-
1
-
-
0025981359
-
Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG
-
Shibutani, S., Takeshita, M. and Grollman, A.P. (1991) Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature, 349, 431-434.
-
(1991)
Nature
, vol.349
, pp. 431-434
-
-
Shibutani, S.1
Takeshita, M.2
Grollman, A.P.3
-
2
-
-
4544273926
-
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase
-
Hsu, G.W., Ober, M., Carell, T. and Beese, L.S. (2004) Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature, 431, 217-221.
-
(2004)
Nature
, vol.431
, pp. 217-221
-
-
Hsu, G.W.1
Ober, M.2
Carell, T.3
Beese, L.S.4
-
3
-
-
34250900982
-
Base-excision repair of oxidative DNA damage
-
David, S.S., O'Shea, V.L. and Kundu, S. (2007) Base-excision repair of oxidative DNA damage. Nature, 447, 941-950.
-
(2007)
Nature
, vol.447
, pp. 941-950
-
-
David, S.S.1
O'Shea, V.L.2
Kundu, S.3
-
4
-
-
84870683808
-
Recent advances in the structural mechanisms of DNA glycosylases
-
Brooks, S.C., Adhikary, S., Rubinson, E.H. and Eichman, B.F. (2013) Recent advances in the structural mechanisms of DNA glycosylases. Biochim. Biophys. Acta, 1834, 247-271.
-
(2013)
Biochim. Biophys. Acta
, vol.1834
, pp. 247-271
-
-
Brooks, S.C.1
Adhikary, S.2
Rubinson, E.H.3
Eichman, B.F.4
-
5
-
-
77953654163
-
Detection of damaged DNA bases by DNA glycosylase enzymes
-
Friedman, J.I. and Stivers, J.T. (2010) Detection of damaged DNA bases by DNA glycosylase enzymes. Biochemistry, 49, 4957-4967.
-
(2010)
Biochemistry
, vol.49
, pp. 4957-4967
-
-
Friedman, J.I.1
Stivers, J.T.2
-
6
-
-
38849207616
-
Extrahelical damaged base recognition by DNA glycosylase enzymes
-
Stivers, J.T. (2008) Extrahelical damaged base recognition by DNA glycosylase enzymes. Chemistry, 14, 786-793.
-
(2008)
Chemistry
, vol.14
, pp. 786-793
-
-
Stivers, J.T.1
-
7
-
-
0034387984
-
One- and three-dimensional pathways for proteins to reach specific DNA sites
-
Stanford, N.P., Szczelkun, M.D., Marko, J.F. and Halford, S.E. (2000) One- and three-dimensional pathways for proteins to reach specific DNA sites. EMBO J., 19, 6546-6557.
-
(2000)
EMBO J.
, vol.19
, pp. 6546-6557
-
-
Stanford, N.P.1
Szczelkun, M.D.2
Marko, J.F.3
Halford, S.E.4
-
8
-
-
79957549084
-
Dancing on DNA: Kinetic aspects of search processes on DNA
-
Tafvizi, A., Mirny, L.A. and van Oijen, A.M. (2011) Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem, 12, 1481-1489.
-
(2011)
Chemphyschem
, vol.12
, pp. 1481-1489
-
-
Tafvizi, A.1
Mirny, L.A.2
Van Oijen, A.M.3
-
9
-
-
0019867850
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: Kinetic measurements and conclusions
-
Winter, R.B., Berg, O.G. and Hippel, P.H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry, 20, 6961-6977.
-
(1981)
Biochemistry
, vol.20
, pp. 6961-6977
-
-
Winter, R.B.1
Berg, O.G.2
Hippel, P.H.3
-
10
-
-
0019887628
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
-
Berg, O.G., Winter, R.B. and Hippel, P.H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry, 20, 6929-6948.
-
(1981)
Biochemistry
, vol.20
, pp. 6929-6948
-
-
Berg, O.G.1
Winter, R.B.2
Hippel, P.H.3
-
11
-
-
0019816896
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli lac repressor-operator interaction: Equilibrium measurements
-
Winter, R.B. and Hippel, P.H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli lac repressor-operator interaction: equilibrium measurements. Biochemistry, 20, 6948-6960.
-
(1981)
Biochemistry
, vol.20
, pp. 6948-6960
-
-
Winter, R.B.1
Hippel, P.H.2
-
12
-
-
27644460480
-
Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA
-
Gowers, D.M., Wilson, G.G. and Halford, S.E. (2005) Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl. Acad. Sci. U.S.A., 102, 15883-15888.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 15883-15888
-
-
Gowers, D.M.1
Wilson, G.G.2
Halford, S.E.3
-
13
-
-
3042579602
-
How do site-specific DNA-binding proteins find their targets?
-
Halford, S.E. and Marko, J.F. (2004) How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res., 32, 3040-3052.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3040-3052
-
-
Halford, S.E.1
Marko, J.F.2
-
14
-
-
49449107340
-
Visualizing one-dimensional diffusion of proteins along DNA
-
Gorman, J. and Greene, E.C. (2008) Visualizing one-dimensional diffusion of proteins along DNA. Nat. Struct. Mol. Biol., 15, 768-774.
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 768-774
-
-
Gorman, J.1
Greene, E.C.2
-
15
-
-
84890531231
-
Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging
-
Gahlmann, A. and Moerner, W.E. (2014) Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging. Nat. Rev. Microbiol., 12, 9-22.
-
(2014)
Nat. Rev. Microbiol.
, vol.12
, pp. 9-22
-
-
Gahlmann, A.1
Moerner, W.E.2
-
16
-
-
80053206516
-
Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA
-
Dunn, A.R., Kad, N.M., Nelson, S.R., Warshaw, D.M. and Wallace, S.S. (2011) Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA. Nucleic Acids Res., 39, 7487-7498.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 7487-7498
-
-
Dunn, A.R.1
Kad, N.M.2
Nelson, S.R.3
Warshaw, D.M.4
Wallace, S.S.5
-
17
-
-
84856117713
-
Timing facilitated site transfer of an enzyme on DNA
-
Schonhoft, J.D. and Stivers, J.T. (2012) Timing facilitated site transfer of an enzyme on DNA. Nat. Chem. Biol., 8, 205-210.
-
(2012)
Nat. Chem. Biol.
, vol.8
, pp. 205-210
-
-
Schonhoft, J.D.1
Stivers, J.T.2
-
18
-
-
49449088997
-
Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils
-
Porecha, R.H. and Stivers, J.T. (2008) Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils. Proc. Natl. Acad. Sci. U.S.A., 105, 10791-10796.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 10791-10796
-
-
Porecha, R.H.1
Stivers, J.T.2
-
19
-
-
0141790433
-
Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2
-
Leipold, M.D., Workman, H., Muller, J.G., Burrows, C.J. and David, S.S. (2003) Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2. Biochemistry, 42, 11373-11381.
-
(2003)
Biochemistry
, vol.42
, pp. 11373-11381
-
-
Leipold, M.D.1
Workman, H.2
Muller, J.G.3
Burrows, C.J.4
David, S.S.5
-
20
-
-
40849135868
-
Potent inhibition of human apurinic/apyrimidinic endonuclease 1 by arylstibonic acids
-
Seiple, L.A., Cardellina, J.H., Akee, R. and Stivers, J.T. (2008) Potent inhibition of human apurinic/apyrimidinic endonuclease 1 by arylstibonic acids. Mol. Pharmacol., 73, 669-677.
-
(2008)
Mol. Pharmacol.
, vol.73
, pp. 669-677
-
-
Seiple, L.A.1
Cardellina, J.H.2
Akee, R.3
Stivers, J.T.4
-
21
-
-
0022381905
-
Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis
-
Terry, B.J., Jack, W.E. and Modrich, P. (1985) Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis. J. Biol. Chem., 260, 13130-13137.
-
(1985)
J. Biol. Chem.
, vol.260
, pp. 13130-13137
-
-
Terry, B.J.1
Jack, W.E.2
Modrich, P.3
-
22
-
-
34247862129
-
Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations
-
Radom, C.T., Banerjee, A. and Verdine, G.L. (2007) Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations. J. Biol. Chem., 282, 9182-9194.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 9182-9194
-
-
Radom, C.T.1
Banerjee, A.2
Verdine, G.L.3
-
23
-
-
84876279199
-
DNA translocation by human uracil DNA glycosylase: Role of DNA phosphate charge
-
Schonhoft, J.D., Kosowicz, J.G. and Stivers, J.T. (2013) DNA translocation by human uracil DNA glycosylase: role of DNA phosphate charge. Biochemistry, 52, 2526-2535.
-
(2013)
Biochemistry
, vol.52
, pp. 2526-2535
-
-
Schonhoft, J.D.1
Kosowicz, J.G.2
Stivers, J.T.3
-
24
-
-
84876234449
-
DNA translocation by human uracil DNA glycosylase: The case of single-stranded DNA and clustered uracils
-
Schonhoft, J.D. and Stivers, J.T. (2013) DNA translocation by human uracil DNA glycosylase: the case of single-stranded DNA and clustered uracils. Biochemistry, 52, 2536-2544.
-
(2013)
Biochemistry
, vol.52
, pp. 2536-2544
-
-
Schonhoft, J.D.1
Stivers, J.T.2
-
25
-
-
0034708226
-
Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
-
Bruner, S.D., Norman, D.P. and Verdine, G.L. (2000) Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature, 403, 859-866.
-
(2000)
Nature
, vol.403
, pp. 859-866
-
-
Bruner, S.D.1
Norman, D.P.2
Verdine, G.L.3
-
26
-
-
15844379169
-
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
-
Banerjee, A., Yang, W., Karplus, M. and Verdine, G.L. (2005) Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature, 434, 612-618.
-
(2005)
Nature
, vol.434
, pp. 612-618
-
-
Banerjee, A.1
Yang, W.2
Karplus, M.3
Verdine, G.L.4
-
27
-
-
77951113170
-
Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein
-
Hedglin, M. and O'Brien, P.J. (2010) Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein. ACS Chem. Biol., 5, 427-436.
-
(2010)
ACS Chem. Biol.
, vol.5
, pp. 427-436
-
-
Hedglin, M.1
O'Brien, P.J.2
-
28
-
-
50149091510
-
Correlated cleavage of damaged DNA by bacterial and human 8-oxoguanine-DNA glycosylases
-
Sidorenko, V.S. and Zharkov, D.O. (2008) Correlated cleavage of damaged DNA by bacterial and human 8-oxoguanine-DNA glycosylases. Biochemistry, 47, 8970-8976.
-
(2008)
Biochemistry
, vol.47
, pp. 8970-8976
-
-
Sidorenko, V.S.1
Zharkov, D.O.2
-
29
-
-
79952494759
-
Protein sliding and hopping kinetics on DNA
-
DeSantis, M.C., Li, J.-L. and Wang, Y.M. (2011) Protein sliding and hopping kinetics on DNA. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 83, 021907.
-
(2011)
Phys. Rev. E Stat. Nonlin. Soft Matter Phys.
, vol.83
, pp. 021907
-
-
Desantis, M.C.1
Li, J.-L.2
Wang, Y.M.3
-
30
-
-
47249153641
-
Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA
-
Bonnet, I., Biebricher, A., Porte, P.L., Loverdo, C., Benichou, O., Voituriez, R., Escude, C., Wende, W., Pingoud, A. and Desbiolles, P. (2008) Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res., 36, 4118-4127.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 4118-4127
-
-
Bonnet, I.1
Biebricher, A.2
Porte, P.L.3
Loverdo, C.4
Benichou, O.5
Voituriez, R.6
Escude, C.7
Wende, W.8
Pingoud, A.9
Desbiolles, P.10
-
31
-
-
55249097156
-
Human alkyladenine DNA glycosylase employs a processive search for DNA damage
-
Hedglin, M. and O'Brien, P.J. (2008) Human alkyladenine DNA glycosylase employs a processive search for DNA damage. Biochemistry, 47, 11434-11445.
-
(2008)
Biochemistry
, vol.47
, pp. 11434-11445
-
-
Hedglin, M.1
O'Brien, P.J.2
-
32
-
-
33645807371
-
A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
-
Blainey, P.C., van Oijen, A.M., Banerjee, A., Verdine, G.L. and Xie, X.S. (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. U.S.A., 103, 5752-5757.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 5752-5757
-
-
Blainey, P.C.1
Van Oijen, A.M.2
Banerjee, A.3
Verdine, G.L.4
Xie, X.S.5
-
33
-
-
22444442634
-
Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylase
-
Kuznetsov, N.A., Koval, V.V., Zharkov, D.O., Nevinsky, G.A., Douglas, K.T. and Fedorova, O.S. (2005) Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylase. Nucleic Acids Res., 33, 3919-3931.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 3919-3931
-
-
Kuznetsov, N.A.1
Koval, V.V.2
Zharkov, D.O.3
Nevinsky, G.A.4
Douglas, K.T.5
Fedorova, O.S.6
-
34
-
-
33847718732
-
Kinetic conformational analysis of human 8-oxoguanine-DNA glycosylase
-
Kuznetsov, N.A., Koval, V.V., Nevinsky, G.A., Douglas, K.T., Zharkov, D.O. and Fedorova, O.S. (2007) Kinetic conformational analysis of human 8-oxoguanine-DNA glycosylase. J. Biol. Chem., 282, 1029-1038.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 1029-1038
-
-
Kuznetsov, N.A.1
Koval, V.V.2
Nevinsky, G.A.3
Douglas, K.T.4
Zharkov, D.O.5
Fedorova, O.S.6
-
35
-
-
71449094444
-
Nonspecifically bound proteins spin while diffusing along DNA
-
Blainey, P.C., Luo, G., Kou, S.C., Mangel, W.F., Verdine, G.L., Bagchi, B. and Xie, X.S. (2009) Nonspecifically bound proteins spin while diffusing along DNA. Nat. Struct. Mol. Biol., 16, 1224-1229.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1224-1229
-
-
Blainey, P.C.1
Luo, G.2
Kou, S.C.3
Mangel, W.F.4
Verdine, G.L.5
Bagchi, B.6
Xie, X.S.7
-
36
-
-
84856100220
-
Single-molecule imaging of LacI diffusing along nonspecific DNA
-
Williams, MC and Maher, JL (eds). Springer, New York
-
Wang, Y.M. and Austin, R.H. (2011) Single-molecule imaging of LacI diffusing along nonspecific DNA. In: Williams, MC and Maher, JL (eds). In Biophysics of DNA-Protein Interactions From Single Molecules to Biological Systems. Springer, New York. pp. 9-37.
-
(2011)
Biophysics of DNA-Protein Interactions from Single Molecules to Biological Systems
, pp. 9-37
-
-
Wang, Y.M.1
Austin, R.H.2
-
37
-
-
0024531901
-
Facilitated target location in biological systems
-
Hippel, P.H. and Berg, O.G. (1989) Facilitated target location in biological systems. J. Biol. Chem., 264, 675-678.
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 675-678
-
-
Hippel, P.H.1
Berg, O.G.2
-
38
-
-
0035098395
-
Rates of base excision repair are not solely dependent on levels of initiating enzymes
-
Cappelli, E. (2001) Rates of base excision repair are not solely dependent on levels of initiating enzymes. Carcinogenesis, 22, 387-393.
-
(2001)
Carcinogenesis
, vol.22
, pp. 387-393
-
-
Cappelli, E.1
-
39
-
-
65249099497
-
Fundamental aspects of protein-protein association kinetics
-
Schreiber, G., Haran, G. and Zhou, H.X. (2009) Fundamental aspects of protein-protein association kinetics. Chem. Rev., 109, 839-860.
-
(2009)
Chem. Rev.
, vol.109
, pp. 839-860
-
-
Schreiber, G.1
Haran, G.2
Zhou, H.X.3
-
40
-
-
41049090929
-
Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
-
Zhou, H.X., Rivas, G. and Minton, A.P. (2008) Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu. Rev. Biophys., 37, 375-397.
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 375-397
-
-
Zhou, H.X.1
Rivas, G.2
Minton, A.P.3
-
41
-
-
0036009327
-
Direct visualization of a DNA glycosylase searching for damage
-
Chen, L., Haushalter, K.A., Lieber, C.M. and Verdine, G.L. (2002) Direct visualization of a DNA glycosylase searching for damage. Chem. Biol., 9, 345-350.
-
(2002)
Chem. Biol.
, vol.9
, pp. 345-350
-
-
Chen, L.1
Haushalter, K.A.2
Lieber, C.M.3
Verdine, G.L.4
-
42
-
-
33847057368
-
Interactions of human 8-oxoguanine-DNA glycosylase with singleand double-stranded DNA
-
Kirpota, O.O., Zharkov, D.O., Buneva, V.N. and Nevinskii, G.A. (2006) [Interactions of human 8-oxoguanine-DNA glycosylase with singleand double-stranded DNA]. Mol. Biol. (Mosk.), 40, 1055-1063.
-
(2006)
Mol. Biol. (Mosk.)
, vol.40
, pp. 1055-1063
-
-
Kirpota, O.O.1
Zharkov, D.O.2
Buneva, V.N.3
Nevinskii, G.A.4
|