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(-)-epigallocatechin-3-gallate
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competitive, the inhibitor can form hydrogen bonds with Pro1223, Glu1265, Cys1225, Ser1229 and Arg1309. Hypermethylation of CpG islands in the promoter regions is an important mechanism to silence the expression of many important genes in cancer. (-)-Epigallocatechin-3-gallate can inhibit DNMT activity and reactivate methylation-silenced genes in cancer cells
(N4-fluoroacetyl-5-azacytidine)
efficient inhibitor of DNA methylation in human tumor cell lines
2'-dC
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binding modelling, overview
2'-deoxy-5-aza-cytidine
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binding modelling, overview
2-(1H)-pyrimidinone riboside
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i.e. zebularine, is a more stable, less cytotoxic inhibitor compared to 5-azacytidine probably due to differing stability and reversibility of the covalent bonds. The ternary complexes between the enzyme, 2-(1H)-pyrimidinone inhibitor, and the cofactor S-adenosyl-L-methionine are maintained through the formation of a reversible covalent interaction
2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-chloro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-fluoro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-iodo-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-methoxy-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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2-amino-4-[([(2S,3S,4R,5R)-5-[6-amino-2-(methylsulfanyl)-9H-purin-9-yl]-3,4-dihydroxytetrahydrofuran-2-yl]methyl)sulfanyl]butanoic acid
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2-pyrimidinone
forms a part of inhibitor 1,2-dihydropyrimidin-2-one-5-methylene-(methylsulfonium)-adenosyl, bindng structure and mechanism, overview
5'-(3-aminopropylthio)-5'-deoxyadenosine
5'-(3-carboxypropylthio)-5'-deoxyadenosine
5-Azacytosine
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mechanism-based inhibitor
asCEBPA-1 RNA
competitive with respect to substrate (CMeGG-CCG)12
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asCEBPA-2 RNA
mixed inhibition
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asCEPA-1HPE RNA
competitive with respect to substrate (CMeGG-CCG)12
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asCEPA-2HPE RNA
competitive with respect to substrate (CMeGG-CCG)12
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decitabine
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binding modelling, overview
Mg2+
1 mM, slight inhibition, Dnmt3a; 1 mM, slight inhibition, Dnmt3b
miR-127-3p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-145-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-146a-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-155-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12; micro-RNA. Exogenous miR-155-5p in cells inhibits DNMT1 and induces aberrant DNA methylation of the genome
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miR-16-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-17-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-19b-3p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-20a-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-21-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-373-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-9-3p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-9-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-92-1-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-92a-1-5p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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miR-92a-3p
micro-RNA, competitive with respect to substrate (CMeGG-CCG)12
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Mn2+
strong inhibition, Dnmt3a; strong inhibition, Dnmt3b
native DNA
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non-competitive inhibitor against S-adenosyl-L-methionine
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Ni2+
strong inhibition, Dnmt3a; strong inhibition, Dnmt3b
Nicotine
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decreases glutamic acid decarboxylase 67 promoter methylation by DMT1 in GABAergic interneurons
NSC 106084
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inhibition of Dnmt1
NSC 137546
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inhibition of Dnmt1
NSC 138419
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inhibition of Dnmt1
NSC 14778
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inhibition of Dnmt1; inhibition of Dnmt3b
NSC 158324
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inhibition of Dnmt1
NSC 319745
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inhibition of Dnmt1
NSC 348926
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slight inhibition of Dnmt1
NSC 408488
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inhibition of Dnmt1
NSC 54162
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inhibition of Dnmt1
NSC 56071
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inhibition of Dnmt1
NSC 57893
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inhibition of Dnmt1
NSC 622444
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inhibition of Dnmt1
oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone
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oligodeoxyribonucleotides containing 2-aminopurine
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-
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oligodeoxyribonucleotides containing 5-azacytidine
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5-azacytosine oligodeoxyribonucleotides form complexes with C5 DNA methyltransferases that are irreversible when the 5-azacytosine ring is intact, overview
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poly[d(G-5-azacytidine)]
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-
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procainamide
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binding modelling, overview
procaine
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binding modelling, overview
putrescine
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1 mM, 42% inhibition
retinoblastoma gene product
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a negative regulator of DNA methylation, binds to the allosteric site of hDNMT1 and inhibits methylation, it may regulate methylation spreading
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RG108
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slight inhibition of Dnmt1
S-(1-deazaadenosyl)-L-homocysteine
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S-(2'-deoxy-b -D-ribofuranosyladenosin-5'-yl)-L-homocysteine
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S-(2'-deoxy-beta-D-ribofuranosyladenosin-5'-yl)-L-homocysteine
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S-(3-deazaadenosyl)-L-homocysteine
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S-(8-azaadenosyl)-L-homocysteine
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S-(N-(2-biphenyl-4-ylethyl)-2-chloroadenosyl)-L-homocysteine
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S-(N-(2-biphenyl-4-ylethyl)adenosyl)-L-homocysteine
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S-(N-(3,5-dimethoxybenzyl)adenosyl)-L-homocysteine
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S-(N-(pyridin-4-ylmethyl)adenosyl)-L-homocysteine
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S-(N-benzyladenosyl)-L-homocysteine
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S-(N-phenyladenosyl)-L-homocysteine
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S-(N-phenylethyladenosyl)-L-homocysteine
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S-(N-phenylpropyladenosyl)-L-homocysteine
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S-(N6 -benzoyladenosin-5'-yl)-L-homocysteine
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S-(N6-benzoyladenosin-5'-yl)-L-homocysteine
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S-adenosin-5'-yl-L-homocysteine methylamide
S-adenosyl-L-homocysteine
S-cytid-5'-yl-L-homocysteine
S-inosin-5'-yl-L-homocysteine
S-nebularinehomocysteine
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S-Tubercidinylhomocysteine
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[1,2-dihydropyrimidin-2-one]-5-methylene-(methylsulfonium)-adenosyl
with 2-pyrimidinone ring
5'-(3-aminopropylthio)-5'-deoxyadenosine
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5'-(3-aminopropylthio)-5'-deoxyadenosine
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5'-(3-carboxypropylthio)-5'-deoxyadenosine
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5'-(3-carboxypropylthio)-5'-deoxyadenosine
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5-aza-2'-deoxycytidine
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5-aza-2'-deoxycytidine
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5-azacytidine
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5-azacytidine
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zebularine is a more stable, less cytotoxic inhibitor compared to 5-azacytidine probably due to differing stability and reversibility of the covalent bonds
5-azacytidine
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binding modelling, overview
5-fluorocytosine
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mechanism-based inhibitor
6-thioguanine
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incorporation of 6-thioguanine perturbs cytosine methylation at the CpG dinucleotide site by DNA methyltransferases in vitro and acts as a DNA demethylating agent in vivo. Presence of 6-thioguanine at the unmethylated CpG site abolished almost completely the methylation of its 5' adjacent cytosine by HpaII
6-thioguanine
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incorporation of 6-thioguanine perturbs cytosine methylation at the CpG dinucleotide site by DNA methyltransferases in vitro and acts as a DNA demethylating agent in vivo. Presence of 6-thioguanine at the unmethylated CpG site abolished almost completely the methylation of its 5' adjacent cytosine by DNMT1
hydralazine
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inhibition of Dnmt1
hydralazine
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binding modelling, overview
KCl
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above 100 mM
KCl
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above 0.1 M, inhibition may be simply due to dissociation of the DNA-enzyme complex
NaCl
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incubation of native calf thymus DNA in presence of 40 mM NaCl results in 50% inhibition, more than 90% inhibition at 200 mM. With denatured calf thymus DNA, low concentrations of NaCl, up to 90 mM stimulate, 50% inhibition at 175 mM
NaCl
Dnmt3a, inhibits activity around physiological ionic strength; Dnmt3b, inhibits activity around physiological ionic strength
NaCl
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above 0.1 M, inhibition may be simply due to dissociation of the DNA-enzyme complex
oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone
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oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone at the enzymatic target site are competitive inhibitors of both prokaryotic and mammalian DNA C5 methyltransferases, overview
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oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone
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S-adenosin-5'-yl-L-homocysteine methylamide
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S-adenosin-5'-yl-L-homocysteine methylamide
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S-adenosyl-L-ethionine
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non-competitive inhibitor against DNA
S-adenosyl-L-ethionine
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IC50: 0.05 mM
S-adenosyl-L-homocysteine
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S-adenosyl-L-homocysteine
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S-adenosyl-L-homocysteine
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S-adenosyl-L-homocysteine
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S-adenosyl-L-homocysteine
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product inhibition of Dnmt1; product inhibition of Dnmt3b
S-adenosyl-L-homocysteine
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potent competitive inhibitor
S-adenosyl-L-homocysteine
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half-inhibition at 0.02 mM
S-cytid-5'-yl-L-homocysteine
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S-cytid-5'-yl-L-homocysteine
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S-inosin-5'-yl-L-homocysteine
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S-inosin-5'-yl-L-homocysteine
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spermidine
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1 mM, 59% inhibition
spermidine
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at millimolar concentrations
spermine
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1 mM, 97% inhibition
spermine
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at millimolar concentrations
additional information
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methylation specificity is affected by gene copy number and induction levels
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additional information
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inhibitor binding kinetics
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additional information
synthesis of 2-amino-3-cyano-4-halopyridine-C-nucleosides (dXPCN) and oligodeoxyribonucleotides containing dXPCN, as inhibitors of DNMT. Oligodeoxyribonucleotides have a cyano group as an electron-withdrawing group at the C3 position of the pyridine ring. Oligodeoxyribonucleotides containing dXPCN effectively form a complex with DNMTs and exhibit cell antiproliferation activity against human cancer cells
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additional information
not inhibited by 0.045 mM 2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-methoxy-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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additional information
not inhibited by 0.045 mM 2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-methoxy-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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additional information
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not inhibited by 0.045 mM 2-amino-4-([[(2S,3S,4R,5R)-5-(6-amino-2-methoxy-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl]sulfanyl)butanoic acid
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additional information
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no inhibition of Dnmt3b by NSC 56071, NSC 348926, NSC 106084, NSC 622444, NSC 408488, NSC 137546, NSC 345763, NSC 54162, NSC 154957, NSC 158324, NSC 57893, and NSC 138419; virtual inhibitor screeening, molecular modeling with Dnmt1, overview. No inhibition of Dnmt1 by NSC 345763, NSC 154957, and NSC 158324
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additional information
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inhibitor screening by molecular docking and molecular dynamics simulations
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additional information
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stimulating proteins from murine P815 mastocytoma cells stimulate both de novo and maintenance activity of DNA methyltransferase about 3fold. They enhance the methylation of any natural DNA and of poly[(dI-dC)*(dI-dC)] but inhibit methylation of poly[(dG-dC)*(dG-dC)]
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additional information
Dnmt3a is fully active at physiological potassium concentration of K+
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additional information
Dnmt3a is fully active at physiological potassium concentration of K+
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additional information
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Dnmt3a is fully active at physiological potassium concentration of K+
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additional information
inhibitory effects by methyl donor analogs, base analogs, cations, and cationic amines on rice DNA MTase; inhibitory effects by methyl donor analogs, base analogs, cations, and cationic amines on rice DNA MTase
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additional information
inhibitory effects by methyl donor analogs, base analogs, cations, and cationic amines on rice DNA MTase; inhibitory effects by methyl donor analogs, base analogs, cations, and cationic amines on rice DNA MTase
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additional information
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inhibitory effects by methyl donor analogs, base analogs, cations, and cationic amines on rice DNA MTase; inhibitory effects by methyl donor analogs, base analogs, cations, and cationic amines on rice DNA MTase
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