-
1
-
-
0037007175
-
Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases
-
Jeltsch A. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem. 3 (2002) 274-293
-
(2002)
Chembiochem.
, vol.3
, pp. 274-293
-
-
Jeltsch, A.1
-
2
-
-
4344685527
-
Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex
-
Hopkins B.B., and Reich N.O. Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex. J. Biol. Chem. 279 (2004) 37049-37060
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 37049-37060
-
-
Hopkins, B.B.1
Reich, N.O.2
-
3
-
-
0028010888
-
HhaI methyltransferase flips its target base out of the DNA helix
-
Klimasauskas S., Kumar S., Roberts R.J., and Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76 (1994) 357-369
-
(1994)
Cell
, vol.76
, pp. 357-369
-
-
Klimasauskas, S.1
Kumar, S.2
Roberts, R.J.3
Cheng, X.4
-
4
-
-
0031667109
-
Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base
-
O'Gara M., Horton J.R., Roberts R.J., and Cheng X. Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nature Struct. Biol. 5 (1998) 872-877
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 872-877
-
-
O'Gara, M.1
Horton, J.R.2
Roberts, R.J.3
Cheng, X.4
-
5
-
-
0029068629
-
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing
-
Reinisch K.M., Chen L., Verdine G.L., and Lipscomb W.N. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82 (1995) 143-153
-
(1995)
Cell
, vol.82
, pp. 143-153
-
-
Reinisch, K.M.1
Chen, L.2
Verdine, G.L.3
Lipscomb, W.N.4
-
6
-
-
0034746572
-
Structure of the N6-adenine DNA methyltransferase M center dot Taql in complex with DNA and a cofactor analog
-
Goedecke K., Pignot M., Goody R.S., Scheidig A.J., and Weinhold E. Structure of the N6-adenine DNA methyltransferase M center dot Taql in complex with DNA and a cofactor analog. Nature Struct. Biol. 8 (2001) 121-125
-
(2001)
Nature Struct. Biol.
, vol.8
, pp. 121-125
-
-
Goedecke, K.1
Pignot, M.2
Goody, R.S.3
Scheidig, A.J.4
Weinhold, E.5
-
7
-
-
0030575782
-
A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase
-
O'Gara M., Roberts R.J., and Cheng X. A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase. J. Mol. Biol. 263 (1996) 597-606
-
(1996)
J. Mol. Biol.
, vol.263
, pp. 597-606
-
-
O'Gara, M.1
Roberts, R.J.2
Cheng, X.3
-
8
-
-
0029904839
-
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
-
Slupphaug G., Mol C.D., Kavli B., Arvai A.S., Krokan H.E., and Tainer J.A. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 384 (1996) 87-92
-
(1996)
Nature
, vol.384
, pp. 87-92
-
-
Slupphaug, G.1
Mol, C.D.2
Kavli, B.3
Arvai, A.S.4
Krokan, H.E.5
Tainer, J.A.6
-
9
-
-
0028990179
-
M.HhaI binds tightly to substrates containing mismatches at the target base
-
Klimasauskas S., and Roberts R.J. M.HhaI binds tightly to substrates containing mismatches at the target base. Nucl. Acids Res. 23 (1995) 1388-1395
-
(1995)
Nucl. Acids Res.
, vol.23
, pp. 1388-1395
-
-
Klimasauskas, S.1
Roberts, R.J.2
-
10
-
-
0030572656
-
Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes
-
O'Gara M., Klimasauskas S., Roberts R.J., and Cheng X. Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes. J. Mol. Biol. 261 (1996) 634-645
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 634-645
-
-
O'Gara, M.1
Klimasauskas, S.2
Roberts, R.J.3
Cheng, X.4
-
11
-
-
0034694685
-
Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (Cytosine C5)-methyltransferase
-
Wang P., Brank A.S., Banavali N.K., Nicklaus M.C., Marquez V.E., Christman J.K., and MacKerell Jr. A.D. Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (Cytosine C5)-methyltransferase. J. Am. Chem. Soc. 122 (2000) 12422-12434
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 12422-12434
-
-
Wang, P.1
Brank, A.S.2
Banavali, N.K.3
Nicklaus, M.C.4
Marquez, V.E.5
Christman, J.K.6
MacKerell Jr., A.D.7
-
13
-
-
0037178070
-
Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations
-
Varnai P., and Lavery R. Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations. J. Am. Chem. Soc. 124 (2002) 7272-7273
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 7272-7273
-
-
Varnai, P.1
Lavery, R.2
-
14
-
-
0034663610
-
DNA bending induced by DNA (cytosine-5) methyltransferases
-
Rasko T., Finta C., and Kiss A. DNA bending induced by DNA (cytosine-5) methyltransferases. Nucl. Acids Res. 28 (2000) 3083-3091
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 3083-3091
-
-
Rasko, T.1
Finta, C.2
Kiss, A.3
-
15
-
-
33646088737
-
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase
-
Horton J.R., Liebert K., Bekes M., Jeltsch A., and Cheng X. Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase. J. Mol. Biol. 358 (2006) 559-570
-
(2006)
J. Mol. Biol.
, vol.358
, pp. 559-570
-
-
Horton, J.R.1
Liebert, K.2
Bekes, M.3
Jeltsch, A.4
Cheng, X.5
-
16
-
-
0141507036
-
Structure of the bacteriophage T4 DNA adenine methyltransferase
-
Yang Z., Horton J.R., Zhou L., Zhang X.J., Dong A., Zhang X., et al. Structure of the bacteriophage T4 DNA adenine methyltransferase. Nature Struct. Biol. 10 (2003) 849-855
-
(2003)
Nature Struct. Biol.
, vol.10
, pp. 849-855
-
-
Yang, Z.1
Horton, J.R.2
Zhou, L.3
Zhang, X.J.4
Dong, A.5
Zhang, X.6
-
17
-
-
0033516566
-
DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity
-
Allan B.W., Garcia R., Maegley K., Mort J., Wong D., Lindstrom W., et al. DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity. J. Biol. Chem. 274 (1999) 19269-19275
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 19269-19275
-
-
Allan, B.W.1
Garcia, R.2
Maegley, K.3
Mort, J.4
Wong, D.5
Lindstrom, W.6
-
18
-
-
0035883736
-
AdoMet-dependent methylation, DNA methyltransferases and base flipping
-
Cheng X., and Roberts R.J. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucl. Acids Res. 29 (2001) 3784-3795
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 3784-3795
-
-
Cheng, X.1
Roberts, R.J.2
-
19
-
-
0034214957
-
Spontaneous base flipping in DNA and its possible role in methyltransferase binding
-
Chen Y.Z., Mohan V., and Griffey R.H. Spontaneous base flipping in DNA and its possible role in methyltransferase binding. Phys. Rev. E 62 (2000) 1133-1137
-
(2000)
Phys. Rev. E
, vol.62
, pp. 1133-1137
-
-
Chen, Y.Z.1
Mohan, V.2
Griffey, R.H.3
-
20
-
-
0013411169
-
Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings
-
Keepers J.W., Kollman P.A., Weiner P.K., and James T.L. Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings. Proc. Natl Acad. Sci. USA 79 (1982) 5537-5541
-
(1982)
Proc. Natl Acad. Sci. USA
, vol.79
, pp. 5537-5541
-
-
Keepers, J.W.1
Kollman, P.A.2
Weiner, P.K.3
James, T.L.4
-
21
-
-
0021733122
-
Molecular-mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG).d(CGCGAATTCGCG
-
Keepers J.W., Schmidt P., James T.L., and Kollman P.A. Molecular-mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG).d(CGCGAATTCGCG. Biopolymers 23 (1984) 2901-2929
-
(1984)
Biopolymers
, vol.23
, pp. 2901-2929
-
-
Keepers, J.W.1
Schmidt, P.2
James, T.L.3
Kollman, P.A.4
-
22
-
-
0000777707
-
Energetic coupling between DNA bending and base pair opening
-
Ramstein J., and Lavery R. Energetic coupling between DNA bending and base pair opening. Proc. Natl Acad. Sci. USA 85 (1988) 7231-7235
-
(1988)
Proc. Natl Acad. Sci. USA
, vol.85
, pp. 7231-7235
-
-
Ramstein, J.1
Lavery, R.2
-
23
-
-
9644255719
-
Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI
-
Huang N., and MacKerell Jr. A.D. Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. J. Mol. Biol. 345 (2005) 265-274
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 265-274
-
-
Huang, N.1
MacKerell Jr., A.D.2
-
24
-
-
0027338134
-
Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-l-methionine
-
Cheng X., Kumar S., Posfai J., Pflugrath J.W., and Roberts R.J. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-l-methionine. Cell 74 (1993) 299-307
-
(1993)
Cell
, vol.74
, pp. 299-307
-
-
Cheng, X.1
Kumar, S.2
Posfai, J.3
Pflugrath, J.W.4
Roberts, R.J.5
-
25
-
-
3242714355
-
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase
-
Horton J.R., Ratner G.., Banavali N.K., Huang N., Choi Y., Maier M.A., et al. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucl. Acids Res. 32 (2004) 3877-3886
-
(2004)
Nucl. Acids Res.
, vol.32
, pp. 3877-3886
-
-
Horton, J.R.1
Ratner, G..2
Banavali, N.K.3
Huang, N.4
Choi, Y.5
Maier, M.A.6
-
26
-
-
3843090592
-
The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes
-
Estabrook R.A., Lipson R., Hopkins B., and Reich N. The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes. J. Biol. Chem. 279 (2004) 31419-31428
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 31419-31428
-
-
Estabrook, R.A.1
Lipson, R.2
Hopkins, B.3
Reich, N.4
-
27
-
-
0028920604
-
The mechanism of inhibition of DNA-(cytosine-C5)-methyltransferases by 5-azacytosine is likely to involve methyl transfer to the inhibitor
-
Gabbara S., and Bhagwat A.S. The mechanism of inhibition of DNA-(cytosine-C5)-methyltransferases by 5-azacytosine is likely to involve methyl transfer to the inhibitor. Biochem. J. 307 (1995) 87-92
-
(1995)
Biochem. J.
, vol.307
, pp. 87-92
-
-
Gabbara, S.1
Bhagwat, A.S.2
-
28
-
-
0039765141
-
Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase
-
Lindstrom Jr. W.M., Flynn J., and Reich N.O. Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase. J. Biol. Chem. 275 (2000) 4912-4919
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 4912-4919
-
-
Lindstrom Jr., W.M.1
Flynn, J.2
Reich, N.O.3
-
29
-
-
0030448581
-
Targeted base stacking disruption by the EcoRI DNA methyltransferase
-
Allan B.W., and Reich N.O. Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35 (1996) 14757-14762
-
(1996)
Biochemistry
, vol.35
, pp. 14757-14762
-
-
Allan, B.W.1
Reich, N.O.2
-
30
-
-
0027318633
-
The DNA-binding affinity of HhaI methylase is increased by a single amino-acid substitution in the catalytic center
-
Mi S., and Roberts R.J. The DNA-binding affinity of HhaI methylase is increased by a single amino-acid substitution in the catalytic center. Nucl. Acids Res. 21 (1993) 2459-2464
-
(1993)
Nucl. Acids Res.
, vol.21
, pp. 2459-2464
-
-
Mi, S.1
Roberts, R.J.2
-
31
-
-
0038392721
-
Catalytic mechanism of DNA-(cytosine-C5)-methyltransferases revisited: covalent intermediate formation is not essential for methyl group transfer by the murine Dnmt3a enzyme
-
Reither S., Li F., Gowher H., and Jeltsch A. Catalytic mechanism of DNA-(cytosine-C5)-methyltransferases revisited: covalent intermediate formation is not essential for methyl group transfer by the murine Dnmt3a enzyme. J. Mol. Biol. 329 (2003) 675-684
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 675-684
-
-
Reither, S.1
Li, F.2
Gowher, H.3
Jeltsch, A.4
-
32
-
-
0033499867
-
In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b
-
Hsieh C.L. In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b. Mol. Cell. Biol. 19 (1999) 8211-8218
-
(1999)
Mol. Cell. Biol.
, vol.19
, pp. 8211-8218
-
-
Hsieh, C.L.1
-
33
-
-
0036142089
-
Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro
-
Lin I.G., Han L., Taghva A., O'Brien L.E., and Hsieh C.L. Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro. Mol. Cell. Biol. 22 (2002) 704-723
-
(2002)
Mol. Cell. Biol.
, vol.22
, pp. 704-723
-
-
Lin, I.G.1
Han, L.2
Taghva, A.3
O'Brien, L.E.4
Hsieh, C.L.5
-
34
-
-
0030789978
-
DNA containing 4′-thio-2′-deoxycytidine inhibits methylation by HhaI methyltransferase
-
Kumar S., Horton J.R., Jones G.D., Walker R.T., Roberts R.J., and Cheng X. DNA containing 4′-thio-2′-deoxycytidine inhibits methylation by HhaI methyltransferase. Nucl. Acids Res. 25 (1997) 2773-2783
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 2773-2783
-
-
Kumar, S.1
Horton, J.R.2
Jones, G.D.3
Walker, R.T.4
Roberts, R.J.5
Cheng, X.6
-
35
-
-
0034624023
-
Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase
-
Vilkaitis G., Dong A., Weinhold E., Cheng X., and Klimasauskas S. Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J. Biol. Chem. 275 (2000) 38722-38730
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 38722-38730
-
-
Vilkaitis, G.1
Dong, A.2
Weinhold, E.3
Cheng, X.4
Klimasauskas, S.5
-
36
-
-
31144473532
-
Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes
-
Neely R.K., Daujotyte D., Grazulis S., Magennis S.W., Dryden D.T., Klimasauskas S., and Jones A.C. Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucl. Acids Res. 33 (2005) 6953-6960
-
(2005)
Nucl. Acids Res.
, vol.33
, pp. 6953-6960
-
-
Neely, R.K.1
Daujotyte, D.2
Grazulis, S.3
Magennis, S.W.4
Dryden, D.T.5
Klimasauskas, S.6
Jones, A.C.7
-
37
-
-
0029053632
-
Disruption of the target G-C base-pair by the HhaI methyltransferase
-
Klimasauskas S., and Roberts R.J. Disruption of the target G-C base-pair by the HhaI methyltransferase. Gene 157 (1995) 163-164
-
(1995)
Gene
, vol.157
, pp. 163-164
-
-
Klimasauskas, S.1
Roberts, R.J.2
-
39
-
-
0036306053
-
Free energy and structural pathways of base flipping in a DNA GCGC containing sequence
-
Banavali N.K., and MacKerell Jr. A.D. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J. Mol. Biol. 319 (2002) 141-160
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 141-160
-
-
Banavali, N.K.1
MacKerell Jr., A.D.2
-
40
-
-
0037335588
-
Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations
-
Giudice E., Varnai P., and Lavery R. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucl. Acids Res. 31 (2003) 1434-1443
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 1434-1443
-
-
Giudice, E.1
Varnai, P.2
Lavery, R.3
-
41
-
-
0033569621
-
Active site dynamics of the HhaI methyltransferase: insights from computer simulation
-
Lau E.Y., and Bruice T.C. Active site dynamics of the HhaI methyltransferase: insights from computer simulation. J. Mol. Biol. 293 (1999) 9-18
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 9-18
-
-
Lau, E.Y.1
Bruice, T.C.2
-
42
-
-
84889120137
-
Improved methods for building protein models in electron-density maps and the location of errors in these models
-
Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
-
(1991)
Acta Crystallog. sect. A
, vol.47
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
43
-
-
3543012707
-
Crystallography and NMR system: a new software suite for macromolecular structure determination
-
Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
-
(1998)
Acta Crystallog. sect. D
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
-
44
-
-
0033609041
-
Measurement of the absolute temporal coupling between DNA binding and base flipping
-
Allan B.W., Reich N.O., and Beechem J.M. Measurement of the absolute temporal coupling between DNA binding and base flipping. Biochemistry 38 (1999) 5308-5314
-
(1999)
Biochemistry
, vol.38
, pp. 5308-5314
-
-
Allan, B.W.1
Reich, N.O.2
Beechem, J.M.3
-
45
-
-
20444480973
-
DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping
-
Su T.J., Tock M.R., Egelhaaf S.U., Poon W.C., and Dryden D.T. DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping. Nucl. Acids Res. 33 (2005) 3235-3244
-
(2005)
Nucl. Acids Res.
, vol.33
, pp. 3235-3244
-
-
Su, T.J.1
Tock, M.R.2
Egelhaaf, S.U.3
Poon, W.C.4
Dryden, D.T.5
-
46
-
-
33747786756
-
-
Youngblood, B., Shieh, F., De Los Rios, S., Perona, J. J. & Reich, N. (2006). Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase M.HhaI. J. Mol. Biol. (in press).
-
-
-
|