-
1
-
-
0016273515
-
DNA ligase: Structure, mechanism, and function
-
Lehman, I.R. (1974) DNA ligase: Structure, mechanism, and function. Science 186, 790-797.
-
(1974)
Science
, vol.186
, pp. 790-797
-
-
Lehman, I.R.1
-
2
-
-
0037127211
-
Mechanism underlying replication protein A stimulation of DNA Ligase I
-
Ranalli, T.A., DeMott, M.S. & Bambara, R.A. (2002) Mechanism underlying replication protein A stimulation of DNA Ligase I. J. Biol. Chem. 277, 1719-1727.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 1719-1727
-
-
Ranalli, T.A.1
DeMott, M.S.2
Bambara, R.A.3
-
3
-
-
0032486375
-
DNA ligase I selectively affects DNA synthesis by DNA polymerases delta and epsilon suggesting differential functions in DNA replication and repair
-
Mossi, R., Ferrari, E. & Hubscher, U. (1998) DNA ligase I selectively affects DNA synthesis by DNA polymerases delta and epsilon suggesting differential functions in DNA replication and repair. J. Biol. Chem. 273, 14322-14330.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 14322-14330
-
-
Mossi, R.1
Ferrari, E.2
Hubscher, U.3
-
4
-
-
0031972353
-
Structure and function of mammalian DNA ligases
-
Tomkinson, A.E. & Mackey, Z.B. (1998) Structure and function of mammalian DNA ligases. Mutation Res. 407, 1-9.
-
(1998)
Mutation Res.
, vol.407
, pp. 1-9
-
-
Tomkinson, A.E.1
Mackey, Z.B.2
-
5
-
-
0032126647
-
DNA ligase I is recruited to sites of DNA replication by an interaction with proliferating cell nuclear antigen: Identification of a common targeting mechanism for the assembly of replication factories
-
Montecucco, A., Rossi, R., Levin, D.S., Gary, R., Park, M.S., Motycka, T.A., Ciarrocchi, G., Villa, A., Biamonti, G. & Tomkinson, A.E. (1998) DNA ligase I is recruited to sites of DNA replication by an interaction with proliferating cell nuclear antigen: Identification of a common targeting mechanism for the assembly of replication factories. EMBO J. 17, 3786-3795.
-
(1998)
EMBO J.
, vol.17
, pp. 3786-3795
-
-
Montecucco, A.1
Rossi, R.2
Levin, D.S.3
Gary, R.4
Park, M.S.5
Motycka, T.A.6
Ciarrocchi, G.7
Villa, A.8
Biamonti, G.9
Tomkinson, A.E.10
-
6
-
-
0033569841
-
Delayed DNA joining at 3′ mismatches by human DNA ligases
-
Bhagwat, A.S., Sanderson, R.J. & Lindahl, T. (1999) Delayed DNA joining at 3′ mismatches by human DNA ligases. Nucleic Acids Res. 27, 4028-4033.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4028-4033
-
-
Bhagwat, A.S.1
Sanderson, R.J.2
Lindahl, T.3
-
7
-
-
0032478802
-
The action of DNA ligase at abasic sites in DNA
-
Bogenhagen, D.F. & Pinz, K.G. (1998) The action of DNA ligase at abasic sites in DNA. J. Biol. Chem. 273, 7888-7893.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 7888-7893
-
-
Bogenhagen, D.F.1
Pinz, K.G.2
-
8
-
-
0342350255
-
Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair
-
Levin, D.S., McKenna, A.E., Motycka, T.A., Matsumoto, Y. & Tomkinson, A.E. (2000) Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. Curr. Biol. 10, 919-922.
-
(2000)
Curr. Biol.
, vol.10
, pp. 919-922
-
-
Levin, D.S.1
McKenna, A.E.2
Motycka, T.A.3
Matsumoto, Y.4
Tomkinson, A.E.5
-
9
-
-
0035191378
-
Crystal structure of an Xrcc4-DNA ligase IV complex
-
Sibanda, B.L., Critchlow, S.E., Begun, J., Pei, X.Y., Jackson, S.P., Blundell, T.L. & Pellegrini, L. (2001) Crystal structure of an Xrcc4-DNA ligase IV complex. Nat. Struct. Biol. 8, 1015-1019.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 1015-1019
-
-
Sibanda, B.L.1
Critchlow, S.E.2
Begun, J.3
Pei, X.Y.4
Jackson, S.P.5
Blundell, T.L.6
Pellegrini, L.7
-
10
-
-
0032185230
-
DNA ligase IV is essential for V(D)J recombination and DNA double-strand break repair in human precursor lymphocytes
-
Grawunder, U., Zimmer, D., Fugmann, S., Schwarz, K. & Lieber, M.R. (1998) DNA ligase IV is essential for V(D)J recombination and DNA double-strand break repair in human precursor lymphocytes. Mol. Cell 2, 477-484.
-
(1998)
Mol. Cell
, vol.2
, pp. 477-484
-
-
Grawunder, U.1
Zimmer, D.2
Fugmann, S.3
Schwarz, K.4
Lieber, M.R.5
-
11
-
-
0035903103
-
Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radio-sensitivity
-
Riballo, E., Doherty, A.J., Dai, Y., StiN, T., Oettinger, M.A., Jeggo, P.A. & Kysela, B. (2001) Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radio-sensitivity. J. Biol. Chem. 276, 31124-31132.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 31124-31132
-
-
Riballo, E.1
Doherty, A.J.2
Dai, Y.3
Stiff, T.4
Oettinger, M.A.5
Jeggo, P.A.6
Kysela, B.7
-
12
-
-
0035834067
-
DNA ligase IV-deficient cells are more resistant to ionizing radiation in the absence of Ku70: Implications for DNA double-strand break repair
-
Adachi, N., Ishino, T., Ishii, Y., Takeda, S. & Koyama, H. (2001) DNA ligase IV-deficient cells are more resistant to ionizing radiation in the absence of Ku70: Implications for DNA double-strand break repair. Proc. Natl. Acad. Sci. USA 98, 12109-12113.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 12109-12113
-
-
Adachi, N.1
Ishino, T.2
Ishii, Y.3
Takeda, S.4
Koyama, H.5
-
13
-
-
0029166107
-
Mammalian DNA ligase III: Molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination
-
Chen, J., Tomkinson, A.E., Ramos, W., Mackey, Z.B., Dane-hower, S., Walter, C.A., Schultz, R.A., Besterman, J.M. & Husain, I. (1995) Mammalian DNA ligase III: Molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. Mol. Cell Biol. 15, 5412-5422.
-
(1995)
Mol. Cell Biol.
, vol.15
, pp. 5412-5422
-
-
Chen, J.1
Tomkinson, A.E.2
Ramos, W.3
Mackey, Z.B.4
Danehower, S.5
Walter, C.A.6
Schultz, R.A.7
Besterman, J.M.8
Husain, I.9
-
14
-
-
0035818603
-
Intermediates in V(D)J recombination: A stable RAG1/2 complex sequesters cleaved RSS ends
-
Jones, J.M. & Gellert, M. (2001) Intermediates in V(D)J recombination: A stable RAG1/2 complex sequesters cleaved RSS ends. Proc. Natl. Acad. Sci. USA 98, 12926-12931.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 12926-12931
-
-
Jones, J.M.1
Gellert, M.2
-
15
-
-
0028102267
-
Biochemistry of homologous recombination in Escherichia coli
-
Kowalczykowski,S.C.,Dixon,D.A.,Eggleston,A.K.,Lauder,S.D. & Rehrauer, W.M. (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58, 401-465.
-
(1994)
Microbiol. Rev.
, vol.58
, pp. 401-465
-
-
Kowalczykowski, S.C.1
Dixon, D.A.2
Eggleston, A.K.3
Lauder, S.D.4
Rehrauer, W.M.5
-
16
-
-
0037126846
-
2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases
-
2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases. J. Biol. Chem. 277, 1695-1704.
-
(2002)
J. Biol Chem.
, vol.277
, pp. 1695-1704
-
-
Cherepanov, A.V.1
De Vries, S.2
-
17
-
-
0029938467
-
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7
-
Subramanya, H.S., Doherty, A.J., Ashford, S.R. & Wigley, D.B. (1996) Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85, 607-615.
-
(1996)
Cell
, vol.85
, pp. 607-615
-
-
Subramanya, H.S.1
Doherty, A.J.2
Ashford, S.R.3
Wigley, D.B.4
-
18
-
-
0029969958
-
Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization
-
Doherty, A.J., Ashford, S.R., Subramanya, H.S. & Wigley, D.B. (1996) Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization. J. Biol. Chem. 271, 11083-11089.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 11083-11089
-
-
Doherty, A.J.1
Ashford, S.R.2
Subramanya, H.S.3
Wigley, D.B.4
-
19
-
-
0033634655
-
Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining
-
Odell, M., Sriskanda, V., Shuman, S. & Nikolov, D.B. (2000) Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol. Cell 6, 1183-1193.
-
(2000)
Mol. Cell
, vol.6
, pp. 1183-1193
-
-
Odell, M.1
Sriskanda, V.2
Shuman, S.3
Nikolov, D.B.4
-
20
-
-
12944286563
-
+-dependent DNA ligase from Thermus filiformis
-
+-dependent DNA ligase from Thermus filiformis. Acta Crystallogr. D Biol. Crystallogr. 56, 357-358.
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 357-358
-
-
Lee, J.Y.1
Kim, H.K.2
Chang, C.3
Eom, S.H.4
Hwang, K.Y.5
Cho, Y.6
Yu, Y.G.7
Ryu, S.E.8
Kwon, S.T.9
Suh, S.W.10
-
21
-
-
0034161570
-
+-dependent DNA ligase: Modular architecture and functional implications
-
+-dependent DNA ligase: Modular architecture and functional implications. EMBO J. 19, 1119-1129.
-
(2000)
EMBO J.
, vol.19
, pp. 1119-1129
-
-
Lee, J.Y.1
Chang, C.2
Song, H.K.3
Moon, J.4
Yang, J.K.5
Kim, H.K.6
Kwon, S.T.7
Suh, S.W.8
-
23
-
-
0035965270
-
+-dependent DNA ligase encoded by a eukaryotic virus
-
Sriskanda, V., Moyer, R.W. & Shuman, S. (2001) NAD(+)-dependent DNA ligase encoded by a eukaryotic virus. J. Biol. Chem. 276, 36100-36109.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 36100-36109
-
-
Sriskanda, V.1
Moyer, R.W.2
Shuman, S.3
-
24
-
-
0034734323
-
DNA ligases in the repair and replication of DNA
-
Timson, D.J., Singleton, M.R. & Wigley, D.B. (2000) DNA ligases in the repair and replication of DNA. Mutation Res. 460, 301-318.
-
(2000)
Mutation Res.
, vol.460
, pp. 301-318
-
-
Timson, D.J.1
Singleton, M.R.2
Wigley, D.B.3
-
25
-
-
0034635347
-
Nick recognition by DNA ligases
-
Doherty, A.J. & DaNorn, T.R. (2000) Nick recognition by DNA ligases. J. Mol. Biol. 296, 43-56.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 43-56
-
-
Doherty, A.J.1
Dafforn, T.R.2
-
26
-
-
0037155931
-
Role of nucleotidyl transferase motif V in strand joining by Chlorella virus DNA ligase
-
Sriskanda, V. & Shuman, S. (2002) Role of nucleotidyl transferase motif V in strand joining by Chlorella virus DNA ligase. J. Biol. Chem. 277, 9661-9667.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 9661-9667
-
-
Sriskanda, V.1
Shuman, S.2
-
27
-
-
0030585422
-
Closing the gap on DNA ligase
-
Shuman, S. (1996) Closing the gap on DNA ligase. Structure 4, 653-656.
-
(1996)
Structure
, vol.4
, pp. 653-656
-
-
Shuman, S.1
-
28
-
-
0031090688
-
Common fold, common function, common origin?
-
Suck, D. (1997) Common fold, common function, common origin? Nat. Struct. Biol. 4, 161-165.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 161-165
-
-
Suck, D.1
-
29
-
-
0027479161
-
OB (oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences
-
Murzin, A.G. (1993) OB (oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences. EMBO J. 12, 861-867.
-
(1993)
EMBO J.
, vol.12
, pp. 861-867
-
-
Murzin, A.G.1
-
30
-
-
0038228666
-
X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes
-
Hakansson, K., Doherty, A.J., Shuman, S. & Wigley, D.B. (1997) X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell 89, 545-553.
-
(1997)
Cell
, vol.89
, pp. 545-553
-
-
Hakansson, K.1
Doherty, A.J.2
Shuman, S.3
Wigley, D.B.4
-
31
-
-
0029906410
-
Characterization of proteolytic fragments of bacteriophage T7 DNA ligase
-
Doherty, A.J., Ashford, S.R. & Wigley, D.B. (1996) Characterization of proteolytic fragments of bacteriophage T7 DNA ligase. Nucleic Acids Res. 24, 2281-2287.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 2281-2287
-
-
Doherty, A.J.1
Ashford, S.R.2
Wigley, D.B.3
-
32
-
-
0033553405
-
Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA
-
Odell, M. & Shuman, S. (1999) Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. J. Biol. Chem. 274, 14032-14039.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 14032-14039
-
-
Odell, M.1
Shuman, S.2
-
33
-
-
0033534370
-
Functional domains of an ATP-dependent DNA ligase
-
Doherty, A.J. & Wigley, D.B. (1999) Functional domains of an ATP-dependent DNA ligase. J. Mol. Biol. 285, 63-71.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 63-71
-
-
Doherty, A.J.1
Wigley, D.B.2
-
34
-
-
0034327406
-
Structural and mechanistic conservation in DNA ligases
-
Doherty, A.J. & Suh, S.W. (2000) Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res. 28, 4051-4058.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4051-4058
-
-
Doherty, A.J.1
Suh, S.W.2
-
35
-
-
0033581011
-
DNA polymerases: Structural diversity and common mechanisms
-
Steitz, T.A. (1999) DNA polymerases: Structural diversity and common mechanisms. J. Biol. Chem. 274, 17395-17398.
-
(1999)
J. Biol Chem.
, vol.274
, pp. 17395-17398
-
-
Steitz, T.A.1
-
36
-
-
0028881713
-
Polymerase structures and function: Variations on a theme?
-
Joyce, C.M. & Steitz, T.A. (1995) Polymerase structures and function: Variations on a theme? J. Bacteriol. 177, 6321-6329.
-
(1995)
J. Bacteriol.
, vol.177
, pp. 6321-6329
-
-
Joyce, C.M.1
Steitz, T.A.2
-
37
-
-
0035369086
-
Structure of the replicating complex of a pol alpha family DNA polymerase
-
Franklin, M.C., Wang, J. & Steitz, T.A. (2001) Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105, 657-667.
-
(2001)
Cell
, vol.105
, pp. 657-667
-
-
Franklin, M.C.1
Wang, J.2
Steitz, T.A.3
-
38
-
-
0035826622
-
Insight into the catalytic mechanism of DNA polymerase beta: Structures of intermediate complexes
-
Arndt, J.W., Gong, W., Zhong, X., Showalter, A.K., Liu, J., Dunlap, C.A., Lin, Z., Paxson, C., Tsai, M.D. & Chan, M.K. (2001) Insight into the catalytic mechanism of DNA polymerase beta: Structures of intermediate complexes. Biochemistry 40, 5368-5375.
-
(2001)
Biochemistry
, vol.40
, pp. 5368-5375
-
-
Arndt, J.W.1
Gong, W.2
Zhong, X.3
Showalter, A.K.4
Liu, J.5
Dunlap, C.A.6
Lin, Z.7
Paxson, C.8
Tsai, M.D.9
Chan, M.K.10
-
39
-
-
0030930760
-
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
-
Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J. & Pelletier, H. (1997) Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism. Biochemistry 36, 11205-11215.
-
(1997)
Biochemistry
, vol.36
, pp. 11205-11215
-
-
Sawaya, M.R.1
Prasad, R.2
Wilson, S.H.3
Kraut, J.4
Pelletier, H.5
-
40
-
-
0028049441
-
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP
-
Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. & Kraut, J. (1994) Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science 264, 1891-1903.
-
(1994)
Science
, vol.264
, pp. 1891-1903
-
-
Pelletier, H.1
Sawaya, M.R.2
Kumar, A.3
Wilson, S.H.4
Kraut, J.5
-
41
-
-
0032535528
-
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation
-
Li, Y., Korolev, S. & Waksman, G. (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation. EMBO J. 17, 7514-7525.
-
(1998)
EMBO J.
, vol.17
, pp. 7514-7525
-
-
Li, Y.1
Korolev, S.2
Waksman, G.3
-
42
-
-
0034698001
-
A-form conformational motifs in ligand-bound DNA structures
-
Lu, X.J., Shakked, Z. & Olson, W.K. (2000) A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300, 819-840.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 819-840
-
-
Lu, X.J.1
Shakked, Z.2
Olson, W.K.3
-
43
-
-
0032518524
-
Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
-
Kiefer, J.R., Mao, C., Braman, J.C. & Beese, L.S. (1998) Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391, 304-307.
-
(1998)
Nature
, vol.391
, pp. 304-307
-
-
Kiefer, J.R.1
Mao, C.2
Braman, J.C.3
Beese, L.S.4
-
44
-
-
0030586279
-
A model for DNA polymerase translocation: Worm-like movement of DNA within the binding cleft
-
WlassoN, W.A., Dymshits, G.M. & Lavrik, O.I. (1996) A model for DNA polymerase translocation: Worm-like movement of DNA within the binding cleft. FEBS Lett. 390, 6-9.
-
(1996)
FEBS Lett.
, vol.390
, pp. 6-9
-
-
Wlassoff, W.A.1
Dymshits, G.M.2
Lavrik, O.I.3
-
45
-
-
0027231782
-
Structure of DNA polymerase I Klenow fragment bound to duplex DNA
-
Beese, L.S., Derbyshire, V. & Steitz, T.A. (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260, 352-355.
-
(1993)
Science
, vol.260
, pp. 352-355
-
-
Beese, L.S.1
Derbyshire, V.2
Steitz, T.A.3
-
46
-
-
0027244844
-
Evidence of DNA bending in transcription complexes imaged by scanning force microscopy
-
Rees, W.A., Keller, R.W., Vesenka, J.P., Yang, G. & Bustamante, C. (1993) Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science 260, 1646-1649.
-
(1993)
Science
, vol.260
, pp. 1646-1649
-
-
Rees, W.A.1
Keller, R.W.2
Vesenka, J.P.3
Yang, G.4
Bustamante, C.5
-
47
-
-
0032518398
-
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution
-
Doublie, S., Tabor, S., Long, A.M., Richardson, C.C. & Ellenberger, T. (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391, 251-258.
-
(1998)
Nature
, vol.391
, pp. 251-258
-
-
Doublie, S.1
Tabor, S.2
Long, A.M.3
Richardson, C.C.4
Ellenberger, T.5
-
48
-
-
0034214208
-
Characterization of the 'helix clamp' motif of HIV-1 reverse transcriptase using MALDI-TOF MS and surface plasmon resonance
-
Lin, S., Long, S., Ramirez, S.M., Cotter, R.J. & Woods, A.S. (2000) Characterization of the 'helix clamp' motif of HIV-1 reverse transcriptase using MALDI-TOF MS and surface plasmon resonance. Anal. Chem. 72, 2635-2640.
-
(2000)
Anal. Chem.
, vol.72
, pp. 2635-2640
-
-
Lin, S.1
Long, S.2
Ramirez, S.M.3
Cotter, R.J.4
Woods, A.S.5
-
49
-
-
0018397705
-
Bent DNA: Visualization of a base-paired and stacked A-B conformational junction
-
Selsing, E., Wells, R.D., Alden, C.J. & Arnott, S. (1979) Bent DNA: Visualization of a base-paired and stacked A-B conformational junction. J. Biol. Chem. 254, 5417-5422.
-
(1979)
J. Biol. Chem.
, vol.254
, pp. 5417-5422
-
-
Selsing, E.1
Wells, R.D.2
Alden, C.J.3
Arnott, S.4
-
50
-
-
0027935377
-
The solution structure of the r (gcg) d (TATACCC): D (GGGTA-TACGC) Okazaki fragment contains two distinct duplex morphologies connected by a junction
-
Salazar, M., FedoroN, O., Zhu, L. & Reid, B.R. (1994) The solution structure of the r (gcg) d (TATACCC): D (GGGTA-TACGC) Okazaki fragment contains two distinct duplex morphologies connected by a junction. J. Mol. Biol. 241, 440-455.
-
(1994)
J. Mol. Biol.
, vol.241
, pp. 440-455
-
-
Salazar, M.1
Fedoroff, O.2
Zhu, L.3
Reid, B.R.4
-
52
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
Jones, S., van Heyningen, P., Berman, H.M. & Thornton, J.M. (1999) Protein-DNA interactions: A structural analysis. J. Mol. Biol. 287, 877-896.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 877-896
-
-
Jones, S.1
Van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
54
-
-
0021770861
-
A base-centred explanation of the B-to-A transition in DNA
-
Calladine, C.R. & Drew, H.R. (1984) A base-centred explanation of the B-to-A transition in DNA. J. Mol. Biol. 178, 773-782.
-
(1984)
J. Mol. Biol.
, vol.178
, pp. 773-782
-
-
Calladine, C.R.1
Drew, H.R.2
-
55
-
-
0031722426
-
An analysis of the relationship between hydration and protein-DNA interactions
-
Woda, J., Schneider, B., Patel, K., Mistry, K. & Berman, H.M. (1998) An analysis of the relationship between hydration and protein-DNA interactions. Biophys. J. 75, 2170-2177.
-
(1998)
Biophys. J.
, vol.75
, pp. 2170-2177
-
-
Woda, J.1
Schneider, B.2
Patel, K.3
Mistry, K.4
Berman, H.M.5
-
56
-
-
0000127073
-
Sequence-specific recognition of double helical nucleic acids by proteins
-
Seeman, N.C., Rosenberg, J.M. & Rich, A. (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73, 804-808.
-
(1976)
Proc. Natl. Acad. Sci. USA
, vol.73
, pp. 804-808
-
-
Seeman, N.C.1
Rosenberg, J.M.2
Rich, A.3
-
57
-
-
0000619168
-
Comparison of nucleotide interactions in water, proteins, and vacuum: Model for DNA polymerase fidelity
-
Petruska, J., Sowers, L.C. & Goodman, M.F. (1986) Comparison of nucleotide interactions in water, proteins, and vacuum: Model for DNA polymerase fidelity. Proc. Natl. Acad. Sci. USA 83, 1559-1562.
-
(1986)
Proc. Natl. Acad. Sci. USA
, vol.83
, pp. 1559-1562
-
-
Petruska, J.1
Sowers, L.C.2
Goodman, M.F.3
-
58
-
-
0023056536
-
Salt induced B-A transition of poly (dG) poly (dC) and the stabilization of A form by its methylation
-
Nishimura, Y., Torigoe, C. & Tsuboi, M. (1986) Salt induced B-A transition of poly (dG) poly (dC) and the stabilization of A form by its methylation. Nucleic Acids Res. 14, 2737-2748.
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 2737-2748
-
-
Nishimura, Y.1
Torigoe, C.2
Tsuboi, M.3
-
59
-
-
0016266033
-
The B to A transition of DNA in solution
-
Ivanov, V.I., Minchenkova, L.E., Minyat, E.E., Frank-Kamenetskii, M.D. & Schyolkina, A.K. (1974) The B to A transition of DNA in solution. J. Mol. Biol. 87, 817-833.
-
(1974)
J. Mol. Biol.
, vol.87
, pp. 817-833
-
-
Ivanov, V.I.1
Minchenkova, L.E.2
Minyat, E.E.3
Frank-Kamenetskii, M.D.4
Schyolkina, A.K.5
-
60
-
-
0028241531
-
Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes
-
Nekludova, L. & Pabo, C.O. (1994) Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. Proc. Natl. Acad. Sci. USA 91, 6948-6952.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 6948-6952
-
-
Nekludova, L.1
Pabo, C.O.2
-
61
-
-
0028315988
-
Determinants of repressor/operator recognition from the structure of the trp operator binding site
-
Shakked, Z., Guzikevich-Guerstein, G., Frolow, F., Rabinovich, D., Joachimiak, A. & Sigler, P.B. (1994) Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature 368, 469-473.
-
(1994)
Nature
, vol.368
, pp. 469-473
-
-
Shakked, Z.1
Guzikevich-Guerstein, G.2
Frolow, F.3
Rabinovich, D.4
Joachimiak, A.5
Sigler, P.B.6
-
62
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson, W.K., Gorin, A.A., Lu, X.J., Hock, L.M. & Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA 95, 11163-11168.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
63
-
-
0034326316
-
B-form to A-form conversion by a 3′-terminal ribose: Crystal structure of the chimera d (CCACTAGTG) r (G)
-
Wahl, M.C. & Sundaralingam, M. (2000) B-form to A-form conversion by a 3′-terminal ribose: Crystal structure of the chimera d (CCACTAGTG) r (G). Nucleic Acids Res. 28, 4356-4363.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4356-4363
-
-
Wahl, M.C.1
Sundaralingam, M.2
-
64
-
-
0028618356
-
Crystal structure of the highly distorted chimeric decamer r (C) d (CGGCGCCG) r (G) spermine complex-spermine binding to phosphate only and minor groove tertiary base-pairing
-
Ban, C., Ramakrishnan, B. & Sundaralingam, M. (1994) Crystal structure of the highly distorted chimeric decamer r (C) d (CGGCGCCG) r (G) spermine complex-spermine binding to phosphate only and minor groove tertiary base-pairing. Nucleic Acids Res. 22, 5466-5476.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 5466-5476
-
-
Ban, C.1
Ramakrishnan, B.2
Sundaralingam, M.3
-
65
-
-
0028350664
-
A single 2′-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d (CCGGC) r (G) d (CCGG) with a novel intermolecular G-C base-paired quadruplet
-
Ban, C., Ramakrishnan, B. & Sundaralingam, M. (1994) A single 2′-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d (CCGGC) r (G) d (CCGG) with a novel intermolecular G-C base-paired quadruplet. J. Mol. Biol. 236, 275-285.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 275-285
-
-
Ban, C.1
Ramakrishnan, B.2
Sundaralingam, M.3
-
66
-
-
0030582341
-
Prokaryotic DNA ligases unwind superhelical DNA
-
Ivanchenko, M., van Holde, K. & Zlatanova, J. (1996) Prokaryotic DNA ligases unwind superhelical DNA, Biochem. Biophys. Res. Commun. 226, 498-505.
-
(1996)
Biochem. Biophys. Res. Commun.
, vol.226
, pp. 498-505
-
-
Ivanchenko, M.1
Van Holde, K.2
Zlatanova, J.3
-
67
-
-
33947547892
-
Molecular architecture and biological reactions
-
Pauling, L. (1946) Molecular architecture and biological reactions. Chem. Engng. News 24, 1375-1377.
-
(1946)
Chem. Engng. News
, vol.24
, pp. 1375-1377
-
-
Pauling, L.1
-
68
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland, D.E.J. (1958) Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44, 98-104.
-
(1958)
Proc. Natl. Acad. Sci. USA
, vol.44
, pp. 98-104
-
-
Koshland, D.E.J.1
-
70
-
-
0032518177
-
Chlorella virus DNA ligase: Nick recognition and mutational analysis
-
Sriskanda, V. & Shuman, S. (1998) Chlorella virus DNA ligase: Nick recognition and mutational analysis. Nucleic Acids Res. 26, 525-531.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 525-531
-
-
Sriskanda, V.1
Shuman, S.2
-
71
-
-
0031858138
-
Apparent pore size of polyacrylamide gels: Comparison of gels cast and run in Tris-acetate-EDTA and Tris-borate-EDTA buNers
-
Stellwagen, N.C. (1998) Apparent pore size of polyacrylamide gels: Comparison of gels cast and run in Tris-acetate-EDTA and Tris-borate-EDTA buNers. Electrophoresis 19, 1542-1547.
-
(1998)
Electrophoresis
, vol.19
, pp. 1542-1547
-
-
Stellwagen, N.C.1
-
72
-
-
0022970697
-
DNA ligase from Drosophila melanogaster embryos. Purification and physical characterization
-
Rabin, B.A., Hawley, R.S. & Chase, J.W. (1986) DNA ligase from Drosophila melanogaster embryos. Purification and physical characterization. J. Biol. Chem. 261, 10637-10645.
-
(1986)
J. Biol. Chem.
, vol.261
, pp. 10637-10645
-
-
Rabin, B.A.1
Hawley, R.S.2
Chase, J.W.3
-
73
-
-
0034653795
-
+-dependent DNA ligase from the hyperthermophile Aquifex aeolicus
-
+-dependent DNA ligase from the hyperthermophile Aquifex aeolicus. Nucleic Acids Res. 28, 1447-1454.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1447-1454
-
-
Tong, J.1
Barany, F.2
Cao, W.3
-
74
-
-
0033527667
-
DNA structure and polymerase fidelity
-
Timsit, Y. (1999) DNA structure and polymerase fidelity. J. Mol. Biol. 293, 835-853.
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 835-853
-
-
Timsit, Y.1
-
75
-
-
0023708040
-
Water: An integral part of nucleic acid structure
-
Westhof, E. (1988) Water: An integral part of nucleic acid structure. Annu. Rev. Biophys. Biophys. Chem. 17, 125-144.
-
(1988)
Annu. Rev. Biophys. Biophys. Chem.
, vol.17
, pp. 125-144
-
-
Westhof, E.1
-
76
-
-
0003890119
-
-
W.H. Freeman, New York, USA
-
Kornberg, A. & Baker, T.A. (1992) In DNA Replication, pp. 307-322. W.H. Freeman, New York, USA.
-
(1992)
DNA Replication
, pp. 307-322
-
-
Kornberg, A.1
Baker, T.A.2
-
77
-
-
0030929525
-
Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing
-
Rumbaugh, J.A., Murante, R.S., Shi, S. & Bambara, R.A. (1997) Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing. J. Biol. Chem. 272, 22591-22599.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 22591-22599
-
-
Rumbaugh, J.A.1
Murante, R.S.2
Shi, S.3
Bambara, R.A.4
-
78
-
-
0030767872
-
Ligation of RNA-containing duplexes by Vaccinia DNA ligase
-
Sekiguchi, J. & Shuman, S. (1997) Ligation of RNA-containing duplexes by Vaccinia DNA ligase. Biochemistry 36, 9073-9079.
-
(1997)
Biochemistry
, vol.36
, pp. 9073-9079
-
-
Sekiguchi, J.1
Shuman, S.2
-
79
-
-
0032145356
-
Specificity and fidelity of strand joining by Chlorella virus DNA ligase
-
Sriskanda, V. & Shuman, S. (1998) Specificity and fidelity of strand joining by Chlorella virus DNA ligase. Nucleic Acids Res. 26, 3536-3541.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 3536-3541
-
-
Sriskanda, V.1
Shuman, S.2
-
80
-
-
0029950158
-
Characterization of DNA ligase from the fungus Coprinus cinereus
-
Matsuda, S., Sakaguchi, K., Tsukada, K. & Teraoka, H. (1996) Characterization of DNA ligase from the fungus Coprinus cinereus. Eur. J. Biochem. 237, 691-697.
-
(1996)
Eur. J. Biochem.
, vol.237
, pp. 691-697
-
-
Matsuda, S.1
Sakaguchi, K.2
Tsukada, K.3
Teraoka, H.4
-
81
-
-
0029817836
-
DNA ligase IV from HeLa cell nuclei
-
Robins, P. & Lindahl, T. (1996) DNA ligase IV from HeLa cell nuclei. J. Biol. Chem. 271, 24257-24261.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 24257-24261
-
-
Robins, P.1
Lindahl, T.2
-
82
-
-
0025790388
-
Three distinct DNA ligases in mammalian cells
-
Tomkinson, A.E., Roberts, E., Daly, G., Totty, N.F. & Lindahl, T. (1991) Three distinct DNA ligases in mammalian cells. J. Biol. Chem. 266, 21728-21735.
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 21728-21735
-
-
Tomkinson, A.E.1
Roberts, E.2
Daly, G.3
Totty, N.F.4
Lindahl, T.5
-
83
-
-
0016304026
-
Structures for the polynucleotide complexes poly (dA) with poly (dT) and poly (dT) with poly (dA) with poly (dT)
-
Arnott, S. & Selsing, E. (1974) Structures for the polynucleotide complexes poly (dA) with poly (dT) and poly (dT) with poly (dA) with poly (dT). J. Mol. Biol. 88, 509-521.
-
(1974)
J. Mol. Biol.
, vol.88
, pp. 509-521
-
-
Arnott, S.1
Selsing, E.2
-
84
-
-
0026722438
-
A-DNA in solution as studied by diverse approaches
-
Ivanov, V.I. & Krylov, D. (1992) A-DNA in solution as studied by diverse approaches. Methods Enzymol. 211, 111-127.
-
(1992)
Methods Enzymol.
, vol.211
, pp. 111-127
-
-
Ivanov, V.I.1
Krylov, D.2
-
85
-
-
0035193091
-
Sequence-dependent B-A transition in DNA evaluated with dimeric and trimeric scales
-
Tolstorukov, M.Y., Ivanov, V.I., Malenkov, G.G., Jernigan, R.L. & Zhurkin, V.B. (2001) Sequence-dependent B-A transition in DNA evaluated with dimeric and trimeric scales. Biophys. J. 81, 3409-3421.
-
(2001)
Biophys. J.
, vol.81
, pp. 3409-3421
-
-
Tolstorukov, M.Y.1
Ivanov, V.I.2
Malenkov, G.G.3
Jernigan, R.L.4
Zhurkin, V.B.5
-
86
-
-
0027190862
-
The DNA strand in DNA. RNA hybrid duplexes is neither B-form nor A-form in solution
-
Salazar, M., Fedoroff, O.Y., Miller, J.M., Ribeiro, N.S. & Reid, B.R. (1993) The DNA strand in DNA. RNA hybrid duplexes is neither B-form nor A-form in solution. Biochemistry 32, 4207-4215.
-
(1993)
Biochemistry
, vol.32
, pp. 4207-4215
-
-
Salazar, M.1
Fedoroff, O.Y.2
Miller, J.M.3
Ribeiro, N.S.4
Reid, B.R.5
-
87
-
-
0034615785
-
An A-type double helix of DNA having B-type puckering of the deoxyribose rings
-
Trantirek, L., Stefl, R., Vorlickova, M., Koca, J., Sklenar, V. & Kypr, J. (2000) An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J. Mol. Biol. 297, 907-922.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 907-922
-
-
Trantirek, L.1
Stefl, R.2
Vorlickova, M.3
Koca, J.4
Sklenar, V.5
Kypr, J.6
-
88
-
-
0029375390
-
Crystal structures of B-form DNA-RNA chimers complexed with distamycin
-
Chen, X., Ramakrishnan, B. & Sundaralingam, M. (1995) Crystal structures of B-form DNA-RNA chimers complexed with distamycin. Nat. Struct. Biol. 2, 733-735.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 733-735
-
-
Chen, X.1
Ramakrishnan, B.2
Sundaralingam, M.3
|