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Literature summary for 3.1.26.4 extracted from

  • Plashkevych, O.; Li, Q.; Chattopadhyaya, J.
    How RNase HI (Escherichia coli) promoted site-selective hydrolysis works on RNA in duplex with carba-LNA and LNA substituted antisense strands in an antisense strategy context? (2017), Mol. Biosyst., 13, 921-938 .
    View publication on PubMed

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information detailed kinetic study of 36 single modified AON-RNA heteroduplexes with the enzyme Escherichia coli

Organism

Organism UniProt Comment Textmining
Escherichia coli
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-
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Reaction

Reaction Comment Organism Reaction ID
Endonucleolytic cleavage to a 5'-phosphomonoester mechanism of RNase H mediated cleavage of the RNA, overview Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(1S,3R,4R,5R,7S)-1-[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
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Escherichia coli ?
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?
(1S,3R,4R,5R,7S)-3-[4-(benzylamino)-5-methyl-2-oxopyrimidin-1(2H)-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
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Escherichia coli ?
-
?
(1S,3R,4R,5S,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
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Escherichia coli ?
-
?
(1S,3R,4R,5S,7S)-3-(2-acetamido-6-oxo-5,6-dihydro-9H-purin-9-yl)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
-
Escherichia coli ?
-
?
(1S,3R,4R,5S,7S)-3-[4-(benzylamino)-5-methyl-2-oxopyrimidin-1(2H)-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
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Escherichia coli ?
-
?
(1S,3R,4R,5S,7S)-3-[6-(benzylamino)-9H-purin-9-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-ol + H2O
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Escherichia coli ?
-
?
(1S,3R,4R,5S,7S)-3-[6-(benzylamino)-9H-purin-9-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
-
Escherichia coli ?
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?
1-[(1R,5S,7R,8S)-8-(benzyloxy)-5-[(benzyloxy)methyl]-6-oxabicyclo[3.2.1]octan-7-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
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Escherichia coli ?
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?
1-[(1S,3R,4R,5R,7S)-7-(benzyloxy)-1-[(benzyloxy)methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
-
Escherichia coli ?
-
?
1-[(1S,3R,4R,5R,7S)-7-[bis(4-methoxyphenyl)(phenyl)methoxy]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
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Escherichia coli ?
-
?
1-[(1S,3R,4R,5S,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
-
Escherichia coli ?
-
?
1-[(1S,3R,4R,5S,7S)-7-(benzyloxy)-1-[(benzyloxy)methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
-
Escherichia coli ?
-
?
4-(benzylamino)-1-[(1S,3R,4R,5R,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidin-2(1H)-one + H2O
-
Escherichia coli ?
-
?
4-(benzylamino)-1-[(1S,3R,4R,5S,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidin-2(1H)-one + H2O
-
Escherichia coli ?
-
?
additional information substitution of a single native nucleotide in the antisense strand (AON) by locked nucleic acid (LNA) or by diastereomerically pure carba-LNA results in site-dependent modulation of RNase H1 promoted cleavage of complementary mRNA strands by 2 to 5 fold at 5'-GpN-3' cleavage sites, giving up to 70% of the RNA cleavage products. The 2nd best cleavage site, being the 5'-ApN-3' sites, cleaves up to 23%, depending upon the substitution site in 36 isosequential complementary AONs. A comparison of the modified AON promoted RNA cleavage rates with that of the native AON shows that sequence-specificity is considerably enhanced as a result of modification. Clearly, relatively weaker 5'-purine (Pu)-pyrimidine (Py)-3' stacking in the complementary RNA strand is preferred (giving about 90% of total cleavage products), which plays an important role in RNase H promoted RNA cleavage. A plausible mechanism of RNase H mediated cleavage of the RNA has been proposed to be 2fold, dictated by the balancing effect of the aromatic character of the purine aglycone: first, the locally formed 9-guanylate ion alters the adjoining sugar-phosphate backbone around the scissile phosphate, transforming its sugar N/S conformational equilibrium, to preferential S-type, causing preferential cleavage at 5'-GpN-3' sites around the center of 20 mer complementary mRNA. Second, the weaker nearest-neighbor strength of 5'-Pu-p-Py-3' stacking promotes preferential 5'-GpN-3' and 5'-ApN-3' cleavage, providing about 90% of the total products, compared to about 50% in that of the native one, because of the cLNA/LNA substituent effect on the neighboring 5'-Pu-p-Py-3' sites, providing both local steric flexibility and additional hydration. This facilitates both the water and water/Mg2+ ion availability at the cleavage site causing sequence-specific hydrolysis of the phosphodiester bond of scissile phosphate Escherichia coli ?
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?
N-(9-[(1S,3R,4R,5S,7S)-7-(benzyloxy)-1-[(benzyloxy)methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-6-oxo-6,9-dihydro-5H-purin-2-yl)acetamide + H2O
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Escherichia coli ?
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?
N-benzyl-9-[(1S,3R,4R,5S,7S)-1-([bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-7-[(trimethylsilyl)oxy]-2-oxabicyclo[2.2.1]heptan-3-yl)-9H-purin-6-amine + H2O
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Escherichia coli ?
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?
N-[9-[(1S,3R,4R,5S,7S)-1-([bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-6-oxo-6,9-dihydro-5H-purin-2-yl)acetamide + H2O
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Escherichia coli ?
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?
N-[9-[(1S,3R,4R,5S,7S)-7-hydroxy-1-(hydroxymethyl)-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-6-oxo-6,9-dihydro-5H-purin-2-yl]acetamide + H2O
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Escherichia coli ?
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?
[(1S,3R,4R,5S,7S)-3-[6-(benzylamino)-9H-purin-9-yl]-5-methyl-7-[(trimethylsilyl)oxy]-2-oxabicyclo[2.2.1]heptan-1-yl]methanol + H2O
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Escherichia coli ?
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?

Synonyms

Synonyms Comment Organism
RNase HI
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Escherichia coli