-
1
-
-
84923948943
-
Heterogeneous polymerase fdelity and mismatch repair bias genome variation and composition
-
Lujan, S.A., Clausen, A.R., Clark, A.B., MacAlpine, H.K., MacAlpine, D.M., Malc, E.P., Mieczkowski, P.A., Burkholder, A.B., Fargo, D.C., Gordenin, D.A. et al. (2014) Heterogeneous polymerase fdelity and mismatch repair bias genome variation and composition. Genome Res., 24, 1751-1764.
-
(2014)
Genome Res.
, vol.24
, pp. 1751-1764
-
-
Lujan, S.A.1
Clausen, A.R.2
Clark, A.B.3
MacAlpine, H.K.4
MacAlpine, D.M.5
Malc, E.P.6
Mieczkowski, P.A.7
Burkholder, A.B.8
Fargo, D.C.9
Gordenin, D.A.10
-
2
-
-
84925497848
-
Hypermutation in human cancer genomes: Footprints and mechanisms
-
Roberts, S.A. and Gordenin, D.A. (2014) Hypermutation in human cancer genomes: footprints and mechanisms. Nat. Rev. Cancer, 14, 786-800.
-
(2014)
Nat. Rev. Cancer
, vol.14
, pp. 786-800
-
-
Roberts, S.A.1
Gordenin, D.A.2
-
3
-
-
84906303775
-
Mechanisms underlying mutational signatures in human cancers
-
Helleday, T., Eshtad, S. and Nik-Zainal, S. (2014) Mechanisms underlying mutational signatures in human cancers. Nat. Rev. Genet., 15, 585-598.
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 585-598
-
-
Helleday, T.1
Eshtad, S.2
Nik-Zainal, S.3
-
4
-
-
84895784747
-
Mechanisms of base substitution mutagenesis in cancer genomes
-
Bacolla, A., Cooper, D.N. and Vasquez, K.M. (2014) Mechanisms of base substitution mutagenesis in cancer genomes. Genes, 5, 108-146.
-
(2014)
Genes
, vol.5
, pp. 108-146
-
-
Bacolla, A.1
Cooper, D.N.2
Vasquez, K.M.3
-
5
-
-
84872287592
-
Regulation of AID, the B-cell genome mutator
-
Keim, C., Kazadi, D., Rothschild, G. and Basu, U. (2013) Regulation of AID, the B-cell genome mutator. Genes Dev., 27, 1-17.
-
(2013)
Genes Dev.
, vol.27
, pp. 1-17
-
-
Keim, C.1
Kazadi, D.2
Rothschild, G.3
Basu, U.4
-
6
-
-
77952102476
-
Determinants of sequence-specifcity within human AID and APOBEC3G
-
Carpenter, M.A., Rajagurubandara, E., Wijesinghe, P. and Bhagwat, A.S. (2010) Determinants of sequence-specifcity within human AID and APOBEC3G. DNA Repair, 9, 579-587.
-
(2010)
DNA Repair
, vol.9
, pp. 579-587
-
-
Carpenter, M.A.1
Rajagurubandara, E.2
Wijesinghe, P.3
Bhagwat, A.S.4
-
7
-
-
84883432724
-
An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers
-
Roberts, S.A., Lawrence, M.S., Klimczak, L.J., Grimm, S.A., Fargo, D., Stojanov, P., Kiezun, A., Kryukov, G.V., Carter, S.L., Saksena, G. et al. (2013) An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat. Genet., 45, 970-976.
-
(2013)
Nat. Genet.
, vol.45
, pp. 970-976
-
-
Roberts, S.A.1
Lawrence, M.S.2
Klimczak, L.J.3
Grimm, S.A.4
Fargo, D.5
Stojanov, P.6
Kiezun, A.7
Kryukov, G.V.8
Carter, S.L.9
Saksena, G.10
-
8
-
-
84255176375
-
UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin cancer
-
Pfeifer, G.P. and Besaratinia, A. (2012) UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin cancer. Photochem. Photobiol. Sci., 11, 90-97.
-
(2012)
Photochem. Photobiol. Sci.
, vol.11
, pp. 90-97
-
-
Pfeifer, G.P.1
Besaratinia, A.2
-
9
-
-
84884688770
-
Guanine holes are prominent targets for mutation in cancer and inherited disease
-
Bacolla, A., Temiz, N.A., Yi, M., Ivanic, J., Cer, R.Z., Donohue, D.E., Ball, E.V., Mudunuri, U.S., Wang, G., Jain, A. et al. (2013) Guanine holes are prominent targets for mutation in cancer and inherited disease. PLoS Genet., 9, e1003816.
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003816
-
-
Bacolla, A.1
Temiz, N.A.2
Yi, M.3
Ivanic, J.4
Cer, R.Z.5
Donohue, D.E.6
Ball, E.V.7
Mudunuri, U.S.8
Wang, G.9
Jain, A.10
-
10
-
-
84882837534
-
Signatures of mutational processes in human cancer
-
Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Aparicio, S.A., Behjati, S., Biankin, A.V., Bignell, G.R., Bolli, N., Borg, A., Borresen-Dale, A.L. et al. (2013) Signatures of mutational processes in human cancer. Nature, 500, 415-421.
-
(2013)
Nature
, vol.500
, pp. 415-421
-
-
Alexandrov, L.B.1
Nik-Zainal, S.2
Wedge, D.C.3
Aparicio, S.A.4
Behjati, S.5
Biankin, A.V.6
Bignell, G.R.7
Bolli, N.8
Borg, A.9
Borresen-Dale, A.L.10
-
11
-
-
84876523427
-
The origin, evolution, and functional impact of short insertion-deletion variants identifed in 179 human genomes
-
Montgomery, S.B., Goode, D.L., Kvikstad, E., Albers, C.A., Zhang, Z.D., Mu, X.J., Ananda, G., Howie, B., Karczewski, K.J., Smith, K.S. et al. (2013) The origin, evolution, and functional impact of short insertion-deletion variants identifed in 179 human genomes. Genome Res., 23, 749-761.
-
(2013)
Genome Res.
, vol.23
, pp. 749-761
-
-
Montgomery, S.B.1
Goode, D.L.2
Kvikstad, E.3
Albers, C.A.4
Zhang, Z.D.5
Mu, X.J.6
Ananda, G.7
Howie, B.8
Karczewski, K.J.9
Smith, K.S.10
-
12
-
-
84876512111
-
Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome
-
Ananda, G., Walsh, E., Jacob, K.D., Krasilnikova, M., Eckert, K.A., Chiaromonte, F. and Makova, K.D. (2013) Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome. Genome Biol. Evol., 5, 606-620.
-
(2013)
Genome Biol. Evol.
, vol.5
, pp. 606-620
-
-
Ananda, G.1
Walsh, E.2
Jacob, K.D.3
Krasilnikova, M.4
Eckert, K.A.5
Chiaromonte, F.6
Makova, K.D.7
-
13
-
-
84905457336
-
Microsatellite interruptions stabilize primate genomes and exist as population-specifc single nucleotide polymorphisms within individual human genomes
-
Ananda, G., Hile, S.E., Breski, A., Wang, Y., Kelkar, Y., Makova, K.D. and Eckert, K.A. (2014) Microsatellite interruptions stabilize primate genomes and exist as population-specifc single nucleotide polymorphisms within individual human genomes. PLoS Genet., 10, e1004498.
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004498
-
-
Ananda, G.1
Hile, S.E.2
Breski, A.3
Wang, Y.4
Kelkar, Y.5
Makova, K.D.6
Eckert, K.A.7
-
14
-
-
84873559405
-
Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements
-
Sawaya, S., Bagshaw, A., Buschiazzo, E., Kumar, P., Chowdhury, S., Black, M.A. and Gemmell, N. (2013) Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PLoS One, 8, e54710.
-
(2013)
PLoS One
, vol.8
, pp. e54710
-
-
Sawaya, S.1
Bagshaw, A.2
Buschiazzo, E.3
Kumar, P.4
Chowdhury, S.5
Black, M.A.6
Gemmell, N.7
-
15
-
-
84887924524
-
The landscape of microsatellite instability in colorectal and endometrial cancer genomes
-
Kim, T.M., Laird, P.W. and Park, P.J. (2013) The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell, 155, 858-868.
-
(2013)
Cell
, vol.155
, pp. 858-868
-
-
Kim, T.M.1
Laird, P.W.2
Park, P.J.3
-
16
-
-
84870674869
-
Controls of nucleosome positioning in the human genome
-
Gaffney, D.J., McVicker, G., Pai, A.A., Fondufe-Mittendorf, Y.N., Lewellen, N., Michelini, K., Widom, J., Gilad, Y. and Pritchard, J.K. (2012) Controls of nucleosome positioning in the human genome. PLoS Genet., 8, e1003036.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1003036
-
-
Gaffney, D.J.1
McVicker, G.2
Pai, A.A.3
Fondufe-Mittendorf, Y.N.4
Lewellen, N.5
Michelini, K.6
Widom, J.7
Gilad, Y.8
Pritchard, J.K.9
-
17
-
-
84870013758
-
Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy
-
Zhu, X. and Schatz, G.C. (2012) Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy. J. Phys. Chem. B, 116, 13672-13681.
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 13672-13681
-
-
Zhu, X.1
Schatz, G.C.2
-
18
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A. and Schulten, K. (1996) VMD: visual molecular dynamics. J. Mol. Graph. Model., 14, 33-38.
-
(1996)
J. Mol. Graph. Model.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
19
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K. and Schulten, K. (1999) NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys., 151, 283-312.
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
20
-
-
36449003554
-
Constant-pressure molecular-dynamics algorithms
-
Martyna, G.J., Tobias, D.J. and Klein, M.L. (1994) Constant-pressure molecular-dynamics algorithms. J. Chem. Phys., 101, 4177-4189.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
21
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel, A. and Levitt, M. (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol., 103, 227-249.
-
(1976)
J. Mol. Biol.
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
22
-
-
33646205963
-
An effcient real space multigrid QM/MM electrostatic coupling
-
Laino, T., Mohamed, F., Laio, A. and Parrinello, M. (2005) An effcient real space multigrid QM/MM electrostatic coupling. J. Chem. Theory Comput., 1, 1176-1184.
-
(2005)
J. Chem. Theory Comput.
, vol.1
, pp. 1176-1184
-
-
Laino, T.1
Mohamed, F.2
Laio, A.3
Parrinello, M.4
-
23
-
-
0042113153
-
Self-consistent equations including exchange and correlation effects
-
Kohn, W. and Sham, L.J. (1965) Self-consistent equations including exchange and correlation effects. Phys. Rev., 140, A1133-A1138.
-
(1965)
Phys. Rev.
, vol.140
, pp. A1133-A1138
-
-
Kohn, W.1
Sham, L.J.2
-
24
-
-
15344345714
-
Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
-
VandeVondele, J., Krack, M., Mohamed, F., Parrinello, M., Chassaing, T. and Hutter, J. (2005) Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. Comput. Phys. Commun., 167, 103-128.
-
(2005)
Comput. Phys. Commun.
, vol.167
, pp. 103-128
-
-
Vandevondele, J.1
Krack, M.2
Mohamed, F.3
Parrinello, M.4
Chassaing, T.5
Hutter, J.6
-
25
-
-
0000160164
-
Separable dual-space Gaussian pseudopotentials
-
Goedecker, S., Teter, M. and Hutter, J. (1996) Separable dual-space Gaussian pseudopotentials. Phys. Rev. B, 54, 1703-1710.
-
(1996)
Phys. Rev. B
, vol.54
, pp. 1703-1710
-
-
Goedecker, S.1
Teter, M.2
Hutter, J.3
-
26
-
-
4243943295
-
Generalized gradient approximation made simple
-
Perdew, J.P., Burke, K. and Ernzerhof, M. (1996) Generalized gradient approximation made simple. Phys. Rev. Lett., 77, 3865-3868.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 3865-3868
-
-
Perdew, J.P.1
Burke, K.2
Ernzerhof, M.3
-
27
-
-
26444474547
-
Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties
-
Woon, D.E. and Dunning, T.H. (1994) Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties. J. Chem. Phys., 100, 2975-2988.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 2975-2988
-
-
Woon, D.E.1
Dunning, T.H.2
-
28
-
-
36449004033
-
Electrostatic decoupling of periodic images of plane-wave-expanded densities and derived atomic point charges
-
Blöchl, P.E. (1995) Electrostatic decoupling of periodic images of plane-wave-expanded densities and derived atomic point charges. J. Chem. Phys., 103, 7422-7428.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 7422-7428
-
-
Blöchl, P.E.1
-
29
-
-
79953313618
-
Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome
-
Siddle, K.J., Goodship, J.A., Keavney, B. and Santibanez-Koref, M.F. (2011) Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome. Bioinformatics, 27, 895-898.
-
(2011)
Bioinformatics
, vol.27
, pp. 895-898
-
-
Siddle, K.J.1
Goodship, J.A.2
Keavney, B.3
Santibanez-Koref, M.F.4
-
30
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
Abecasis, G.R., Auton, A., Brooks, L.D., DePristo, M.A., Durbin, R.M., Handsaker, R.E., Kang, H.M., Marth, G.T. and McVean, G.A. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Abecasis, G.R.1
Auton, A.2
Brooks, L.D.3
Depristo, M.A.4
Durbin, R.M.5
Handsaker, R.E.6
Kang, H.M.7
Marth, G.T.8
McVean, G.A.9
-
31
-
-
77952136530
-
A draft sequence of the Neandertal genome
-
Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.H. et al. (2010) A draft sequence of the Neandertal genome. Science, 328, 710-722.
-
(2010)
Science
, vol.328
, pp. 710-722
-
-
Green, R.E.1
Krause, J.2
Briggs, A.W.3
Maricic, T.4
Stenzel, U.5
Kircher, M.6
Patterson, N.7
Li, H.8
Zhai, W.9
Fritz, M.H.10
-
32
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein, M.B., Kundaje, A., Hariharan, M., Landt, S.G., Yan, K.K., Cheng, C., Mu, X.J., Khurana, E., Rozowsky, J., Alexander, R. et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91-100.
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
Kundaje, A.2
Hariharan, M.3
Landt, S.G.4
Yan, K.K.5
Cheng, C.6
Mu, X.J.7
Khurana, E.8
Rozowsky, J.9
Alexander, R.10
-
33
-
-
84876529535
-
Factorbook.org: A Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
-
Wang, J., Zhuang, J., Iyer, S., Lin, X.Y., Greven, M.C., Kim, B.H., Moore, J., Pierce, B.G., Dong, X., Virgil, D. et al. (2013) Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res., 41, D171-D176.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D171-D176
-
-
Wang, J.1
Zhuang, J.2
Iyer, S.3
Lin, X.Y.4
Greven, M.C.5
Kim, B.H.6
Moore, J.7
Pierce, B.G.8
Dong, X.9
Virgil, D.10
-
34
-
-
84877247843
-
Human polymerase kappa uses a template-slippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions
-
Mukherjee, P., Lahiri, I. and Pata, J.D. (2013) Human polymerase kappa uses a template-slippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions. Nucleic Acids Res., 41, 5024-5035.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 5024-5035
-
-
Mukherjee, P.1
Lahiri, I.2
Pata, J.D.3
-
35
-
-
77954171862
-
The nucleotide composition of microsatellites impacts both replication fdelity and mismatch repair in human colorectal cells
-
Campregher, C., Scharl, T., Nemeth, M., Honeder, C., Jascur, T., Boland, C.R. and Gasche, C. (2010) The nucleotide composition of microsatellites impacts both replication fdelity and mismatch repair in human colorectal cells. Hum. Mol. Genet., 19, 2648-2657.
-
(2010)
Hum. Mol. Genet.
, vol.19
, pp. 2648-2657
-
-
Campregher, C.1
Scharl, T.2
Nemeth, M.3
Honeder, C.4
Jascur, T.5
Boland, C.R.6
Gasche, C.7
-
36
-
-
3042782819
-
Microsatellites: Simple sequences with complex evolution
-
Ellegren, H. (2004) Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet., 5, 435-445.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 435-445
-
-
Ellegren, H.1
-
37
-
-
67649710352
-
The unique structure of A-tracts and intrinsic DNA bending
-
Haran, T.E. and Mohanty, U. (2009) The unique structure of A-tracts and intrinsic DNA bending. Q. Rev. Biophys., 42, 41-81.
-
(2009)
Q. Rev. Biophys.
, vol.42
, pp. 41-81
-
-
Haran, T.E.1
Mohanty, U.2
-
38
-
-
0035997345
-
Long-distance electron transfer through DNA
-
Giese, B. (2002) Long-distance electron transfer through DNA. Annu. Rev. Biochem., 71, 51-70.
-
(2002)
Annu. Rev. Biochem.
, vol.71
, pp. 51-70
-
-
Giese, B.1
-
39
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond, T.J. and Davey, C.A. (2003) The structure of DNA in the nucleosome core. Nature, 423, 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
40
-
-
60349115060
-
Poly(dA:dT) tracts: Major determinants of nucleosome organization
-
Segal, E. and Widom, J. (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr. Opin. Struct. Biol., 19, 65-71.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 65-71
-
-
Segal, E.1
Widom, J.2
-
41
-
-
84864487717
-
The mechanics behind DNA sequence-dependent properties of the nucleosome
-
Chua, E.Y., Vasudevan, D., Davey, G.E., Wu, B. and Davey, C.A. (2012) The mechanics behind DNA sequence-dependent properties of the nucleosome. Nucleic Acids Res., 40, 6338-6352.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 6338-6352
-
-
Chua, E.Y.1
Vasudevan, D.2
Davey, G.E.3
Wu, B.4
Davey, C.A.5
-
42
-
-
84901680089
-
Whole-genome sequencing and comprehensive molecular profling identify new driver mutations in gastric cancer
-
Wang, K., Yuen, S.T., Xu, J., Lee, S.P., Yan, H.H., Shi, S.T., Siu, H.C., Deng, S., Chu, K.M., Law, S. et al. (2014) Whole-genome sequencing and comprehensive molecular profling identify new driver mutations in gastric cancer. Nat. Genet., 46, 573-582.
-
(2014)
Nat. Genet.
, vol.46
, pp. 573-582
-
-
Wang, K.1
Yuen, S.T.2
Xu, J.3
Lee, S.P.4
Yan, H.H.5
Shi, S.T.6
Siu, H.C.7
Deng, S.8
Chu, K.M.9
Law, S.10
-
43
-
-
0034257989
-
Infuence of molecular fexibility on DNA radiosensitivity: A simulation study
-
Viduna, D., Hinsen, K. and Kneller, G. (2000) Infuence of molecular fexibility on DNA radiosensitivity: a simulation study. Phys. Rev. E, 62, 3986-3990.
-
(2000)
Phys. Rev. e
, vol.62
, pp. 3986-3990
-
-
Viduna, D.1
Hinsen, K.2
Kneller, G.3
-
44
-
-
84868144458
-
Probing sequence-specifc DNA fexibility in A-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations
-
Nikolova, E.N., Bascom, G.D., Andricioaei, I. and Al-Hashimi, H.M. (2012) Probing sequence-specifc DNA fexibility in A-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. Biochemistry, 51, 8654-8664.
-
(2012)
Biochemistry
, vol.51
, pp. 8654-8664
-
-
Nikolova, E.N.1
Bascom, G.D.2
Andricioaei, I.3
Al-Hashimi, H.M.4
-
45
-
-
84895808218
-
Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment
-
Brenlla, A., Markiewicz, R.P., Rueda, D. and Romano, L.J. (2014) Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment. Nucleic Acids Res., 42, 2555-2563.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 2555-2563
-
-
Brenlla, A.1
Markiewicz, R.P.2
Rueda, D.3
Romano, L.J.4
-
46
-
-
0035812849
-
Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication
-
Ling, H., Boudsocq, F., Woodgate, R. and Yang, W. (2001) Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell, 107, 91-102.
-
(2001)
Cell
, vol.107
, pp. 91-102
-
-
Ling, H.1
Boudsocq, F.2
Woodgate, R.3
Yang, W.4
-
47
-
-
58149085464
-
DNA sequence context as a determinant of the quantity and chemistry of guanine oxidation produced by hydroxyl radicals and one-electron oxidants
-
Margolin, Y., Shafrovich, V., Geacintov, N.E., DeMott, M.S. and Dedon, P.C. (2008) DNA sequence context as a determinant of the quantity and chemistry of guanine oxidation produced by hydroxyl radicals and one-electron oxidants. J. Biol. Chem., 283, 35569-35578.
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 35569-35578
-
-
Margolin, Y.1
Shafrovich, V.2
Geacintov, N.E.3
Demott, M.S.4
Dedon, P.C.5
-
48
-
-
84863686709
-
8-Oxo-2'-deoxyguanosine as a biomarker of tobacco-smoking-induced oxidative stress
-
Mesaros, C, Arora, J.S., Wholer, A., Vachani, A. and Blair, I.A. (2012) 8-Oxo-2'-deoxyguanosine as a biomarker of tobacco-smoking-induced oxidative stress. Free Radic. Biol. Med, 53, 610-617.
-
(2012)
Free Radic. Biol. Med
, vol.53
, pp. 610-617
-
-
Mesaros, C.1
Arora, J.S.2
Wholer, A.3
Vachani, A.4
Blair, I.A.5
-
49
-
-
67649949088
-
Analysis of 7, 8-dihydro-8-oxo-2'-deoxyguanosine in cellular DNA during oxidative stress
-
Mangal, D., Vudathala, D., Park, J.H., Lee, S.H., Penning, T.M. and Blair, I.A. (2009) Analysis of 7, 8-dihydro-8-oxo-2'-deoxyguanosine in cellular DNA during oxidative stress. Chem. Res. Toxicol., 22, 788-797.
-
(2009)
Chem. Res. Toxicol.
, vol.22
, pp. 788-797
-
-
Mangal, D.1
Vudathala, D.2
Park, J.H.3
Lee, S.H.4
Penning, T.M.5
Blair, I.A.6
-
50
-
-
84858136442
-
Chemical and biological consequences of oxidatively damaged guanine in DNA
-
Delaney, S., Jarem, D.A., Volle, C.B. and Yennie, C.J. (2012) Chemical and biological consequences of oxidatively damaged guanine in DNA. Free Radic. Res., 46, 420-441.
-
(2012)
Free Radic. Res.
, vol.46
, pp. 420-441
-
-
Delaney, S.1
Jarem, D.A.2
Volle, C.B.3
Yennie, C.J.4
-
51
-
-
33646965265
-
Recognition and reaction of metallointercalators with DNA
-
Erkkila, K.E., Odom, DT. and Barton, J.K. (1999) Recognition and reaction of metallointercalators with DNA. Chem. Rev., 99, 2777-2796.
-
(1999)
Chem. Rev.
, vol.99
, pp. 2777-2796
-
-
Erkkila, K.E.1
Odom, D.T.2
Barton, J.K.3
-
52
-
-
77249124863
-
Oxidation of DNA: Damage to nucleobases
-
Kanvah, S., Joseph, J., Schuster, G.B., Barnett, R.N, Cleveland, C.L. and Landman, U. (2010) Oxidation of DNA: damage to nucleobases. Acc. Chem. Res., 43, 280-287.
-
(2010)
Acc. Chem. Res.
, vol.43
, pp. 280-287
-
-
Kanvah, S.1
Joseph, J.2
Schuster, G.B.3
Barnett, R.N.4
Cleveland, C.L.5
Landman, U.6
-
53
-
-
0029773892
-
Theoretical studies of GG-specifc photocleavage of DNA via electron transfer: Signifcant lowering of ionization potential and 5'-localization of HOMO of stacked GG bases in B-form DNA
-
Sugiyama, H. and Saito, I. (1996) Theoretical studies of GG-specifc photocleavage of DNA via electron transfer: signifcant lowering of ionization potential and 5'-localization of HOMO of stacked GG bases in B-form DNA. J. Am. Chem. Soc., 118, 7063-7068.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 7063-7068
-
-
Sugiyama, H.1
Saito, I.2
-
54
-
-
0032539233
-
Sequence dependent long range hole transport in DNA
-
Meggers, E., Michel-Beyerle, M.E. and Giese, B. (1998) Sequence dependent long range hole transport in DNA. J. Am. Chem. Soc., 120, 12950-12955.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 12950-12955
-
-
Meggers, E.1
Michel-Beyerle, M.E.2
Giese, B.3
-
55
-
-
0033119286
-
On the mechanism of long-range electron transfer through DNA
-
Giese, B., Wessely, S., Spormann, M., Lindemann, U., Meggers, E. and Michel-Beyerle, M.E. (1999) On the mechanism of long-range electron transfer through DNA. Angew. Chem. Int. Ed. Engl, 38, 996-998.
-
(1999)
Angew. Chem. Int. Ed. Engl
, vol.38
, pp. 996-998
-
-
Giese, B.1
Wessely, S.2
Spormann, M.3
Lindemann, U.4
Meggers, E.5
Michel-Beyerle, M.E.6
-
56
-
-
29544444893
-
Photoinduced DNA cleavage via electron transfer: Demonstration that guanine residues located 5' to guanine are the most electron-donating sites
-
Saito, I., Takayama, M., Sugiyama, H., Nakatani, K., Tsuchida, A. and Yamamoto, M. (1995) Photoinduced DNA cleavage via electron transfer: demonstration that guanine residues located 5' to guanine are the most electron-donating sites. J. Am. Chem. Soc, 117, 6406-6407.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 6406-6407
-
-
Saito, I.1
Takayama, M.2
Sugiyama, H.3
Nakatani, K.4
Tsuchida, A.5
Yamamoto, M.6
-
57
-
-
0032501424
-
Mapping of the hot spots for DNA damage by one-electron oxidation: Effcacy of GG doublets and GGG triplets as a trap in long-range hole migration
-
Saito, I., Nakamura, T., Nakatani, K., Yoshioka, Y, Yamaguchi, K. and Sugiyama, H. (1998) Mapping of the hot spots for DNA damage by one-electron oxidation: effcacy of GG doublets and GGG triplets as a trap in long-range hole migration. J. Am. Chem. Soc, 120, 12686-12687.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 12686-12687
-
-
Saito, I.1
Nakamura, T.2
Nakatani, K.3
Yoshioka, Y.4
Yamaguchi, K.5
Sugiyama, H.6
-
58
-
-
0033615295
-
Experimental and theoretical studies on the selectivity of GGG triplets toward one-electron oxidation in B-form DNA
-
Yoshioka, Y, Kitagawa, Y, Takano, Y, Yamaguchi, K., Nakamura, T. and Saito, I. (1999) Experimental and theoretical studies on the selectivity of GGG triplets toward one-electron oxidation in B-form DNA. J. Am. Chem. Soc, 121, 8712-8719.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 8712-8719
-
-
Yoshioka, Y.1
Kitagawa, Y.2
Takano, Y.3
Yamaguchi, K.4
Nakamura, T.5
Saito, I.6
-
59
-
-
0000265305
-
Energetics of hole transfer in DNA
-
Voityuk, A.A., Jortner, J., Bixon, M. and Rosch, N (2000) Energetics of hole transfer in DNA. Chem. Phys. Lett., 324, 430-434.
-
(2000)
Chem. Phys. Lett.
, vol.324
, pp. 430-434
-
-
Voityuk, A.A.1
Jortner, J.2
Bixon, M.3
Rosch, N.4
-
60
-
-
27144553173
-
Direct optimization method to study constrained systems within density-functional theory
-
Wu, Q. and Van Voorhis, T. (2005) Direct optimization method to study constrained systems within density-functional theory. Phys. Rev. A., 72, 024502.
-
(2005)
Phys. Rev. A.
, vol.72
, pp. 024502
-
-
Wu, Q.1
Van Voorhis, T.2
-
61
-
-
84883206144
-
DNA oxidative damage in mammalian spermatozoa: Where and why is the male nucleus affected?
-
Noblanc, A., Damon-Soubeyrand, C, Karrich, B., Henry-Berger, J., Cadet, R., Saez, F., Guiton, R., Janny, L., Pons-Rejraji, H, Alvarez, J.G et al. (2013) DNA oxidative damage in mammalian spermatozoa: where and why is the male nucleus affected? Free Radic. Biol. Med., 65, 719-723.
-
(2013)
Free Radic. Biol. Med.
, vol.65
, pp. 719-723
-
-
Noblanc, A.1
Damon-Soubeyrand, C.2
Karrich, B.3
Henry-Berger, J.4
Cadet, R.5
Saez, F.6
Guiton, R.7
Janny, L.8
Pons-Rejraji, H.9
Alvarez, J.G.10
-
62
-
-
84858120472
-
Sequence-dependent variation in the reactivity of 8-Oxo-7, 8-dihydro-2'-deoxyguanosine toward oxidation
-
Lim, K.S., Taghizadeh, K., Wishnok, J.S., Babu, I.R., Shafrovich, V, Geacintov, NE. and Dedon, PC. (2012) Sequence-dependent variation in the reactivity of 8-Oxo-7, 8-dihydro-2'-deoxyguanosine toward oxidation. Chem. Res. Toxicol, 25, 366-373.
-
(2012)
Chem. Res. Toxicol
, vol.25
, pp. 366-373
-
-
Lim, K.S.1
Taghizadeh, K.2
Wishnok, J.S.3
Babu, I.R.4
Shafrovich, V.5
Geacintov, N.E.6
Dedon, P.C.7
-
63
-
-
84862985327
-
Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine
-
Suzuki, M., Kino, K., Morikawa, M., Kobayashi, T., Komori, R. and Miyazawa, H. (2012) Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine. Molecules, 17, 6705-6715.
-
(2012)
Molecules
, vol.17
, pp. 6705-6715
-
-
Suzuki, M.1
Kino, K.2
Morikawa, M.3
Kobayashi, T.4
Komori, R.5
Miyazawa, H.6
-
64
-
-
79952105312
-
Coarse-grained time-dependent density functional simulation of charge transfer in complex systems: Application to hole transfer in DNA
-
Kubar, T. and Elstner, M. (2010) Coarse-grained time-dependent density functional simulation of charge transfer in complex systems: application to hole transfer in DNA. J. Phys. Chem. B, 114, 11221-11240.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 11221-11240
-
-
Kubar, T.1
Elstner, M.2
-
65
-
-
72949112529
-
Solvent effects on ionization potentials of guanine runs and chemically modifed guanine in duplex DNA: Effect of electrostatic interaction and its reduction due to solvent
-
Yokojima, S., Yoshiki, N, Yanoi, W. and Okada, A. (2009) Solvent effects on ionization potentials of guanine runs and chemically modifed guanine in duplex DNA: effect of electrostatic interaction and its reduction due to solvent. J. Phys. Chem. B, 113, 16384-16392.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 16384-16392
-
-
Yokojima, S.1
Yoshiki, N.2
Yanoi, W.3
Okada, A.4
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