메뉴 건너뛰기




Volumn 117, Issue 39, 2013, Pages 11617-11622

Effect of 8-oxoguanine on DNA structure and deformability

Author keywords

[No Author keywords available]

Indexed keywords

DEFORMATION; MOLECULAR DYNAMICS; REPAIR;

EID: 84885133326     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp407562t     Document Type: Article
Times cited : (19)

References (44)
  • 1
    • 0033520969 scopus 로고    scopus 로고
    • Quality Control by DNA Repair
    • Lindahl, T.; Wood, R. D. Quality Control by DNA Repair Science 1999, 286, 1897-1905
    • (1999) Science , vol.286 , pp. 1897-1905
    • Lindahl, T.1    Wood, R.D.2
  • 2
    • 10944251591 scopus 로고    scopus 로고
    • Repair and Genetic Consequences of Endogenous DNA Base Damage in Mammalian Cells
    • Barnes, D. E.; Lindahl, T. Repair and Genetic Consequences of Endogenous DNA Base Damage in Mammalian Cells Annu. Rev. Genet. 2004, 38, 445-476
    • (2004) Annu. Rev. Genet. , vol.38 , pp. 445-476
    • Barnes, D.E.1    Lindahl, T.2
  • 4
    • 0034708226 scopus 로고    scopus 로고
    • Structural Basis for Recognition and Repair of the Endogenous Mutagen 8-Oxoguanine in DNA
    • Bruner, S. D.; Norman, D. P. G.; Verdine, G. L. Structural Basis for Recognition and Repair of the Endogenous Mutagen 8-Oxoguanine in DNA Nature 2000, 403, 859-866
    • (2000) Nature , vol.403 , pp. 859-866
    • Bruner, S.D.1    Norman, D.P.G.2    Verdine, G.L.3
  • 6
    • 84861557377 scopus 로고    scopus 로고
    • Sequence-Dependent Structural Variation in DNA Undergoing Intrahelical Inspection by the DNA Glycosylase MutM
    • Sung, R.-J.; Zhang, M.; Qi, Y.; Verdine, G. L. Sequence-Dependent Structural Variation in DNA Undergoing Intrahelical Inspection by the DNA Glycosylase MutM J. Biol. Chem. 2012, 287, 18044-18054
    • (2012) J. Biol. Chem. , vol.287 , pp. 18044-18054
    • Sung, R.-J.1    Zhang, M.2    Qi, Y.3    Verdine, G.L.4
  • 7
    • 84875993659 scopus 로고    scopus 로고
    • Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM
    • Sung, R.-J.; Zhang, M.; Qi, Y.; Verdine, G. L. Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM J. Biol. Chem. 2013, 288, 10012-10023
    • (2013) J. Biol. Chem. , vol.288 , pp. 10012-10023
    • Sung, R.-J.1    Zhang, M.2    Qi, Y.3    Verdine, G.L.4
  • 9
    • 84865283412 scopus 로고    scopus 로고
    • Atomistic Modeling of Protein-DNA Interaction Specificity: Progress and Applications
    • Liu, L. A.; Bradley, P. Atomistic Modeling of Protein-DNA Interaction Specificity: Progress and Applications Curr. Opin. Struct. Biol. 2012, 22, 397-405
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 397-405
    • Liu, L.A.1    Bradley, P.2
  • 13
    • 0034714010 scopus 로고    scopus 로고
    • 1 A Crystal Structures of B-DNA Reveal Sequence-Specific Binding and Groove-Specific Bending of DNA by Magnesium and Calcium
    • Chiu, T. K.; Dickerson, R. E. 1 A Crystal Structures of B-DNA Reveal Sequence-Specific Binding and Groove-Specific Bending of DNA by Magnesium and Calcium J. Mol. Biol. 2000, 301, 915-945
    • (2000) J. Mol. Biol. , vol.301 , pp. 915-945
    • Chiu, T.K.1    Dickerson, R.E.2
  • 15
    • 0028783875 scopus 로고
    • Influence of the Oxidatively Damaged Adduct 8-Oxodeoxyguanosine on the Conformation, Energetics, and Thermodynamic Stability of a DNA Duplex
    • Plum, G. E.; Grollman, A. P.; Johnson, F.; Breslauer, K. J. Influence of the Oxidatively Damaged Adduct 8-Oxodeoxyguanosine on the Conformation, Energetics, and Thermodynamic Stability of a DNA Duplex Biochemistry 1995, 34, 16148-16160
    • (1995) Biochemistry , vol.34 , pp. 16148-16160
    • Plum, G.E.1    Grollman, A.P.2    Johnson, F.3    Breslauer, K.J.4
  • 17
    • 80053405018 scopus 로고    scopus 로고
    • Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base Pair Oligodeoxynucleotide Duplex
    • Crenshaw, C. M.; Wade, J. E.; Arthanari, H.; Frueh, D.; Lane, B. F.; Nunez, M. E. Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base Pair Oligodeoxynucleotide Duplex Biochemistry 2011, 50, 8463-8477
    • (2011) Biochemistry , vol.50 , pp. 8463-8477
    • Crenshaw, C.M.1    Wade, J.E.2    Arthanari, H.3    Frueh, D.4    Lane, B.F.5    Nunez, M.E.6
  • 18
    • 84860477162 scopus 로고    scopus 로고
    • Frontiers in Molecular Dynamics Simulations of DNA
    • Perez, A.; Luque, F. J.; Orozco, M. Frontiers in Molecular Dynamics Simulations of DNA Acc. Chem. Res. 2012, 45, 196-205
    • (2012) Acc. Chem. Res. , vol.45 , pp. 196-205
    • Perez, A.1    Luque, F.J.2    Orozco, M.3
  • 20
    • 84874866920 scopus 로고    scopus 로고
    • Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations
    • Kara, M.; Zacharias, M. Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations Biophys. J. 2013, 104, 1089-1097
    • (2013) Biophys. J. , vol.104 , pp. 1089-1097
    • Kara, M.1    Zacharias, M.2
  • 21
    • 34250318638 scopus 로고    scopus 로고
    • Refinenement of the AMBER Force Field for Nucleic Acids: Improving the Description of Alpha/Gamma Conformers
    • Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinenement of the AMBER Force Field for Nucleic Acids: Improving the Description of Alpha/Gamma Conformers Biophys. J. 2007, 92, 3817-3829
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham III, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 24
    • 24344466194 scopus 로고    scopus 로고
    • Structural and Dynamic Effects of Single 7-Hydro-8-oxoguanine Bases Located in a Frameshift Target DNA Sequence
    • Barone, F.; Lankas, F.; Spackova, N.; Sponer, J.; Karran, P.; Bignami, M.; Mazzei, F. Structural and Dynamic Effects of Single 7-Hydro-8-oxoguanine Bases Located in a Frameshift Target DNA Sequence Biophys. Chem. 2005, 118, 31-41
    • (2005) Biophys. Chem. , vol.118 , pp. 31-41
    • Barone, F.1    Lankas, F.2    Spackova, N.3    Sponer, J.4    Karran, P.5    Bignami, M.6    Mazzei, F.7
  • 25
    • 77950643237 scopus 로고    scopus 로고
    • Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns
    • Naome, A.; Schyman, P.; Laaksonen, A.; Vercauteren, D. P. Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns J. Phys. Chem. B 2010, 114, 4789-4801
    • (2010) J. Phys. Chem. B , vol.114 , pp. 4789-4801
    • Naome, A.1    Schyman, P.2    Laaksonen, A.3    Vercauteren, D.P.4
  • 27
    • 70450267492 scopus 로고    scopus 로고
    • On the Parameterization of Rigid Base and Basepair Models of DNA from Molecular Dynamics Simulations
    • Lankas, F.; Gonzalez, O.; Heffler, L. M.; Stoll, G.; Moakher, M.; Maddocks, J. H. On the Parameterization of Rigid Base and Basepair Models of DNA from Molecular Dynamics Simulations Phys. Chem. Chem. Phys. 2009, 11, 10565-10588
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 10565-10588
    • Lankas, F.1    Gonzalez, O.2    Heffler, L.M.3    Stoll, G.4    Moakher, M.5    Maddocks, J.H.6
  • 28
    • 84872584744 scopus 로고    scopus 로고
    • Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale
    • Schlick, T. Royal Society of Chemistry: London, Vol.
    • Lankas, F. Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale. In Innovations in Biomolecular Modeling and Simulations; Schlick, T., Ed.; Royal Society of Chemistry: London, 2012; Vol. 2; pp 3-32.
    • (2012) Innovations in Biomolecular Modeling and Simulations , vol.2 , pp. 3-32
    • Lankas, F.1
  • 29
    • 84879084489 scopus 로고    scopus 로고
    • Theoretical Models of DNA Flexibility
    • Drsata, T.; Lankas, F. Theoretical Models of DNA Flexibility WIREs Comput. Mol. Sci. 2013, 3, 355-363
    • (2013) WIREs Comput. Mol. Sci. , vol.3 , pp. 355-363
    • Drsata, T.1    Lankas, F.2
  • 31
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures
    • Lu, X.-J.; Olson, W. K. 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures Nucleic Acids Res. 2003, 31, 5108-5121
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 32
    • 35548987996 scopus 로고    scopus 로고
    • Sequence-Dependent DNA Deformability Studied Using Molecular Dynamics Simulations
    • Fujii, S.; Kono, H.; Takenaka, S.; Go, N.; Sarai, A. Sequence-Dependent DNA Deformability Studied Using Molecular Dynamics Simulations Nucleic Acids Res. 2007, 35, 6063-6074
    • (2007) Nucleic Acids Res. , vol.35 , pp. 6063-6074
    • Fujii, S.1    Kono, H.2    Takenaka, S.3    Go, N.4    Sarai, A.5
  • 33
  • 35
    • 1242314385 scopus 로고    scopus 로고
    • DNA Fine Structure and Dynamics in Crystals and in Solution: The Impact of BI/BII Backbone Conformations
    • Djuranovic, D.; Hartmann, B. DNA Fine Structure and Dynamics in Crystals and in Solution: The Impact of BI/BII Backbone Conformations Biopolymers 2004, 73, 356-368
    • (2004) Biopolymers , vol.73 , pp. 356-368
    • Djuranovic, D.1    Hartmann, B.2
  • 38
    • 0242290881 scopus 로고    scopus 로고
    • DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
    • Lankas, F.; Sponer, J.; Langowski, J.; Cheatham, T. E., III. DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations Biophys. J. 2003, 85, 2872-2883
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankas, F.1    Sponer, J.2    Langowski, J.3    Cheatham III, T.E.4
  • 40
    • 33751003527 scopus 로고    scopus 로고
    • Indirect Readout: Detection of Optimized Subsequences and Calculation of Relative Binding Affinities Using Different DNA Elastic Potentials
    • Becker, N. B.; Wolff, L.; Everaers, R. Indirect Readout: Detection of Optimized Subsequences and Calculation of Relative Binding Affinities Using Different DNA Elastic Potentials Nucleic Acids Res. 2006, 34, 5638-5649
    • (2006) Nucleic Acids Res. , vol.34 , pp. 5638-5649
    • Becker, N.B.1    Wolff, L.2    Everaers, R.3
  • 41
    • 40449135396 scopus 로고    scopus 로고
    • Determining Promoter Location Based on DNA Structure First-Principles Calculations
    • Goni, J. R.; Perez, A.; Torrents, D.; Orozco, M. Determining Promoter Location Based on DNA Structure First-Principles Calculations Genome Biol. 2007, 8, R263
    • (2007) Genome Biol. , vol.8 , pp. 263
    • Goni, J.R.1    Perez, A.2    Torrents, D.3    Orozco, M.4
  • 44
    • 34548187754 scopus 로고    scopus 로고
    • From Rigid Base Pairs to Semiflexible Polymers: Coarse-Graining DNA
    • Becker, N.; Everaers, R. From Rigid Base Pairs to Semiflexible Polymers: Coarse-Graining DNA Phys. Rev. E 2007, 76, 021923
    • (2007) Phys. Rev. e , vol.76 , pp. 021923
    • Becker, N.1    Everaers, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.