-
1
-
-
0035967930
-
The DNA polymerase III holoenzyme: An asymmetric dimeric replicative complex with leading and lagging strand polymerases
-
Glover, B. P., and McHenry, C. S. (2001) The DNA polymerase III holoenzyme: an asymmetric dimeric replicative complex with leading and lagging strand polymerases, Cell 105, 925-934.
-
(2001)
Cell
, vol.105
, pp. 925-934
-
-
Glover, B.P.1
McHenry, C.S.2
-
2
-
-
0003890119
-
-
2nd ed.,W. H. Freeman & Company, New York
-
Kornberg, A., and Baker, T. A. (1992) DNA Replication, 2nd ed.,W. H. Freeman & Company, New York.
-
(1992)
DNA Replication
-
-
Kornberg, A.1
Baker, T.A.2
-
3
-
-
34547730912
-
Characterization of a triple DNA polymerase replisome
-
McInerney, P., Johnson, A., Katz, F., and O'Donnell, M. (2007) Characterization of a triple DNA polymerase replisome, Mol. Cell 27, 527-538.
-
(2007)
Mol. Cell
, vol.27
, pp. 527-538
-
-
McInerney, P.1
Johnson, A.2
Katz, F.3
O'Donnell, M.4
-
4
-
-
22244478079
-
Cellular DNA replicases: Components and dynamics at the replication fork
-
Johnson, A., and O'Donnell, M. (2005) Cellular DNA replicases: components and dynamics at the replication fork, Annu. Rev. Biochem. 74, 283-315.
-
(2005)
Annu. Rev. Biochem
, vol.74
, pp. 283-315
-
-
Johnson, A.1
O'Donnell, M.2
-
5
-
-
26844566830
-
Structure and mechanism of DNA polymerases
-
Rothwell, P. J., and Waksman, G. (2005) Structure and mechanism of DNA polymerases, Adv. Protein Chem. 71, 401-440.
-
(2005)
Adv. Protein Chem
, vol.71
, pp. 401-440
-
-
Rothwell, P.J.1
Waksman, G.2
-
6
-
-
0029026635
-
DNA polymerase III holoenzyme: Structure and function of a chromosomal replicating machine
-
Kelman, Z., and O'Donnell, M. (1995) DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine, Annu. Rev. Biochem. 64, 171-200.
-
(1995)
Annu. Rev. Biochem
, vol.64
, pp. 171-200
-
-
Kelman, Z.1
O'Donnell, M.2
-
7
-
-
0033199713
-
Did DNA replication evolve twice independently?
-
Leipe, D. D., Aravind, L., and Koonin, E. V. (1999) Did DNA replication evolve twice independently? Nucleic Acids Res. 27, 3389-3401.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3389-3401
-
-
Leipe, D.D.1
Aravind, L.2
Koonin, E.V.3
-
8
-
-
33748146483
-
Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III
-
Lamers, M. H., Georgescu, R. E., Lee, S. G., O'Donnell, M., and Kuriyan, J. (2006) Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III, Cell 126, 881-892.
-
(2006)
Cell
, vol.126
, pp. 881-892
-
-
Lamers, M.H.1
Georgescu, R.E.2
Lee, S.G.3
O'Donnell, M.4
Kuriyan, J.5
-
9
-
-
33748146034
-
The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases
-
Bailey, S., Wing, R. A., and Steitz, T. A. (2006) The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases, Cell 126, 893-904.
-
(2006)
Cell
, vol.126
, pp. 893-904
-
-
Bailey, S.1
Wing, R.A.2
Steitz, T.A.3
-
10
-
-
0033593355
-
Identification of the acidic residues in the active site of DNA polymerase III
-
Pritchard, A. E., and McHenry, C. S. (1999) Identification of the acidic residues in the active site of DNA polymerase III, J. Mol. Biol. 285, 1067-1080.
-
(1999)
J. Mol. Biol
, vol.285
, pp. 1067-1080
-
-
Pritchard, A.E.1
McHenry, C.S.2
-
11
-
-
33745087407
-
-
2+-dependent exonuclease within a bacterial replicase, Nat. Struct. Mol. Biol. 13, 458-459.
-
2+-dependent exonuclease within a bacterial replicase, Nat. Struct. Mol. Biol. 13, 458-459.
-
-
-
-
12
-
-
0028603484
-
Escherichia coli DNA polymerase III holoenzyme footprints three helical turns of its primer
-
Reems, J. A., and McHenry, C. S. (1994) Escherichia coli DNA polymerase III holoenzyme footprints three helical turns of its primer, J. Biol. Chem. 269, 33091-33096.
-
(1994)
J. Biol. Chem
, vol.269
, pp. 33091-33096
-
-
Reems, J.A.1
McHenry, C.S.2
-
13
-
-
0029929070
-
The helix-hairpin-helix DNA-binding motif: A structural basis for nonsequence-specific recognition of DNA
-
Doherty, A. J., Serpell, L. C., and Ponting, C. P. (1996) The helix-hairpin-helix DNA-binding motif: a structural basis for nonsequence-specific recognition of DNA, Nucleic Acids Res. 24, 2488-2497.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 2488-2497
-
-
Doherty, A.J.1
Serpell, L.C.2
Ponting, C.P.3
-
14
-
-
0034661711
-
Common fold in helix-hairpin-helix proteins
-
Shao, X., and Grishin, N. V. (2000) Common fold in helix-hairpin-helix proteins, Nucleic Acids Res. 28, 2643-2650.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 2643-2650
-
-
Shao, X.1
Grishin, N.V.2
-
15
-
-
23444443484
-
Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: Asymmetric DNA binding and cleavage mechanisms
-
Nishino, T., Komori, K., Ishino, Y., and Morikawa, K. (2005) Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: asymmetric DNA binding and cleavage mechanisms, Structure 13, 1183-1192.
-
(2005)
Structure
, vol.13
, pp. 1183-1192
-
-
Nishino, T.1
Komori, K.2
Ishino, Y.3
Morikawa, K.4
-
16
-
-
33947177875
-
Comparative analysis of eubacterial DNA polymerase III alpha subunits
-
Zhao, X.-Q., Hu, J.-F., and Yu, J. (2006) Comparative analysis of eubacterial DNA polymerase III alpha subunits, Genomics Proteomics Bioinf. 4, 203-211.
-
(2006)
Genomics Proteomics Bioinf
, vol.4
, pp. 203-211
-
-
Zhao, X.-Q.1
Hu, J.-F.2
Yu, J.3
-
17
-
-
0027479161
-
OB(oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for nonhomologous sequences
-
Murzin, A. G. (1993) OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for nonhomologous sequences, EMBO J. 12, 861-867.
-
(1993)
EMBO J
, vol.12
, pp. 861-867
-
-
Murzin, A.G.1
-
18
-
-
0012767432
-
Nucleic acid recognition by OB-fold proteins
-
Theobald, D. L., Mitton-Fry, R. M., and Wuttke, D. S. (2003) Nucleic acid recognition by OB-fold proteins, Annu. Rev. Biophys. Biomol. Struct. 32, 115-133.
-
(2003)
Annu. Rev. Biophys. Biomol. Struct
, vol.32
, pp. 115-133
-
-
Theobald, D.L.1
Mitton-Fry, R.M.2
Wuttke, D.S.3
-
19
-
-
0036913982
-
OB-fold domains: A snapshot of the evolution of sequence, structure, and function
-
Arcus, V. (2002) OB-fold domains: a snapshot of the evolution of sequence, structure, and function, Curr. Opin. Struct. Biol. 12, 794-801.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 794-801
-
-
Arcus, V.1
-
20
-
-
0035748996
-
Comparison of performance in successive CASP experiments
-
Venclovas, Č., Zemla, A., Fidelis, K., and Moult, J. (2001) Comparison of performance in successive CASP experiments, Proteins: Struct., Funct., Genet. 45, 163-170.
-
(2001)
Proteins: Struct., Funct., Genet
, vol.45
, pp. 163-170
-
-
Venclovas, C.1
Zemla, A.2
Fidelis, K.3
Moult, J.4
-
21
-
-
30344454371
-
Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment
-
Venclovas, Č., and Margelevičius, M. (2005) Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment, Proteins: Struct., Funct., Genet. 61, 99-105.
-
(2005)
Proteins: Struct., Funct., Genet
, vol.61
, pp. 99-105
-
-
Venclovas, C.1
Margelevičius, M.2
-
22
-
-
2442684052
-
Sequence-structure mapping errors in the PDB: OB-fold domains
-
Venclovas, Č., Ginalski, K., and Kang, C. (2004) Sequence-structure mapping errors in the PDB: OB-fold domains, Protein Sci. 13, 1594-1602.
-
(2004)
Protein Sci
, vol.13
, pp. 1594-1602
-
-
Venclovas, C.1
Ginalski, K.2
Kang, C.3
-
23
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
24
-
-
23244443772
-
Dual binding modes for an HMG domain from human HMGB2 on DNA
-
McCauley, M., Hardwidge, P. R., Maher, L. J., 3rd, and Williams, M. C. (2005) Dual binding modes for an HMG domain from human HMGB2 on DNA, Biophys. J. 89, 353-364.
-
(2005)
Biophys. J
, vol.89
, pp. 353-364
-
-
McCauley, M.1
Hardwidge, P.R.2
Maher 3rd, L.J.3
Williams, M.C.4
-
25
-
-
33847154255
-
Mechanisms of DNA binding determined in optical tweezers experiments
-
McCauley, M. J., and Williams, M. C. (2007) Mechanisms of DNA binding determined in optical tweezers experiments, Biopolymers 85, 154-168.
-
(2007)
Biopolymers
, vol.85
, pp. 154-168
-
-
McCauley, M.J.1
Williams, M.C.2
-
26
-
-
34249797273
-
Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching
-
Vladescu, I., McCauley, M., Nunez, M. E., Rouzina, I., and Williams, M. C. (2007) Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching, Nat. Methods 4, 517-522.
-
(2007)
Nat. Methods
, vol.4
, pp. 517-522
-
-
Vladescu, I.1
McCauley, M.2
Nunez, M.E.3
Rouzina, I.4
Williams, M.C.5
-
27
-
-
1042298812
-
Mechanical measurement of single molecule binding rates: Kinetics of DNA helix-destabilization by T4 gene 32 protein
-
Pant, K., Karpel, R. L., Rouzina, I., and Williams, M. C. (2004) Mechanical measurement of single molecule binding rates: kinetics of DNA helix-destabilization by T4 gene 32 protein, J. Mol. Biol. 336, 851-870.
-
(2004)
J. Mol. Biol
, vol.336
, pp. 851-870
-
-
Pant, K.1
Karpel, R.L.2
Rouzina, I.3
Williams, M.C.4
-
28
-
-
18844364649
-
Salt dependent binding of T4 gene 32 protein to single- and double-stranded DNA: Single molecule force spectroscopy measurements
-
Pant, K., Karpel, R. L., Rouzina, I., and Williams, M. C. (2005) Salt dependent binding of T4 gene 32 protein to single- and double-stranded DNA: single molecule force spectroscopy measurements, J. Mol. Biol. 349, 317-330.
-
(2005)
J. Mol. Biol
, vol.349
, pp. 317-330
-
-
Pant, K.1
Karpel, R.L.2
Rouzina, I.3
Williams, M.C.4
-
29
-
-
33845975656
-
Single molecule force spectroscopy of salt-dependent bacteriophage T7 gene 2.5 protein binding to single-stranded DNA
-
Shokri, L., Marintcheva, B., Richardson, C. C., Rouzina, I., and Williams, M. C. (2006) Single molecule force spectroscopy of salt-dependent bacteriophage T7 gene 2.5 protein binding to single-stranded DNA, J. Biol. Chem. 281, 38689-38696.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 38689-38696
-
-
Shokri, L.1
Marintcheva, B.2
Richardson, C.C.3
Rouzina, I.4
Williams, M.C.5
-
30
-
-
0035146646
-
Force-induced melting of the DNA double helix. 1. Thermodynamic analysis
-
Rouzina, I., and Bloomfield, V. A. (2001) Force-induced melting of the DNA double helix. 1. Thermodynamic analysis, Biophys. J. 80, 882-893.
-
(2001)
Biophys. J
, vol.80
, pp. 882-893
-
-
Rouzina, I.1
Bloomfield, V.A.2
-
31
-
-
51049121185
-
DNA overstretching in the presence of glyoxal: Structural evidence of force-induced melting
-
Epub ahead of print. DOI: 10.1529/biophysj.1108. 132688
-
Shokri, L., McCauley, M. J., Rouzina, I., and Williams, M. C. (2008) DNA overstretching in the presence of glyoxal: structural evidence of force-induced melting, Biophys. J. Epub ahead of print. DOI: 10.1529/biophysj.1108. 132688.
-
(2008)
Biophys. J
-
-
Shokri, L.1
McCauley, M.J.2
Rouzina, I.3
Williams, M.C.4
-
32
-
-
0036106380
-
Salt dependence of the elasticity and overstretching transition of single DNA molecules
-
Wenner, J. R., Williams, M. C., Rouzina, I., and Bloomfield, V. A. (2002) Salt dependence of the elasticity and overstretching transition of single DNA molecules, Biophys. J. 82, 3160-3169.
-
(2002)
Biophys. J
, vol.82
, pp. 3160-3169
-
-
Wenner, J.R.1
Williams, M.C.2
Rouzina, I.3
Bloomfield, V.A.4
-
33
-
-
32644440043
-
Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins
-
Cruceanu, M., Urbaneja, M. A., Hixson, C. V., Johnson, D. G., Datta, S. A., Fivash, M. J., Stephen, A. G., Fisher, R. J., Gorelick, R. J., Casas-Finet, J. R., Rein, A., Rouzina, I., and Williams, M. C. (2006) Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins, Nucleic Acids Res. 34, 593-605.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 593-605
-
-
Cruceanu, M.1
Urbaneja, M.A.2
Hixson, C.V.3
Johnson, D.G.4
Datta, S.A.5
Fivash, M.J.6
Stephen, A.G.7
Fisher, R.J.8
Gorelick, R.J.9
Casas-Finet, J.R.10
Rein, A.11
Rouzina, I.12
Williams, M.C.13
-
34
-
-
0035253862
-
Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding
-
Bochkareva, E., Belegu, V., Korolev, S., and Bochkarev, A. (2001) Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding, EMBO J. 20, 612-618.
-
(2001)
EMBO J
, vol.20
, pp. 612-618
-
-
Bochkareva, E.1
Belegu, V.2
Korolev, S.3
Bochkarev, A.4
-
35
-
-
0035812836
-
Structural analysis of DNA replication fork reversal by RecG
-
Singleton, M. R., Scaife, S., and Wigley, D. B. (2001) Structural analysis of DNA replication fork reversal by RecG, Cell 107, 79-89.
-
(2001)
Cell
, vol.107
, pp. 79-89
-
-
Singleton, M.R.1
Scaife, S.2
Wigley, D.B.3
-
36
-
-
0029052511
-
Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA
-
Shamoo, Y., Friedman, A. M., Parsons, M. R., Konigsberg, W. H., and Steitz, T. A. (1995) Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA, Nature 376, 362-366.
-
(1995)
Nature
, vol.376
, pp. 362-366
-
-
Shamoo, Y.1
Friedman, A.M.2
Parsons, M.R.3
Konigsberg, W.H.4
Steitz, T.A.5
-
37
-
-
35748980855
-
HMGB binding to DNA: Single and double box motifs
-
McCauley, M. J., Zimmerman, J., Maher, L. J., 3rd, and Williams, M. C. (2007) HMGB binding to DNA: single and double box motifs, J. Mol. Biol. 374, 993-1004.
-
(2007)
J. Mol. Biol
, vol.374
, pp. 993-1004
-
-
McCauley, M.J.1
Zimmerman, J.2
Maher 3rd, L.J.3
Williams, M.C.4
-
38
-
-
0016175370
-
Theoretical aspects of DNA-protein interactions: Cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice
-
McGhee, J. D., and von Hippel, P. H. (1974) Theoretical aspects of DNA-protein interactions: cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice, J. Mol. Biol. 86, 469-489.
-
(1974)
J. Mol. Biol
, vol.86
, pp. 469-489
-
-
McGhee, J.D.1
von Hippel, P.H.2
-
39
-
-
33748261227
-
Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity
-
Sun, S., Geng, L., and Shamoo, Y. (2006) Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity, Proteins: Struct., Funct., Bioinf. 65, 231-238.
-
(2006)
Proteins: Struct., Funct., Bioinf. 65
, pp. 231-238
-
-
Sun, S.1
Geng, L.2
Shamoo, Y.3
-
40
-
-
0000893081
-
Cocrystal structure of an editing complex of Klenow fragment with DNA
-
Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R., and Steitz, T. A. (1988) Cocrystal structure of an editing complex of Klenow fragment with DNA, Proc. Natl. Acad. Sci. U.S.A. 85, 8924-8928.
-
(1988)
Proc. Natl. Acad. Sci. U.S.A
, vol.85
, pp. 8924-8928
-
-
Freemont, P.S.1
Friedman, J.M.2
Beese, L.S.3
Sanderson, M.R.4
Steitz, T.A.5
-
41
-
-
0028246888
-
Escherichia coli single-stranded DNA-binding protein: Multiple DNA-binding modes and cooperativities
-
Lohman, T. M., and Ferrari, M. E. (1994) Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities, Annu. Rev. Biochem. 63, 527-570.
-
(1994)
Annu. Rev. Biochem
, vol.63
, pp. 527-570
-
-
Lohman, T.M.1
Ferrari, M.E.2
-
43
-
-
0037286741
-
Optical-trap force transducer that operates by direct measurement of light momentum
-
Smith, S. B., Cui, Y., and Bustamante, C. (2003) Optical-trap force transducer that operates by direct measurement of light momentum, Methods Enzymol. 361, 134-162.
-
(2003)
Methods Enzymol
, vol.361
, pp. 134-162
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
44
-
-
0036600949
-
Force spectroscopy of single DNA and RNA molecules
-
Williams, M. C., and Rouzina, I. (2002) Force spectroscopy of single DNA and RNA molecules, Curr. Opin. Struct. Biol. 12, 330-336.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 330-336
-
-
Williams, M.C.1
Rouzina, I.2
-
45
-
-
0031047888
-
Stretching DNA with optical tweezers
-
Wang, M. D., Yin, H., Landick, R., Gelles, J., and Block, S. M. (1997) Stretching DNA with optical tweezers, Biophys. J. 72, 1335-1346.
-
(1997)
Biophys. J
, vol.72
, pp. 1335-1346
-
-
Wang, M.D.1
Yin, H.2
Landick, R.3
Gelles, J.4
Block, S.M.5
-
47
-
-
0036009140
-
Thermodynamics of DNA interactions from single molecule stretching experiments
-
Williams, M. C., Rouzina, I., and Bloomfield, V. A. (2002) Thermodynamics of DNA interactions from single molecule stretching experiments, Acc. Chem. Res. 35, 159-166.
-
(2002)
Acc. Chem. Res
, vol.35
, pp. 159-166
-
-
Williams, M.C.1
Rouzina, I.2
Bloomfield, V.A.3
-
48
-
-
0030024985
-
Overstretching BDNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith, S. B., Cui, Y. J., and Bustamante, C. (1996) Overstretching BDNA: the elastic response of individual double-stranded and single-stranded DNA molecules, Science 271, 795-799.
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.J.2
Bustamante, C.3
|