3.1.26.13: retroviral ribonuclease H
This is an abbreviated version!
For detailed information about retroviral ribonuclease H, go to the full flat file.
Word Map on EC 3.1.26.13
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3.1.26.13
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integrase
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hiv-rt
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rna-dna
-
template-primer
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moloney
-
polypurine
-
transcriptases
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minus-strand
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3'-azido-3'-deoxythymidine
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nnrti
-
primer-template
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nonnucleoside
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drug development
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medicine
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analysis
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pharmacology
- 3.1.26.13
-
integrase
- hiv-rt
- rna-dna
-
template-primer
-
moloney
-
polypurine
- transcriptases
-
minus-strand
- 3'-azido-3'-deoxythymidine
-
nnrti
-
primer-template
-
nonnucleoside
- drug development
- medicine
- analysis
- pharmacology
Reaction
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. =
Synonyms
HIV reverse transcriptase ribonuclease H, HIV reverse transcriptase-associated RNase H, HIV RNase H, HIV RT RNaseH, HIV RT-associated RNase H, HIV-1 reverse transcriptase, HIV-1 reverse transcriptase ribonuclease H, HIV-1 reverse transcriptase RNase H, HIV-1 RH, HIV-1 ribonuclease H, HIV-1 ribonuclease H domain, HIV-1 RNase H, HIV-1 RT-associated RNase H, human immunodeficiency virus reverse transcriptase, human immunodeficiency virus reverse transcriptase-associated ribonuclease H, human immunodeficiency virus reverse transcriptase-associated RNase H, human immunodeficiency virus RT-associated RNase H, M-MuLV RT RNase H, reverse transcriptase, reverse transcriptase-associated ribonuclease H, reverse transcriptase-associated RNase H, reverse-transcriptase-associated ribonuclease H, ribonuclease H, ribonuclease H domain in HIV-1 reverse transcriptase, RNase H, RNase H activity of HIV-1 reverse transcriptase, RNase H domain of HIV-1 reverse transcriptase, RNase H of HIV-1 subtype C, RNaseH, RNH, RNHHIV, RT RNase H, RT-RNase H
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3.1.26.13 retroviral ribonuclease HAdvanced search results
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results (Substrates Products
Substrates Products on EC 3.1.26.13 - retroviral ribonuclease H
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SUBSTRATE 
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-end-labeled 267 nt-long RNA annealed to 20 nt-long synthetic DNA + H2O
?
-
-
-
-
?
5'-rGrGrGrCrGrArArUrUrCrGrArGrCrUrCrGrGrUrArCrCrC-dGdGdGdGdAdTdCdCdTdCdTdAdG-3'/3'-dTdCdGdAdGdCdCdAdTdGdGdG-dCdCdCdCdTdAdGdGdAdGdTdC-5' + H2O
5'-rGrGrGrCrGrArArUrUrCrGrArGrCrUrCrGrGrUrArCrCrC/dGdGdGdGdAdTdCdCdTdCdTdAdG-3' + 3'-dTdCdGdAdGdCdCdAdTdGdGdG/dCdCdCdCdTdAdGdGdAdGdTdC-5'
-
model substrate, designed to be structurally similar to the DNA-extended tRNA created by initiation of minus-strand DNA synthesis during retroviral replication, contains sequences from the HIV genome and sequences unrelated to the HIV viral genome
hydrolysis of the phosphodiester bond at the DNA-RNA junction
-
?
5'-rGrGrGrUrCrCrCrUrGrUrUrCrGrGrGrCrGrCrCrA-dCdTdGdCdTdAdGdAdGdAdTdTdTdTdT-3'/3'-dGdAdCdAdAdGdCdCdCdGdCdGdGdT-dGdAdCdGdAdTdCdTdCdTdAdAdAdAdA-5' + H2O
5'-rGrGrGrUrCrCrCrUrGrUrUrCrGrGrGrCrGrCrCrA/dCdTdGdCdTdAdGdAdGdAdTdTdTdTdT-3' + 3'-dGdAdCdAdAdGdCdCdCdGdCdGdGdT/dGdAdCdGdAdTdCdTdCdTdAdAdAdAdA-5'
-
model substrate containing sequences from the HIV genome, designed to be structurally similar to the DNA-extended tRNA created by initiation of minus-strand DNA synthesis during retroviral replication. The DNA-extended RNA was a template and was annealed to a DNA oligonucleotide that primed reverse transcription of the RNA in the template
hydrolysis of the phosphodiester bond at the DNA-RNA junction
-
?
5-rGrGrGrCrGrArArUrUrCrGrArGrCrUrCrGrGrUrArCrCrC-dGdGdGdGdAdTdCdCdTdCdTdAdG-3 + 3-dTdCdGdAdGdCdCdAdTdGdGdG-dCdCdCdCdTdAdGdGdAdGdTdC-5' + H2O
?
5-rGrGrGrUrCrCrCrUrGrUrUrCrGrGrGrCrGrCrCrA-dCdTdGdCdTdAdGdAdGdAdTdTdTdTdT-3 + 3-dGdAdCdAdAdGdCdCdCdGdCdGdGdT-dGdAdCdGdAdTdCdTdCdTdAdAdAdAdA-5 + H2O
?
HTS-1 + H2O
?
-
RNA/DNA duplex substrate HTS-1 (RNA 5'-gaucugagccuggagcu-3'-fluorescein annealed to DNA 3'-CTAGACTCGGACCCTCGA-5'-dabsyl) is a high sensitivity duplex that assesses non-specific internal cleavage
-
-
?
HTS-2 + H2O
?
-
HTS-2 (RNA 5'-cugguuagaccagaucugagccugggagcu-3'-fluorescein annealed to DNA 3'-GGTCTAGACTCGGACCCTCGA-5'-dabsyl) provides a duplex with a recessed DNA 3'-terminus and measures 3'-DNA directed or polymerase directed RNase H cleavage
-
-
?
HTS-3 + H2O
?
-
HTS-3 (RNA 5'-accagaucugagccugggagcu-3'-fluorescein annealed to DNA 3'-GACCAATCTGGTCTAGACTCGGACCCTCGA-5'-dabsyl) measures 5'-RNA-directed RNase H cleavage
-
-
?
poly(A)+ mRNA primed with oligo(dT) + H2O
double-stranded DNA copies between 1.3 and 9.9 kilobases in length + ?
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multifunctional enzyme containing RNase H and reverse transcriptase activity
-
-
?
poly(dT)-poly(rA) + H2O
?
-
substrate poly(dC)-poly(rG) is markedly preferred over substrate poly(dT)-poly(rA)
-
-
?
RNA-DNA hybrid containing the polypurine tract + H2O
?
-
extension of the polypurine tract primer by at least 2 nucleotides is sufficient for recognition and correct cleavage by RNase H at the RNA-DNA junction to remove the primer. Primer removal occurs by cleavage one nucleotide away from the RNA-DNA junction. The same polypurine tract specificity determinants responsible for generation of the polypurine tract primer also direct polypurine tract primer removal. Once the primer has been extended and removed from the nascent plus-strand DNA, reinitiation at the resulting plus-strand primer terminus does not occur
-
-
?
5-rGrGrGrCrGrArArUrUrCrGrArGrCrUrCrGrGrUrArCrCrC-dGdGdGdGdAdTdCdCdTdCdTdAdG-3 + 3-dTdCdGdAdGdCdCdAdTdGdGdG-dCdCdCdCdTdAdGdGdAdGdTdC-5' + H2O
?
-
model substrate, designed to be structurally similar to the DNA-extended tRNA created by initiation of minus-strand DNA synthesis during retroviral replication, contains sequences from the HIV genome and sequences unrelated to the HIV viral genome
hydrolysis of the substrate to leave a single ribonucleotide 5-phosphate at the 5-terminus of the model DNA genome
-
?
5-rGrGrGrCrGrArArUrUrCrGrArGrCrUrCrGrGrUrArCrCrC-dGdGdGdGdAdTdCdCdTdCdTdAdG-3 + 3-dTdCdGdAdGdCdCdAdTdGdGdG-dCdCdCdCdTdAdGdGdAdGdTdC-5' + H2O
?
-
model substrate, designed to be structurally similar to the DNA-extended tRNA created by initiation of minus-strand DNA synthesis during retroviral replication, contains sequences from the HIV genome and sequences unrelated to the HIV viral genome
hydrolysis of the substrate to leave a single ribonucleotide 5-phosphate at the 5-terminus of the model DNA genome
-
?
5-rGrGrGrUrCrCrCrUrGrUrUrCrGrGrGrCrGrCrCrA-dCdTdGdCdTdAdGdAdGdAdTdTdTdTdT-3 + 3-dGdAdCdAdAdGdCdCdCdGdCdGdGdT-dGdAdCdGdAdTdCdTdCdTdAdAdAdAdA-5 + H2O
?
-
model substrate containing sequences from the HIV genome, designed to be structurally similar to the DNA-extended tRNA created by initiation of minus-strand DNA synthesis during retroviral replication. The DNA-extended RNA was a template and was annealed to a DNA oligonucleotide that primed reverse transcription of the RNA in the template
hydrolysis of the substrate to leave a single ribonucleotide 5'-phosphate at the 5'-terminus of the model DNA genome
-
?
5-rGrGrGrUrCrCrCrUrGrUrUrCrGrGrGrCrGrCrCrA-dCdTdGdCdTdAdGdAdGdAdTdTdTdTdT-3 + 3-dGdAdCdAdAdGdCdCdCdGdCdGdGdT-dGdAdCdGdAdTdCdTdCdTdAdAdAdAdA-5 + H2O
?
-
model substrate containing sequences from the HIV genome, designed to be structurally similar to the DNA-extended tRNA created by initiation of minus-strand DNA synthesis during retroviral replication. The DNA-extended RNA is a template and is annealed to a DNA oligonucleotide that primed reverse transcription of the RNA in the template
hydrolysis of the substrate to leave a single ribonucleotide 5-phosphate at the 5-terminus of the model DNA genome
-
?
RNA-DNA hybrid + H2O
?
-
5'-GTTTTCTTTTCCCCCCTGAC-3'-fluorescein/5'-CAAAAGAAAAGGGGGGACUG-3'-dabcyl
-
-
?
additional information
?
-
-
evaluation of activity by enzyme's ability to select and extend the 3' polypurine tract primers into (+) strand DNA. Evaluation via concerted and two-step reactions for (+) strand priming, the latter of which allows discrimination between selection end extension events
3' polypurine tract primer selection appears to represent a specialized form of RNase H activity that is more sensitive to minor structural alterations within this domain
-
?
additional information
?
-
-
no substrate: single-stranded RNA or the DNA component of DNA-RNA hybrids. Products consist primarily of monomers, dimers, and trimers with 3'-OH groups
-
-
?
additional information
?
-
-
the HIV polymerase and RNase H active sites are separated by a distance equivalent to the length of a 15-nucleotide RNA-DNA heteroduplex
-
-
?
additional information
?
-
-
a nick separating an upstream RNA and a downstream RNA annealed to DNA is essentially ignored by RNase H, indicating that the RNA 5' end at a nick is not sufficient to position 5' end-directed cleavages. Cleavage sites that are located close to the 5' end of the downstream RNA are not recognized in the absence of the upstream RNA, and the 5' ends of the shorter upstream RNAs enhance cleavage at these sites. The recognition of an internal cleavage site depends on local sequence features found both upstream and downstream of the cleavage site, designated as the -1/+1 position. Preferred nucleotides have been identified in the flanking sequences spanning positions -14 to +1
-
-
?
additional information
?
-
-
interdependence of the polymerase and RNase H activities of HIV-1 reverse transcription during viral DNA synthesis
-
-
?
additional information
?
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RNase H acts at or about 14 to 18 nucleotides from the 5' end of the template, the cleavage site for the RNase H is therefore held at around this distance behind the DNA polymerase activity. For the intact protein, the RNase H and reverse transcriptase activities may work in a coupled or coordinate manner. More than 80% of the residual 5' oligonucleotides remain base paired to the RNA-directed DNA product. Under certain conditions, these short RNAs can act as efficient primers for an associated DNA-directed DNA synthesis in the reverse direction
-
-
?
additional information
?
-
-
study on specificity of RNase H cleavage by use of synthetic DNA-RNA hybrids based on the same 81-base RNA template. First series of RNase H substrates is prepared with complementary DNA oligonucleotides of different lengths, ranging from 6 to 20 nucleotides, all of which share a common 5' end and are successively shorter at their 3' ends. The second series of oligonucleotides has a common 3' end but shorter 5' ends. The DNA oligonucleotides in the third series are all 20 bases long but have non-complementary stretches at either the 5' end, 3' end, or both ends. Enzyme cleaves fairly efficiently if the duplex region is at least eight bases long, but not if it is shorter. Although enzyme requires the substrate to have a region of RNA-DNA duplex, Moloney murine leukemia virus RT can cleave RNA outside the region that is part of the RNA-DNA duplex. The polymerase domain of HIV-1 RT uses certain mismatched segments of RNA-DNA to position the enzyme for RNase H cleavage. A mismatched region near the RNase H domain can interfere with RNase H cleavage, cleavage is usually but not always more efficient if the mismatched segment is deleted
-
-
?
additional information
?
-
-
substrate heteropolymeric 90-nt 5' end-labeled RNA template-annealed to a 36-nt DNA primer is cleaved by wild-type p66/p51 RT precisely at the RNA/DNA junction to liberate a 20-nt (+) strand DNA
-
-
?
additional information
?
-
-
substrates consist 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 M 13 subclone or a phagemid transcription vector subclone. The corresponding hybrids are fully base-paired
products formed from the fully complementary hybrid consist of a nonuniform distribution of oligonucleotides ranging in size from 4 to 15 nt
-
?
additional information
?
-
-
substrates consist 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 M 13 subclone or a phagemid transcription vector subclone. The corresponding hybrids carry a 5'-mismatch of seven nucleotides
products are a few prominent intermediates of 24-42 nt in size with relatively little accumulation of larger products
-
?
additional information
?
-
-
the recognition and precise cleavage of the polypurine tract of the human immunodeficiency virus type 1 is an essential step in HIV-1 reverse transcription. Mutations at positions 2 and 5 of the 3'-end of the polypurine tract do significantly alter the cleavage specificity at the polypurine tract/U3 junction. The structure of the polypurine tract primer, rather than the base-specific contacts between the polypurine tract and HIV-1 RT, are the primary determinants of RNase H cleavage specificity at the polypurine tract/U3 junction
-
-
?
additional information
?
-
-
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. Enzyme strongly prefers A or U at the +1 position and C or G at the -2 position, and A is disfavored at the -4 position. 5' End-directed cleavages occur when sites are positioned between the 13th and 20th nucleotides from the RNA 5' end. The extent of 5' end-directed cleavages observed in substrates containing a free recessed RNA 5' end is most comparable to substrates with a gap of 2 or 3 bases between the upstream and downstream RNAs
-
-
?
additional information
?
-
-
5'end-directed RNase H of reverse transcriptase
-
-
?
additional information
?
-
-
HIV-1 reverse transcriptase has two enzymatic functions, DNA polymerase and RNase H activities
-
-
?
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids, substrate binding and reaction mechanism, overview
-
-
?
additional information
?
-
-
cleavage of DNA-RNA and RNA-DNA primer templates
-
-
?
additional information
?
-
-
RNA-DNA duplex substrate from a 41-mer 5'-labeled 32P-heteropolymeric RNA template kim40R annealed to complementary 32-mer DNA oligomer kim32D
-
-
?
additional information
?
-
-
RNA-DNA substrate in a tRNA removal assay, the cleavage patterns for the recombinant HIV-1 reverse transcriptase and mutant p51-G-TCR construct correspond to the release of the 11mer RNA, corresponding with the authentic cleavage identified in vivo. The relative activity of the isolated HIV-1 RNaseH(p51-G-TCR) is comparable to that of the full-length HIV reverse transcriptase
-
-
?
additional information
?
-
RNA/DNA hybrid duplex substrate
-
-
?
additional information
?
-
-
substrate is 18-nucleotide 3'-fluourescein-labeled RNA annealed to a complementary 18-nucleotide 5'-dabsyl-labeled DNA
-
-
?
additional information
?
-
-
the tC5U-p12 hybrid is used as reaction substrate the RNase H activity
-
-
?
additional information
?
-
-
conserved residues in the connection subdomain and C-terminal ribonuclease H, RNase H, domain of HIV-1 RT contact the nascent DNA primer and modulate the trajectory of the template relative to the RNase H catalytic center. Within the RNase H domain, these residues include Thr473, Glu475, Lys476, Tyr501, and Ile505, while His539 and Asn474 interact with the scissile phosphate of the RNA template,m substrate recognition and binding, overview
-
-
?
additional information
?
-
-
a 5'-32P-labeled AZT-MP chain-terminated RNA/DNA template/primer substrate
-
-
?
additional information
?
-
-
a DNA/RNA hybrid can simultaneously engage both active sites. Of the tested interconverting reverse transcriptase-DNA/RNA species, 43% are active for both sites simultaneously, 27% show only polymerase activity, and the remaining 30% are nonproductive. A string of at least 4-6 nucleotides downstream of the cleaving site is required for efficient RNA cleavage. During processive nucleotide incorporation, sequential rounds of RNA cleavage occur each time after about 6 nucleotides are incorporated, during processive primer extension, diphosphate release is rate-limiting. Although polymerization is efficient and processive, RNase H is inefficient and periodic. This combination allows the two catalytic centers of HIVRT to work simultaneously at similar speeds without being tightly coupled
-
-
?
additional information
?
-
-
HIV RNase H cleaves viral RNA at multiple stages of reverse transcription with at least three distinct modes: random internal cleavages, DNA 3' end-directed and polymerase dependent cleavages, and RNA 5' end-directed cleavages. A biochemical assay uses the HTS-1 RNA/DNA substrate to specifically probe random internal cleavage, which is believed to be the dominant mode of RNA cutting
-
-
?
additional information
?
-
a 18-nucleotide 3'-fluorescein-labeled RNA is annealed to a complementary 18-nucleotide 5'-dabsyl-labeled DNA. Cleavage of the HIV-1 polypurine tract (PPT) primer is performed with a 29 nt Cy5-labeled RNA (5'-Cy5-UUU UAA AAG AAA AGGGGG G*AC UGG AAG GG-3', where * represents the PPT 3' terminus) hybridized to a 40 nt DNA (5'-ATT AGCCCT TCC AGT CCC CCC TTT TCT TTT AAA AAG TGG C-3'). For cytopathicity assays, HIV-1 virus strain RF is used to infect CEM-SS cells
-
-
?
additional information
?
-
-
a 18-nucleotide 3'-fluorescein-labeled RNA is annealed to a complementary 18-nucleotide 5'-dabsyl-labeled DNA. Cleavage of the HIV-1 polypurine tract (PPT) primer is performed with a 29 nt Cy5-labeled RNA (5'-Cy5-UUU UAA AAG AAA AGGGGG G*AC UGG AAG GG-3', where * represents the PPT 3' terminus) hybridized to a 40 nt DNA (5'-ATT AGCCCT TCC AGT CCC CCC TTT TCT TTT AAA AAG TGG C-3'). For cytopathicity assays, HIV-1 virus strain RF is used to infect CEM-SS cells
-
-
?
additional information
?
-
-
RNA/DNA duplex substrate HTS-1 (RNA 5'-gaucugagccuggagcu-3'-fluorescein annealed to DNA 3'-CTAGACTCGGACCCTCGA-5'-dabsyl) is a high sensitivity duplex that assesses non-specific internal cleavage
-
-
?
additional information
?
-
-
RNA/DNA duplex substrate HTS-1 (RNA 5'-gaucugagccuggagcu-3'-fluorescein annealed to DNA 3'-CTAGACTCGGACCCTCGA-5'-dabsyl) is a high sensitivity duplex that assesses non-specific internal cleavage
-
-
?
additional information
?
-
-
RNA/DNA duplex substrate HTS-1 (RNA 5'-gaucugagccugggagcu-3'-fluorescein annealed to DNA 3'-CTAGACTCGGACCCTCGA-5'-dabsyl) is a high sensitivity duplex assessing non-specific internal cleavage
-
-
?
additional information
?
-
-
RNA/DNA duplex substrate HTS-1 (RNA 5'-gaucugagccugggagcu-3'-fluorescein annealed to DNA 3'-CTAGACTCGGACCCTCGA-5'-dabsyl) is a high sensitivity duplex assessing non-specific internal cleavage
-
-
?
additional information
?
-
-
RNase H activity is determined using oligomeric substrates. 5'-Fluorescein-labeled 29 bp RNA/DNA hybrid (R29/D29), 12 bp RNA/RNA duplex (R12/R12), and 12 bp DNA/DNA duplex (D12/D12) are prepared by hybridizing 5'-fluorescein-labeled 29 b RNA (5'-aauagagaaaaagaaaaaagauggcaaag-3'), 12 b RNA (5'-cggagaugacgg-3'), and 12 b DNA (5'-CGGAGAUGACGG-3') with a 1.5 molar equivalent of the complementary DNA
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-
?
additional information
?
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usage of DNA/RNA hybrid substrates for enzyme activity assay. The majority of species represent the active form of RTx02DNA/RNA complexes that can perform both activities simultaneously. Efficient RNase H cleavage required at least four ribonucleotides downstream of the cutting site
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-
?
additional information
?
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when the RNA/DNA hybrid is immobilized at the polymerase active site, RNase H cleavage occurs, experimentally verifying that the substrate can simultaneously interact with both active sites, analysis of the mechanism of the coordination of the two activities. Cross-linking of HIV-1 RT with RNA/DNA hybrids, inhibition of complex formation by salt and heparin. Purified HIV-1 RT D186C, M184C and Q258C variants are tethered to appropriately modified CL3 substrates, and RNase H activity within the cross-linked complexes is determined, overview
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-
?
additional information
?
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cleavage of DNA-RNA and RNA-DNA primer templates
-
-
?
additional information
?
-
-
RNA-DNA duplex substrate from a 41-mer 5'-labeled 32P-heteropolymeric RNA template kim40R annealed to complementary 32-mer DNA oligomer kim32D
-
-
?
additional information
?
-
RNA/DNA hybrid duplex substrate
-
-
?
additional information
?
-
a 18-nucleotide 3'-fluorescein-labeled RNA is annealed to a complementary 18-nucleotide 5'-dabsyl-labeled DNA. Cleavage of the HIV-1 polypurine tract (PPT) primer is performed with a 29 nt Cy5-labeled RNA (5'-Cy5-UUU UAA AAG AAA AGGGGG G*AC UGG AAG GG-3', where * represents the PPT 3' terminus) hybridized to a 40 nt DNA (5'-ATT AGCCCT TCC AGT CCC CCC TTT TCT TTT AAA AAG TGG C-3'). For cytopathicity assays, HIV-1 virus strain RF is used to infect CEM-SS cells
-
-
?
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids, substrate binding and reaction mechanism, overview
-
-
?
additional information
?
-
Human immunodeficiency virus type 1 group M subtype B
5' end labeled RNA-DNA heteroduplexe substrates aligned from commercial RNA and DNA oligonucleotides are used
-
-
?
additional information
?
-
Human immunodeficiency virus type 1 group M subtype B
activity of wild-type enzyme is determined with the RNA/DNA template-primer R33B/20A, comparison of HIV-1 group O subtype B ESP49 and HIV-1 group M subtype B BH10
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-
?
additional information
?
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Human immunodeficiency virus type 1 group M subtype B
hybrid RNA/DNA 5'-GAUCUGAGCCUGGGAGCU-fluorescin-3' and 5'-dabsyl-AGCTCCCAGGCTCAGATC-3' are used for RNase H activity assays
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-
?
additional information
?
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Human immunodeficiency virus type 1 group M subtype B
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usage of DNA/RNA hybrid substrates for enzyme activity assay. The isolated RNH domain of reverse transcriptase (RT), folded by itself, is not catalytically active, due to lack of the substrate handle region, but exhibits a native-like protein fold
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-
?
additional information
?
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Human immunodeficiency virus type 1 group M subtype B BH10
-
usage of DNA/RNA hybrid substrates for enzyme activity assay. The isolated RNH domain of reverse transcriptase (RT), folded by itself, is not catalytically active, due to lack of the substrate handle region, but exhibits a native-like protein fold
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-
?
additional information
?
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Human immunodeficiency virus type 1 group M subtype B BH10
hybrid RNA/DNA 5'-GAUCUGAGCCUGGGAGCU-fluorescin-3' and 5'-dabsyl-AGCTCCCAGGCTCAGATC-3' are used for RNase H activity assays
-
-
?
additional information
?
-
Human immunodeficiency virus type 1 group M subtype B BH10
activity of wild-type enzyme is determined with the RNA/DNA template-primer R33B/20A, comparison of HIV-1 group O subtype B ESP49 and HIV-1 group M subtype B BH10
-
-
?
additional information
?
-
Human immunodeficiency virus type 1 group M subtype B BH10
5' end labeled RNA-DNA heteroduplexe substrates aligned from commercial RNA and DNA oligonucleotides are used
-
-
?
additional information
?
-
Human immunodeficiency virus type 1 group O subtype B
-
activities of wild-type and mutant enzymes are determined with the RNA/DNA template-primer R33B/20A, comparison of HIV-1 group O subtype B ESP49 and HIV-1 group M subtype B BH10
-
-
?
additional information
?
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Human immunodeficiency virus type 1 group O subtype B ESP49
-
activities of wild-type and mutant enzymes are determined with the RNA/DNA template-primer R33B/20A, comparison of HIV-1 group O subtype B ESP49 and HIV-1 group M subtype B BH10
-
-
?
additional information
?
-
-
a nick separating an upstream RNA and a downstream RNA annealed to DNA is essentially ignored by RNase H, indicating that the RNA 5' end at a nick is not sufficient to position 5' end-directed cleavages. Cleavage sites that are located close to the 5' end of the downstream RNA are not recognized in the absence of the upstream RNA, and the 5' ends of the shorter upstream RNAs enhance cleavage at these sites. The recognition of an internal cleavage site depends on local sequence features found both upstream and downstream of the cleavage site, designated as the -1/+1 position. Preferred nucleotides have been identified in the flanking sequences spanning positions -11 to +1
-
-
?
additional information
?
-
-
study on specificity of RNase H cleavage by use of synthetic DNA-RNA hybrids based on the same 81-base RNA template. First series of RNase H substrates is prepared with complementary DNA oligonucleotides of different lengths, ranging from 6 to 20 nucleotides, all of which share a common 5' end and are successively shorter at their 3' ends. The second series of oligonucleotides has a common 3' end but shorter 5' ends. The DNA oligonucleotides in the third series are all 20 bases long but have non-complementary stretches at either the 5' end, 3' end, or both ends. Enzyme cleaves fairly efficiently if the duplex region is at least eight bases long, but not if it is shorter. Although enzyme requires the substrate to have a region of RNA-DNA duplex, Moloney murine leukemia virus RT can cleave RNA outside the region that is part of the RNA-DNA duplex. The polymerase domain of Moloney murine leukemia virus RT does not use the same mismatched segments to define the position for RNase H cleavage
-
-
?
additional information
?
-
-
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. Enzyme strongly prefers A or U at the +1 position and C or G at the -2 position. 5' End-directed cleavages occurr when sites are positioned between the 13th and 20th nucleotides from the RNA 5' end. The extent of 5' end-directed cleavages observed in substrates containing a free recessed RNA 5' end is most comparable to substrates with a gap of 2 or 3 bases between the upstream and downstream RNAs
-
-
?
additional information
?
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Moloney murine leukemia virus reverse transcriptase, M-MuLV RT, is a domain structured enzyme that has the N-terminally located DNA polymerization activity and C-terminally located RNase H activity, which interferes with the efficient synthesis of long cDNA molecules
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Moloney murine leukemia virus reverse transcriptase, MMLV RT, shows DNA polymerization activity and RNase H activity. Stabilization of the reverse transcriptase activity by eliminating the RNase H activity, overview
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retroviral reverse transcriptase also possesses a ribonuclease H activity, an enzyme which cleaves the RNA strand of RNA/DNA hetroduplex
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DNA binding by M-MuLV RT assay using 5'-end labeled 48/36 bp RNA-DNA oligonucleotide duplex, method, overview. RNA-DNA hybrid binding and 5'-end labeled 48/36 bp RNA-DNA oligonucleotide duplex by M-MuLV RT derivatives, overview
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substrate is a 3H-UTP-labeled RNA: RNA-DNA hybrid, synthesis, overview
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the active site of the RNase H function contains four acidic residues, D443, E478, D498, and D549, that likely coordinate two divalent metal ions that are essential for catalysis
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