1.13.2 5'-fluorescein-labeled RNA/DNA hybrid + H2O - Halobacterium sp. NRC-1 ? - ? 429812 3.1.13.2 CGK1 + H2O RNase H substrate CGK1 is obtained by annealing 5'-cap-labelled R1 5'-m7Gppp*GmAAUACUCAAGCUAUGCAUC-3' with DNA oligonucleotide D1. The RNA oligonucleotide is blocked at the 5' end by adding a guanosyl-5'-5'-guanosine triphosphate cap structure Human immunodeficiency virus 1 ? - ? 400645 3.1.13.2 DNA-15-nucleotide-RNA hybrid + H2O - Human immunodeficiency virus 1 ? - ? 452589 3.1.13.2 DNA-16-nucleotide-RNA hybrid + H2O - Human immunodeficiency virus 1 ? - ? 452590 3.1.13.2 DNA-17-nucleotide-RNA hybrid + H2O - Human immunodeficiency virus 1 ? - ? 452591 3.1.13.2 DNA-18-nucleotide-RNA hybrid + H2O - Human immunodeficiency virus 1 ? - ? 452592 3.1.13.2 DNA-DNA hybrid duplex + H2O - Human Immunodeficiency Virus ? - ? 364121 3.1.13.2 DNA-DNA hybrid duplex + H2O - Human Immunodeficiency Virus HXB2 ? - ? 364121 3.1.13.2 DNA-RNA duplex + H2O - murine leukemia virus ? - ? 380600 3.1.13.2 DNA-RNA duplex + H2O - Human immunodeficiency virus 1 ? - ? 380600 3.1.13.2 DNA-RNA hybrid + H2O - Escherichia coli ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Homo sapiens ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Arabidopsis thaliana ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Hepatitis B virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Human Immunodeficiency Virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Human spumaretrovirus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Moloney murine leukemia virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Halalkalibacterium halodurans ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Sulfurisphaera tokodaii ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Xenotropic MuLV-related virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Halobacterium sp. ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O RNA-DNA hybrid structures: thermodynamics of recognition and impact on reverse viral replication Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O the RNase H primer grip is important for viral replication and replication fidelity, mutational analysis, overview murine leukemia virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O cleavage pattern to 3' end of wild-type and mutant reverse transcriptase/RNase H, HIV-1 reverse transcriptase employs the DNA 3' end-directed primary/secondary RNase H cleavage mechanism during synthesis and strand transfer Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O cleavage site recognition and specificity, mechanism, in vitro synthesis of substrates, overview Moloney murine leukemia virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O cleavage site recognition and specificity, mechanism, in vitro synthesis of substrates, overview Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O cleavage site specificity at -17, -12 and -8 from the 5' end positions of the RNA strand in 3' to 5' direction, overview human foamy virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O fluorescent-labeled RNA-DNA duplex of 15, 16, 17, or 18 nucleotide-RNA and in each case 18 nucleotide-DNA, overview Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O formed by commercial R1 RNA and D1 DNA oligonucleotides, the His-tag affects the cleavage pattern of recombinant RNaseh domain Human Immunodeficiency Virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O in vitro synthesis of substrates, overview Moloney murine leukemia virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O in vitro synthesis of substrates, overview Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O RNA-DNA hybrid structures: thermodynamics of recognition and impact on reverse transcriptase-mediated RNase H activity, cleavage sites Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O substrate preparation, overview Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O the RNase H catalytic efficiency and specificity is influences by the RNase H primer grip contacting the DNA primer strand and positioning the template strand near the RNase H active site, overview murine leukemia virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O recessed 5'-end RNA substrates CGK1 annealed from RNA R1, i.e. 5'-GAAUACUCAAGCUAUGCAUC-3', and DNA D1, i.e. 5'-GATGCATAGCTTGAGTATTCTATAGTGAGTCGTATTAA-3', substrate labeling with fluorescein at the 3' end and with dabcyl at the 5' end Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O RNase H specifically hydrolyzes the RNA strand of a RNA/DNA heteroduplex, the ribonuclease H hydrolytic activity is part of the reverse transcriptase Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O RNase H specifically hydrolyzes the RNA strand of a RNA/DNA heteroduplex, the ribonuclease H hydrolytic activity is part of the reverse transcriptase Human immunodeficiency virus 2 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O the RNaseH activity of HIV-1 reverse transcriptase cleaves the viral genome concomitant with minus strand synthesis during pausing of the reverse transcriptase activity, RNase H cleavage on a hairpin containing RNA template system, overview, pause-related 3' end-directed secondary cuts decreased primer extendibility, relationship between cleavage of the RNA template and extension of a DNA primer, mechanism, overview Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O 3 distinct cleavage modes have been described for retroviral RNases H that are referred to as internal, DNA 3'-end-directed and RNA 5'-end-directed cleavages Avian sarcoma leukosis virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O RNase H cleaves precisely one nucleotide from the tRNA/DNA junction, leaving a ribo-A on the 3' end of the viral minus-strand DNA Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O sequence preference for internal cleavage. 3 distinct cleavage modes are described for retroviral RNases H that are referred to as internal, DNA 3'-end-directed and RNA 5'-end-directed cleavages Moloney murine leukemia virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O a Cy3-Tr35/Pd22 RNA-DNA hybrid is cut at approximately 18 base pair upstream from the 3' primer end Human immunodeficiency virus 1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O a Cy3-Tr35/Pd22 RNA-DNA hybrid is cut at approximately 19 base pair upstream from the 3' primer end Moloney murine leukemia virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O a Cy3-Tr35/Pd22 RNA-DNA hybrid is cut at approximately 19 base pair upstream from the 3' primer end Xenotropic MuLV-related virus ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Sulfurisphaera tokodaii DSM 16993 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Halobacterium sp. NRC-1 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Halalkalibacterium halodurans DSM 18197 ? - ? 380601 3.1.13.2 DNA-RNA hybrid + H2O - Human immunodeficiency virus 1 DNA + RNA nucleotides - ? 390206 3.1.13.2 DNA-RNA hybrid + H2O - Human immunodeficiency virus 1 DNA nucleotides + RNA nucleotides - ? 391872 3.1.13.2 DNA-RNA hybrid duplex + H2O - Herpes simplex virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Avian myeloblastosis virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Rous sarcoma virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - feline leukemia virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - RD-feline leukemia virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Mason-Pfizer monkey virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Moloney murine leukemia virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Rauscher leukemia virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - mouse mammary tumor virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Woolly monkey sarcoma virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Harvey murine sarcoma virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Rous-associated virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Hepatitis B virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Human immunodeficiency virus 1 oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Human Immunodeficiency Virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Moloney murine leukemia virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety 4-30 nucleotides in length ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O limited hydrolysis of ribopolymers when complementary DNA strand is missing or in presence of a complementary RNA strand Avian myeloblastosis virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O poor substrate: poly(rG)-poly(dC) Hepatitis B virus oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O only cleavage of RNA from a RNA-DNA-duplex Human immunodeficiency virus 1 oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O the RNase H domain of reverse transcriptase catalyses the cleavage of the RNA within DNA-RNA hybrids, both in a polymerase-dependent or independent fashion. Polymerase-dependent: Cleavage occurring at a distance of 18-20 nucleotides behind DNA polymerization. Polymerase-independent: cleavage of the viral RNA for the initiation of second DNA strand synthesis and for removal of the primer tRNA. Human immunodeficiency virus 1 oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Hepatitis B virus HBV oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O poor substrate: poly(rG)-poly(dC) Hepatitis B virus HBV oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Moloney murine leukemia virus M-MuLV oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Moloney murine leukemia virus M-MuLV oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety 4-30 nucleotides in length ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Herpes simplex virus HSV oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Human Immunodeficiency Virus HXB2 oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA-RNA hybrid duplex + H2O - Harvey murine sarcoma virus MSV-MLV(H) oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety - ? 92983 3.1.13.2 DNA/DNA + H2O RNase H catalysis by the retroviral enzyme appears to involve a two-metal ion mechanism. Unlike cellular RNases H, the retroviral RNase H displays three different modes of cleavage: internal, 3'-end-DNA-directed, and 5'-end-RNA-directed, all three modes of cleavage appear to have essential roles in reverse transcription, overview, cleavage site selection modelling, RNase H activities of human retroviral reverse transcriptases preferentially cleave between two ribonucleotide residues in an RNA chain, and between the penultimate and last ribonucleotide of an extended RNA primer rather than precisely at the RNA-DNA junction, overview Human immunodeficiency virus 1 ? - ? 391873 3.1.13.2 DNA/DNA + H2O RNase H catalysis by the retroviral enzyme appears to involve a two-metal ion mechanism. Unlike cellular RNases H, the retroviral RNase H displays three different modes of cleavage: internal, 3'-end-DNA-directed, and 5'-end-RNA-directed, all three modes of cleavage appear to have essential roles in reverse transcription, overview, RNase H activities of murine retroviral reverse transcriptases preferentially cleave between two ribonucleotide residues in an RNA chain, and between the penultimate and last ribonucleotide of an extended RNA primer rather than precisely at the RNA-DNA junction Moloney murine leukemia virus ? - ? 391873 3.1.13.2 double-stranded RNA + H2O substrate of RNase H1 Sulfurisphaera tokodaii ? - ? 141057 3.1.13.2 double-stranded RNA + H2O substrate of RNase H1 Sulfurisphaera tokodaii DSM 16993 ? - ? 141057 3.1.13.2 HTS-1 RNA-DNA + H2O - Moloney murine leukemia virus ? - ? 430252 3.1.13.2 HTS-1 RNA-DNA + H2O - Human immunodeficiency virus 1 ? - ? 430252 3.1.13.2 HTS-1 RNA-DNA + H2O - Xenotropic MuLV-related virus ? - ? 430252 3.1.13.2 HTS-2 RNA-DNA + H2O - Moloney murine leukemia virus ? - ? 430253 3.1.13.2 HTS-2 RNA-DNA + H2O - Human immunodeficiency virus 1 ? - ? 430253 3.1.13.2 HTS-2 RNA-DNA + H2O - Xenotropic MuLV-related virus ? - ? 430253 3.1.13.2 additional information not: ss DNA Herpes simplex virus ? - ? 89 3.1.13.2 additional information not: ss DNA Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information not: ss RNA Herpes simplex virus ? - ? 89 3.1.13.2 additional information not: ss RNA Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information not: ds RNA Herpes simplex virus ? - ? 89 3.1.13.2 additional information not: ds DNA Herpes simplex virus ? - ? 89 3.1.13.2 additional information not: ds DNA Avian myeloblastosis virus ? - ? 89 3.1.13.2 additional information not: ds DNA Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information not: poly(rU)-poly(dA), DNA-RNA hybrids without a free RNA-end Avian myeloblastosis virus ? - ? 89 3.1.13.2 additional information in Mg2+, hydrolysis of poly(rAdT) appears to be solely endonucleolytic. In Mn2+, hydrolysis of poly(rAdT) is both endonucleolytic and exonucleolytic. With poly(rGdC) as substrate, hydrolysis is both endonucleolytic and exonucleolytic in either Mg2+ or Mn2+ Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the enzyme is essential for retroviral replication Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information the enzyme is essential for retroviral replication Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the enzyme is essential to complete retroviral replication Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information the enzyme is essential to complete retroviral replication Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the enzyme plays a key role in viral proliferation Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the enzyme is part of the viral reverse transcriptase Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the enzyme is part of the viral reverse transcriptase residing on distinct domains of the enzyme with the DNA polymerase activity Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the enzyme is part of the viral reverse transcriptase, RNase H substrate synthesis by the enzyme's RT activity human foamy virus ? - ? 89 3.1.13.2 additional information the enzyme is part of the viral reverse transcriptase, the isolated RNase H domain is inactive at low pH Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the enzyme recognizes 3' ends of DNA and 5' ends of RNA for cleavage, the enzyme cleaves downstream of a nick, recognition of internal cleavage sites, influence of 5' end position of upstream RNA on cleavage of downstream RNA, overview Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information the enzyme recognizes 3' ends of DNA and 5' ends of RNA for cleavage, the enzyme cleaves downstream of a nick, recognition of internal cleavage sites, influence of 5' end position of upstream RNA on cleavage of downstream RNA, overview Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the isolated RNase H domain, part of reverse transcriptase, is catalytically active Human Immunodeficiency Virus ? - ? 89 3.1.13.2 additional information the reverse transcriptase possesses different activity domains and shows RNase H, integrase, and DNA polymerase activities Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information mutations in reverse transcriptase outside of the polymerase domain may have clinical significance in resistance to nucleoside analog RT inhibitors, i.e. NRTIs Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information mutations in reverse transcriptase outside of the polymerase domain may have clinical significance in resistance to nucleoside analog RT inhibitors, i.e. NRTIs Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the RNase H function of HIV RT is required to effectively incorporate viral genetic information into the host cell genome Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the RNase H function of HIV RT is required to effectively incorporate viral genetic information into the host cell genome Human immunodeficiency virus 2 ? - ? 89 3.1.13.2 additional information HIV reverse transcriptase, HIV-RT, contains two distinct protein domains catalyzing DNA polymerase and RNase H activities Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the polymerization-dependent RNase H activity is insufficient to completely degrade the genomic template during minus-strand synthesis, pausing by reverse transcriptase during transcription promotes RNase H cleavages and facilitates strand transfers, overview, cleavage site selection modelling, overview, the isolated MoMLV RNase H domain retains enzymatic activity, but is unable to carry out specific cleavages such as removal of the tRNA or PPT primers in vitro, cleavage specificity of RNase H, overview Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information the polymerization-dependent RNase H activity is insufficient to completely degrade the genomic template during minus-strand synthesis, pausing by reverse transcriptase during transcription promotes RNase H cleavages and facilitates strand transfers, the isolated RNase H domain of HIV-1 is inactive, but nuclease activity is reconstituted by introducing the p51 subunit, by adding the thumb and connection subdomains, or by various N-terminal fusions on the RNase H domain, cleavage specificity of RNase H, overview Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the reverse transcriptase has two enzyme activities, one of which is the RNase H, enzyme-ligand interactions, overview Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information 3 distinct cleavage modes are described for retroviral RNases H that are referred to as internal, DNA 3'-end-directed and RNA 5'-end-directed cleavages Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information 3 distinct cleavage modes have been described for retroviral RNases H that are referred to as internal, DNA 3'-end-directed and RNA 5'-end-directed cleavages Avian sarcoma leukosis virus ? - ? 89 3.1.13.2 additional information 3 distinct cleavage modes have been described for retroviral RNases H that are referred to as internal, DNA 3'-end-directed and RNA 5'-end-directed cleavages Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information cleaves RNA only if the RNA is part of an RNA/DNA duplex Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information during minus-strand DNA synthesis, RNase H degrades viral RNA sequences, generating potential plus-strand DNA primers Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information retroviral RNase H is essential for viral replication Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information retroviral RNases H display three different modes of cleavage: internal, DNA 3' end-directed, and RNA 5' end-directed Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information retroviral RNases H display three different modes of cleavage: internal, DNA 3' end-directed, and RNA 5' end-directed Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information RNA cleavage in the RNA-DNA hybrids by the various mutant HIV-2 reverse transcriptases, in comparison to the wild-type HIV-1 and HIV-2 reverse transcriptases Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information RNA cleavage in the RNA-DNA hybrids by the various mutant HIV-2 reverse transcriptases, in comparison to the wild-type HIV-1 and HIV-2 reverse transcriptases Human immunodeficiency virus 2 ? - ? 89 3.1.13.2 additional information RNase H activity is determined by measuring the [3H]oligo(rA) released from [3H]poly(rA)*p(dT)45 Avian myeloblastosis virus ? - ? 89 3.1.13.2 additional information RNase H activity is determined by measuring the [3H]oligo(rA) released from [3H]poly(rA)*p(dT)45 Moloney murine leukemia virus ? - ? 89 3.1.13.2 additional information RNAse H is implicated in catalysing the degradation of the RNA strand during conversion of the viral genome into double-stranded DNA Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information the reverse transcriptase-associated RNase H activity introduces nicks into the RNA strand that yield low molecular weight bands in urea-containing denaturing PAGE, which are visualized by fluorescence scanning. The p51 preparation does not yield detectable low-molecular-weight bands, indicating that the reverse transcriptase preparation is not contaminated with RNase activities of bacterial origin Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information using specially designed RNA and DNA transfer substrates in vitro to determine how individual invasion sites contribute to the invasion-mediated mechanism of strand transfer, with specific focus on the limits and influences on the apparently crucial intermediate step of hybrid propagation. Investigation of the roles of the RNase H activities of reverse transcriptase and the strand-exchange properties of nucleocapsid protein (NC) Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information both of the enzymatic functions of reverse transcriptase, the DNA polymerase and RNase H, are essential for copying the single-stranded RNA genome found in virions into the double-stranded DNA that is inserted into the host genome by IN Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information RNaseH assays are performed using an 18-nucleotide 3'-fluorescein-labeled RNA annealed to a complementary 18-nucleotide 5'-dabcyl-conjugated DNA. The increase in fluorescence as a result of RNase H hydrolysis is monitored with a Spectramax Gemini EM fluorescence spectrometer Human immunodeficiency virus 1 ? - ? 89 3.1.13.2 additional information LC11-RNase H1 does not exhibit double strand RNase activity Sulfurisphaera tokodaii ? - ? 89 3.1.13.2 additional information heteroduplexes with 5'-O-methylphosphonate units in the antisense strand exhibit a significant increase in RNase H cleavage activity by up to 3fold in comparison with the natural heteroduplex Escherichia coli ? - ? 89 3.1.13.2 additional information Herpes simplex virus 1 DNA polymerase shows also RNase H activity and acts in a 3'-to-5' direction, the activity is dependent on the 3'-to-5' exonuclease active site. No RNase H activity of HSV-1 DNA polymerase on RNA-DNA hybrids with 5' RNA termini Human alphaherpesvirus 1 ? - ? 89 3.1.13.2 additional information phage T4 RNase H shows 5'-3'exonuclease (EC 3.1.13.2) and flap endonuclease (EC 3.1.99.) activities on dsDNA Tequatrovirus T4 ? - ? 89 3.1.13.2 additional information cleavage of RNA:DNA hybrid substrate Hepatitis B virus ? - ? 89 3.1.13.2 additional information in vitro assays are performed utilizing purified wild-type Pol and the D368A exonuclease-deficient mutant, testing the ability of these enzymes to extend a fluorescently labeled DNA hairpin primer-template and degrade dsDNA and RNA-DNA hybrid hairpin substrates over time, assay of RNase H activity using differentially end-labeled templates with 5' or 3' RNA termini, e.g. 6-FAM-labeled hairpin RNA-DNA substrate with a 3' RNA terminus. Wild-type HSV Pol exhibits readily detectable RNase H activity on this substrate in the 3'-to-5' direction, while the mutant is inactive. Neither wild-type nor D368A Pol exhibits detectable RNase H activity on a substrate with a 5' RNA terminus Human alphaherpesvirus 1 ? - ? 89 3.1.13.2 additional information synthetic DNA substrates are used Tequatrovirus T4 ? - ? 89 3.1.13.2 additional information the 3'-5' exoribonuclease activity of the HBV RNaseH is determined. The enzyme also shows endolytic activity (EC 3.1.26.4) in DNA oligonucleotide (ODN)-directed RNA cleavage assays are conducted. Substrate specificity of the HBV RNaseH, overview Hepatitis B virus ? - ? 89 3.1.13.2 additional information not: ss DNA Moloney murine leukemia virus M-MuLV ? - ? 89 3.1.13.2 additional information not: ss RNA Moloney murine leukemia virus M-MuLV ? - ? 89 3.1.13.2 additional information not: ds DNA Moloney murine leukemia virus M-MuLV ? - ? 89 3.1.13.2 additional information not: ss DNA Herpes simplex virus HSV ? - ? 89 3.1.13.2 additional information not: ss RNA Herpes simplex virus HSV ? - ? 89 3.1.13.2 additional information not: ds RNA Herpes simplex virus HSV ? - ? 89 3.1.13.2 additional information not: ds DNA Herpes simplex virus HSV ? - ? 89 3.1.13.2 additional information LC11-RNase H1 does not exhibit double strand RNase activity Sulfurisphaera tokodaii DSM 16993 ? - ? 89 3.1.13.2 poly(rA)n-poly(dT)n - Human immunodeficiency virus 1 ? - ? 364095 3.1.13.2 poly(rA)n-poly(dT)n - Human immunodeficiency virus 2 ? - ? 364095 3.1.13.2 poly(rA)n-poly(dT)n - Human immunodeficiency virus 2 D-194 ? - ? 364095 3.1.13.2 poly(rA)n-poly(dT)n - Human immunodeficiency virus 2 ROD ? - ? 364095 3.1.13.2 poly(rA)n-poly(dT)ne + H2O - Human immunodeficiency virus 1 ? - ? 453963 3.1.13.2 RNA-DNA hybrid + H2O poly(rGdC) Human immunodeficiency virus 1 ribonucleotide 5'-phosphomonoester - ? 93109 3.1.13.2 RNA/DNA hybrid + H2O - Moloney murine leukemia virus ? - ? 390306 3.1.13.2 RNA/DNA hybrid + H2O Cy3-labeled 43-nt RNA strand (5'-GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGG-3') annealed to a 53-nt DNA strand (5'-CCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACC-3') Human immunodeficiency virus 1 ? - ? 390306 3.1.13.2 RNA/DNA hybrid + H2O Cy3-labeled 43-nt RNA strand (5'-GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGG-3') annealed to a 53-nt DNA strand (5'-CCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACC-3') Simian immunodeficiency virus ? - ? 390306 3.1.13.2 RNA/DNA hybrid + H2O Cy3-labeled 43-nt RNA strand (5'-GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGG-3') annealed to a 53-nt DNA strand (5'-CCCTAGTTAGCCAGAGAGCTCCCAGGCTCAGATCTGGTCTAACCAGAGAGACC-3') Human immunodeficiency virus 2 ? - ? 390306 3.1.13.2 RNA/DNA hybrid + H2O i.e. 18 nucleotide 3'-fluorescein-labeled RNA annealed to a complementary 18 nucleotide 5'-dabsyl-modified DNA, RNase H catalysis by the retroviral enzyme appears to involve a two-metal ion mechanism. Unlike cellular RNases H, the retroviral RNase H displays three different modes of cleavage: internal, 3'-end-DNA-directed, and 5'-end-RNA-directed, all three modes of cleavage appear to have essential roles in reverse transcription, overview, substrate binding structure, overview Human immunodeficiency virus 1 ? - ? 390306 3.1.13.2 RNA/DNA hybrid + H2O RNase H catalysis by the retroviral enzyme appears to involve a two-metal ion mechanism. Unlike cellular RNases H, the retroviral RNase H displays three different modes of cleavage: internal,3'-end-DNA-directed, and 5'-end-RNA-directed, all three modes of cleavage appear to have essential roles in reverse transcription, overview Moloney murine leukemia virus ? - ? 390306 3.1.13.2 RNA/DNA hybrid + H2O secondary structure and substrate binding, overview Moloney murine leukemia virus ? - ? 390306 3.1.13.2 single-stranded RNA + H2O - Human immunodeficiency virus 1 ? - ? 93110