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Volumn 94, Issue 9, 2008, Pages 3590-3600

Predicting thymine dimerization yields from molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOSIDE PHOSPHATE; DNA; ORGANIC COMPOUND; PYRIMIDINE DIMER; SOLVENT; THYMIDYLYL (3' 5') THYMIDINE; THYMIDYLYL-(3'-5')-THYMIDINE; THYMINE; WATER;

EID: 43649101919     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.118612     Document Type: Article
Times cited : (88)

References (71)
  • 1
  • 2
    • 24144459117 scopus 로고    scopus 로고
    • Base stacking controls excited-state dynamics in AT DNA
    • Crespo-Hernández, C. E., B. Cohen, and B. Kohler. 2005. Base stacking controls excited-state dynamics in AT DNA. Nature. 436: 1141-1144.
    • (2005) Nature , vol.436 , pp. 1141-1144
    • Crespo-Hernández, C.E.1    Cohen, B.2    Kohler, B.3
  • 4
    • 33846064290 scopus 로고    scopus 로고
    • Crystal structure and photochemical behavior in solution of the 3′-N-sulfamate analogue of thymidylyl(3′-5′)thymidine
    • Moriou, C., M. Thomas, M. T. Adeline, M. T. Martin, A. Chiaroni, S. Pochet, J. L. Fourrey, A. Favre, and P. Clivio. 2007. Crystal structure and photochemical behavior in solution of the 3′-N-sulfamate analogue of thymidylyl(3′-5′)thymidine. J. Org. Chem. 72:43-50.
    • (2007) J. Org. Chem , vol.72 , pp. 43-50
    • Moriou, C.1    Thomas, M.2    Adeline, M.T.3    Martin, M.T.4    Chiaroni, A.5    Pochet, S.6    Fourrey, J.L.7    Favre, A.8    Clivio, P.9
  • 5
    • 34548047708 scopus 로고    scopus 로고
    • Dinucleotide TpT and its 2'-O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries
    • Santini, G. P. H., C. Pakleza, P. Auffinger, C. Moriou, A. Favre, P. Clivio, and J. A. H. Cognet. 2007. Dinucleotide TpT and its 2'-O-Me analogue possess different backbone conformations and flexibilities but similar stacked geometries. J. Phys. Chem. B. 111:9400-9409.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 9400-9409
    • Santini, G.P.H.1    Pakleza, C.2    Auffinger, P.3    Moriou, C.4    Favre, A.5    Clivio, P.6    Cognet, J.A.H.7
  • 6
    • 0021190168 scopus 로고
    • Use of light for footprinting DNA in vivo
    • Becker, M. M., and J. C. Wang. 1984. Use of light for footprinting DNA in vivo. Nature. 309:682-687.
    • (1984) Nature , vol.309 , pp. 682-687
    • Becker, M.M.1    Wang, J.C.2
  • 7
    • 0029058984 scopus 로고
    • UV light as a footprinting agent: Modulation of UV-induced DNA damage by transcription factors bound at the promoters of three human genes
    • Tornaletti, S., and G. P. Pfeifer. 1995. UV light as a footprinting agent: modulation of UV-induced DNA damage by transcription factors bound at the promoters of three human genes. J. Mol. Biol. 249:714-728.
    • (1995) J. Mol. Biol , vol.249 , pp. 714-728
    • Tornaletti, S.1    Pfeifer, G.P.2
  • 8
    • 0014214774 scopus 로고
    • The excited-state precursor of the thymine dimer
    • Eisinger, J., and A. A. Lamola. 1967. The excited-state precursor of the thymine dimer. Biochem. Biophys. Res. Commun. 28:558-565.
    • (1967) Biochem. Biophys. Res. Commun , vol.28 , pp. 558-565
    • Eisinger, J.1    Lamola, A.A.2
  • 10
    • 0002705020 scopus 로고
    • On the mechanism of thymine photodimerization
    • Lamola, A. A., and J. Eisinger. 1968. On the mechanism of thymine photodimerization. Proc. Natl. Acad. Sci. USA. 59:46-51.
    • (1968) Proc. Natl. Acad. Sci. USA , vol.59 , pp. 46-51
    • Lamola, A.A.1    Eisinger, J.2
  • 11
    • 0015913882 scopus 로고
    • Synthetic spectroscopic models related to coenzymes and base pairs. XI. Solid state ultraviolet irradiation of 1,1 ′ -trimethylenebisthymine and photosensitized irradiation of 1,1 ' -polymethylenebisthy- mines
    • Leonard, N. J., R. S. McCredie, M. W. Logue, and R. L. Cundall. 1973. Synthetic spectroscopic models related to coenzymes and base pairs. XI. Solid state ultraviolet irradiation of 1,1 ′ -trimethylenebisthymine and photosensitized irradiation of 1,1 ' -polymethylenebisthy- mines. J. Am. Chem. Soc. 95:2320-2324.
    • (1973) J. Am. Chem. Soc , vol.95 , pp. 2320-2324
    • Leonard, N.J.1    McCredie, R.S.2    Logue, M.W.3    Cundall, R.L.4
  • 12
    • 0024380891 scopus 로고
    • Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin
    • Pehrson, J. R. 1989. Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin. Proc. Natl. Acad. Sci. USA. 86:9149-9153.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 9149-9153
    • Pehrson, J.R.1
  • 13
    • 0014461339 scopus 로고
    • Influence of polynucleotide secondary structure on thymine dimerization
    • Tramer, Z., K. L. Wierzchowski, and D. Shugar. 1969. Influence of polynucleotide secondary structure on thymine dimerization. Acta Bioc-him. Pol. 16:83-107.
    • (1969) Acta Bioc-him. Pol , vol.16 , pp. 83-107
    • Tramer, Z.1    Wierzchowski, K.L.2    Shugar, D.3
  • 14
    • 58649087766 scopus 로고
    • The influence of the interfacial energy of organic solvents on the photochemical dimerization of thymidylyl-(3′-5′)-thymidine
    • Wacker, A., and E. Lodemann. 1965. The influence of the interfacial energy of organic solvents on the photochemical dimerization of thymidylyl-(3′-5′)-thymidine. Angew. Chem. Int. Ed. Engl. 4:150.
    • (1965) Angew. Chem. Int. Ed. Engl , vol.4 , pp. 150
    • Wacker, A.1    Lodemann, E.2
  • 15
    • 85031351225 scopus 로고    scopus 로고
    • Solvent effects on photodegradation of the 18-mer of thymidilic acid
    • thesis. The Ohio State University, Columbus, OH
    • Olmon, E. D. 2005. Solvent effects on photodegradation of the 18-mer of thymidilic acid. Senior honors thesis. The Ohio State University, Columbus, OH.
    • (2005) Senior honors
    • Olmon, E.D.1
  • 16
    • 29644444403 scopus 로고    scopus 로고
    • Effect of denaturation on the photochemistry of pyrimidine bases in isolated DNA
    • Douki, T. 2006. Effect of denaturation on the photochemistry of pyrimidine bases in isolated DNA. J. Photochem. Photobiol. B. 82: 45-52.
    • (2006) J. Photochem. Photobiol. B , vol.82 , pp. 45-52
    • Douki, T.1
  • 18
    • 33750549466 scopus 로고    scopus 로고
    • Low ionic strength reduces cytosine photoreactivity in UVC-irradiated isolated DNA
    • Douki, T. 2006. Low ionic strength reduces cytosine photoreactivity in UVC-irradiated isolated DNA. Photochem. Photobiol. Sci. 5:1045-1051.
    • (2006) Photochem. Photobiol. Sci , vol.5 , pp. 1045-1051
    • Douki, T.1
  • 20
    • 84995071764 scopus 로고
    • Quantum yield of photohydration for dimethyluracil. Concentration and wavelength dependence
    • Rahn, R. O., and H. G. Sellin. 1979. Quantum yield of photohydration for dimethyluracil. Concentration and wavelength dependence. Photochem. Photobiol. 30:317-318.
    • (1979) Photochem. Photobiol , vol.30 , pp. 317-318
    • Rahn, R.O.1    Sellin, H.G.2
  • 21
    • 0021378821 scopus 로고
    • Photochemical addition of amino acids and peptides to DNA
    • Shetlar, M. D., J. Christensen, and K. Hom. 1984. Photochemical addition of amino acids and peptides to DNA. Photochem. Photobiol. 39:125-133.
    • (1984) Photochem. Photobiol , vol.39 , pp. 125-133
    • Shetlar, M.D.1    Christensen, J.2    Hom, K.3
  • 22
    • 0027670837 scopus 로고
    • The photochemistry of adenosine: Intermediates contributing to its photodegradation mechanism in aqueous solution at 298 K and characterization of the major product
    • Arce, R., L. Martínez, and E. Danielsen. 1993. The photochemistry of adenosine: intermediates contributing to its photodegradation mechanism in aqueous solution at 298 K and characterization of the major product. Photochem. Photobiol. 58:318-328.
    • (1993) Photochem. Photobiol , vol.58 , pp. 318-328
    • Arce, R.1    Martínez, L.2    Danielsen, E.3
  • 23
    • 0027604555 scopus 로고
    • Quantum yields and secondary photoreactions of the photoproducts of dTpdT, dTpdC and dTpdU
    • Lemaire, D. G. E., and B. P. Ruzsicska. 1993. Quantum yields and secondary photoreactions of the photoproducts of dTpdT, dTpdC and dTpdU. Photochem. Photobiol. 57:755-769.
    • (1993) Photochem. Photobiol , vol.57 , pp. 755-769
    • Lemaire, D.G.E.1    Ruzsicska, B.P.2
  • 24
    • 0014725117 scopus 로고
    • Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxynucleotides
    • Cantor, C. R., M. M. Warshaw, and H. Shapiro. 1970. Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxynucleotides. Biopolymers. 9:1059-1071.
    • (1970) Biopolymers , vol.9 , pp. 1059-1071
    • Cantor, C.R.1    Warshaw, M.M.2    Shapiro, H.3
  • 25
    • 0001062698 scopus 로고
    • Pyrimidine photodimers
    • Acids. S. Y. Wang, editor. Academic Press, New York
    • Fisher, G. J., and H. E. Johns. 1976. Pyrimidine photodimers. In Photochemistry and Photobiology of Nucleic Acids. S. Y. Wang, editor. Academic Press, New York. 225-294.
    • (1976) Photochemistry and Photobiology of Nucleic , pp. 225-294
    • Fisher, G.J.1    Johns, H.E.2
  • 26
    • 0031196856 scopus 로고    scopus 로고
    • Far-UV-induced dimeric photoproducts in short oligonucleotides: Sequence effects
    • Douki, T., T. Zalizniak, and J. Cadet. 1997. Far-UV-induced dimeric photoproducts in short oligonucleotides: sequence effects. Photochem. Photobiol. 66:171-179.
    • (1997) Photochem. Photobiol , vol.66 , pp. 171-179
    • Douki, T.1    Zalizniak, T.2    Cadet, J.3
  • 27
    • 0017173727 scopus 로고
    • Molecular structure of a deoxyribose-dinucleotide, sodium thymidylyl-(5′-3′)- thymidylate-(5') hydrate (pTpT), and a possible structural model for polythymidylate
    • Camerman, N., J. K. Fawcett, and A. Camerman. 1976. Molecular structure of a deoxyribose-dinucleotide, sodium thymidylyl-(5′-3′)- thymidylate-(5') hydrate (pTpT), and a possible structural model for polythymidylate. J. Mol. Biol. 107:601-621.
    • (1976) J. Mol. Biol , vol.107 , pp. 601-621
    • Camerman, N.1    Fawcett, J.K.2    Camerman, A.3
  • 29
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • Berendsen, H. J. C., D. van der Spoel, and R. van Drunen. 1995. GROMACS: a message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91:43-56.
    • (1995) Comput. Phys. Commun , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 30
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
    • (2001) J. Mol. Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 32
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin, E. J., and V. S. Pande. 2005. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 88:2472-2493.
    • (2005) Biophys. J , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 33
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
    • (1977) J. Comput. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 34
    • 84986440341 scopus 로고
    • Settle: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
    • Miyamoto, S., and P. A. Kollman. 1992. Settle: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comput. Chem. 13:952-962.
    • (1992) J. Comput. Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 36
    • 33846842713 scopus 로고    scopus 로고
    • Lide, D. R, editor, Taylor & Francis, Boca Raton, FL
    • Lide, D. R., editor. 2007. CRC Handbook of Chemistry and Physics. Taylor & Francis, Boca Raton, FL.
    • (2007) CRC Handbook of Chemistry and Physics
  • 38
    • 33646887390 scopus 로고
    • On the limited memory BFGS method for large-scale optimization
    • Liu, D. C., and J. Nocedal. 1989. On the limited memory BFGS method for large-scale optimization. Math. Program. 45: 503-528.
    • (1989) Math. Program , vol.45 , pp. 503-528
    • Liu, D.C.1    Nocedal, J.2
  • 39
    • 0003871536 scopus 로고    scopus 로고
    • Conformational analysis
    • O. M. Becker, A. D. Mackerell Jr, B. Roux, and M. Wanatabe, editors. Marcel Dekker, New York
    • Becker, O. M. 2001. Conformational analysis. In Computational Biochemistry and Biophysics. O. M. Becker, A. D. Mackerell Jr., B. Roux, and M. Wanatabe, editors. Marcel Dekker, New York. 69-90.
    • (2001) Computational Biochemistry and Biophysics , pp. 69-90
    • Becker, O.M.1
  • 40
    • 0025294114 scopus 로고
    • Conformational sampling using high-temperature molecular dynamics
    • Bruccoleri, R. E., and M. Karplus. 1990. Conformational sampling using high-temperature molecular dynamics. Biopolymers. 29:1847-1862.
    • (1990) Biopolymers , vol.29 , pp. 1847-1862
    • Bruccoleri, R.E.1    Karplus, M.2
  • 41
    • 1542742143 scopus 로고    scopus 로고
    • Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence
    • Yang, W., R. Bitetti-Putzer, and M. Karplus. 2004. Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. J. Chem. Phys. 120:2618-2628.
    • (2004) J. Chem. Phys , vol.120 , pp. 2618-2628
    • Yang, W.1    Bitetti-Putzer, R.2    Karplus, M.3
  • 42
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu, X.-J., and W. K. Olson. 2003. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31:5108-5121.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 43
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., M. Billeter, and K. Wüthrich. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:51-55.
    • (1996) J. Mol. Graph , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3
  • 45
    • 0030077218 scopus 로고    scopus 로고
    • Depopulation of highly excited singlet states of DNA model compounds: Quantum yields of 193 and 245 nm photoproducts of pyrimidine monomers and dinucleoside monophosphates
    • Gurzadyan, G. G., and H. Görner. 1996. Depopulation of highly excited singlet states of DNA model compounds: quantum yields of 193 and 245 nm photoproducts of pyrimidine monomers and dinucleoside monophosphates. Photochem. Photobiol. 63:143-153.
    • (1996) Photochem. Photobiol , vol.63 , pp. 143-153
    • Gurzadyan, G.G.1    Görner, H.2
  • 46
    • 84932971076 scopus 로고
    • Strahlenchemische Veränderungen von Thymin und Cytosin in der DNS durch UV-Licht.
    • Dellweg, H., and A. Wacker. 1962. Strahlenchemische Veränderungen von Thymin und Cytosin in der DNS durch UV-Licht. Z. Naturforsch. 17b:827-834.
    • (1962) Z. Naturforsch , vol.17 b , pp. 827-834
    • Dellweg, H.1    Wacker, A.2
  • 47
    • 0000178584 scopus 로고
    • Mechanism of thymine photodimerization
    • Eisinger, J., and A. A. Lamola. 1969. Mechanism of thymine photodimerization. Mol. Photochem. 1:209-223.
    • (1969) Mol. Photochem , vol.1 , pp. 209-223
    • Eisinger, J.1    Lamola, A.A.2
  • 48
    • 0043011175 scopus 로고    scopus 로고
    • Sugar conformational effects on the photochemistry of thymidylyl(3′-5′)thymidine
    • Ostrowski, T., J.-C. Maurizot, M.-T. Adeline, J.-L. Fourrey, and P. Clivio. 2003. Sugar conformational effects on the photochemistry of thymidylyl(3′-5′)thymidine. J. Org. Chem. 68:6502-6510.
    • (2003) J. Org. Chem , vol.68 , pp. 6502-6510
    • Ostrowski, T.1    Maurizot, J.-C.2    Adeline, M.-T.3    Fourrey, J.-L.4    Clivio, P.5
  • 49
    • 0015913863 scopus 로고
    • 3-Thy). Environment of a solid state photochemical reaction
    • 3-Thy). Environment of a solid state photochemical reaction. J. Am. Chem. Soc. 95:2324-2332.
    • (1973) J. Am. Chem. Soc , vol.95 , pp. 2324-2332
    • Frank, J.K.1    Paul, I.C.2
  • 50
    • 0039054621 scopus 로고
    • Nonaqueous solutions of DNA. Denaturation in methanol and ethanol
    • Herskovits, T. T., S. J. Singer, and E. P. Geiduschek. 1961. Nonaqueous solutions of DNA. Denaturation in methanol and ethanol. Arch. Biochem. Biophys. 94:99-114.
    • (1961) Arch. Biochem. Biophys , vol.94 , pp. 99-114
    • Herskovits, T.T.1    Singer, S.J.2    Geiduschek, E.P.3
  • 51
    • 0031972564 scopus 로고    scopus 로고
    • Solvent influence on base stacking
    • Norberg, J., and L. Nilsson. 1998. Solvent influence on base stacking. Biophys. J. 74:394-402.
    • (1998) Biophys. J , vol.74 , pp. 394-402
    • Norberg, J.1    Nilsson, L.2
  • 53
    • 0032500623 scopus 로고    scopus 로고
    • Solution-state structure of a DNA dodecamer duplex containing a cissyn thymine cyclobutane dimer, the major UV photoproduct of DNA
    • McAteer, K., Y. Jing, J. Kao, J.-S. Taylor, and M. A. Kennedy. 1998. Solution-state structure of a DNA dodecamer duplex containing a cissyn thymine cyclobutane dimer, the major UV photoproduct of DNA. J. Mol. Biol. 282:1013-1032.
    • (1998) J. Mol. Biol , vol.282 , pp. 1013-1032
    • McAteer, K.1    Jing, Y.2    Kao, J.3    Taylor, J.-S.4    Kennedy, M.A.5
  • 54
    • 0026098297 scopus 로고
    • NMR studies of bipyrimidine cyclobutane photodimers
    • Koning, M. G., J. J. van Soest, and R. Kaptein. 1991. NMR studies of bipyrimidine cyclobutane photodimers. FEBS J. 195:29-40.
    • (1991) FEBS J , vol.195 , pp. 29-40
    • Koning, M.G.1    van Soest, J.J.2    Kaptein, R.3
  • 55
    • 0023711916 scopus 로고
    • Nuclear magnetic resonance studies of cissyn, trans- syn, and 6-4 photodimers of thymidylyl(3′-5′)thymidine monophosphate and cis-syn photodimers of thymidylyl(3′-5′)thymidine cyanoethyl phosphotriester
    • Kan, L.-S., L. Voituriez, and J. Cadet. 1988. Nuclear magnetic resonance studies of cissyn, trans- syn, and 6-4 photodimers of thymidylyl(3′-5′)thymidine monophosphate and cis-syn photodimers of thymidylyl(3′-5′)thymidine cyanoethyl phosphotriester. Biochemistry. 27:5796-5803.
    • (1988) Biochemistry , vol.27 , pp. 5796-5803
    • Kan, L.-S.1    Voituriez, L.2    Cadet, J.3
  • 56
    • 0027657058 scopus 로고
    • An NMR and conformational investigation of the trans-syn cyclobutane photodimers of dTpdU
    • Tabaczynski, W. A., D. G. E. Lemaire, B. P. Ruzsicska, and J. L. Alderfer. 1993. An NMR and conformational investigation of the trans-syn cyclobutane photodimers of dTpdU. Biopolymers. 33:1365-1375.
    • (1993) Biopolymers , vol.33 , pp. 1365-1375
    • Tabaczynski, W.A.1    Lemaire, D.G.E.2    Ruzsicska, B.P.3    Alderfer, J.L.4
  • 57
    • 0027223848 scopus 로고
    • Identification and structure determination of a third cyclobutane photodimer of thymidyl-(3′ -5′ )-thymine: The trans-syn-II product
    • Kao, J. L. F., S. Nadji, and J.-S. Taylor. 1993. Identification and structure determination of a third cyclobutane photodimer of thymidyl-(3′ -5′ )-thymine: the trans-syn-II product. Chem. Res. Toxicol. 6:561-567.
    • (1993) Chem. Res. Toxicol , vol.6 , pp. 561-567
    • Kao, J.L.F.1    Nadji, S.2    Taylor, J.-S.3
  • 59
    • 0030954859 scopus 로고    scopus 로고
    • A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions
    • Cheatham III, T. E., M. F. Crowley, T. Fox, and P. A. Kollman. 1997. A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc. Natl. Acad. Sci. USA. 94:9626-9630.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 9626-9630
    • Cheatham III, T.E.1    Crowley, M.F.2    Fox, T.3    Kollman, P.A.4
  • 60
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of a/y conformers
    • Pérez, A., I. Marchán, D. Svozil, J. Sponer, T. E. Cheatham III, C. A. Laughton, and M. Orozco. 2007. Refinement of the AMBER force field for nucleic acids: improving the description of a/y conformers. Biophys. J. 92:3817-3829.
    • (2007) Biophys. J , vol.92 , pp. 3817-3829
    • Pérez, A.1    Marchán, I.2    Svozil, D.3    Sponer, J.4    Cheatham III, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 61
    • 4043179941 scopus 로고    scopus 로고
    • DNA and its counterions: A molecular dynamics study
    • Varnai, P., and K. Zakrzewska. 2004. DNA and its counterions: a molecular dynamics study. Nucleic Acids Res. 32:4269-4280.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4269-4280
    • Varnai, P.1    Zakrzewska, K.2
  • 62
    • 0023732135 scopus 로고
    • Origin of DNA helical structure and its sequence dependence
    • Sarai, A., J. Mazur, R. Nussinov, and R. L. Jernigan. 1988. Origin of DNA helical structure and its sequence dependence. Biochemistry. 27:8498-8502.
    • (1988) Biochemistry , vol.27 , pp. 8498-8502
    • Sarai, A.1    Mazur, J.2    Nussinov, R.3    Jernigan, R.L.4
  • 63
    • 0000668404 scopus 로고
    • Characterization of thymidine ultraviolet photo-products. Cyclobutane dimers and 5,6-dihydrothymidines
    • Cadet, J., L. Voituriez, F. E. Hruska, L.-S. Kan, F. A. A. M. de Leeuw, and C. Altona. 1985. Characterization of thymidine ultraviolet photo-products. Cyclobutane dimers and 5,6-dihydrothymidines. Can. J. Chem. 63:2861-2868.
    • (1985) Can. J. Chem , vol.63 , pp. 2861-2868
    • Cadet, J.1    Voituriez, L.2    Hruska, F.E.3    Kan, L.-S.4    de Leeuw, F.A.A.M.5    Altona, C.6
  • 64
    • 0034976275 scopus 로고    scopus 로고
    • Isolation and mass spectrometric characterization of dimeric adenine photoproducts in oligodeoxynucleotides
    • Wang, Y., J.-S. Taylor, and M. L. Gross. 2001. Isolation and mass spectrometric characterization of dimeric adenine photoproducts in oligodeoxynucleotides. Chem. Res. Toxicol. 14:738-745.
    • (2001) Chem. Res. Toxicol , vol.14 , pp. 738-745
    • Wang, Y.1    Taylor, J.-S.2    Gross, M.L.3
  • 65
    • 0011602243 scopus 로고
    • Conical intersections as a mechanistic feature of organic photochemistry
    • Robb, M. A., F. Bernardi, and M. Olivucci. 1995. Conical intersections as a mechanistic feature of organic photochemistry. Pure Appl. Chem. 67:783-789.
    • (1995) Pure Appl. Chem , vol.67 , pp. 783-789
    • Robb, M.A.1    Bernardi, F.2    Olivucci, M.3
  • 66
    • 84985512927 scopus 로고
    • Conical intersections and the mechanism of singlet photoreactions
    • Klessinger, M. 1995. Conical intersections and the mechanism of singlet photoreactions. Angew. Chem. Int. Ed. Engl. 34:549-551.
    • (1995) Angew. Chem. Int. Ed. Engl , vol.34 , pp. 549-551
    • Klessinger, M.1
  • 67
    • 14544286825 scopus 로고    scopus 로고
    • Hirano, S., S. Toyota, and F. Toda. 2005. A new [2 + 2] photodimerization of 5-chloro- and 5-methyl-2-pyridone in their inclusion complexes with 1,1′-biphenyl-2,2′-dicarboxylic acid as a model for DNA damage by photodimerization of its thymine component. Chem. Commun.643-644.
    • Hirano, S., S. Toyota, and F. Toda. 2005. A new [2 + 2] photodimerization of 5-chloro- and 5-methyl-2-pyridone in their inclusion complexes with 1,1′-biphenyl-2,2′-dicarboxylic acid as a model for DNA damage by photodimerization of its thymine component. Chem. Commun.643-644.
  • 68
    • 33646879004 scopus 로고    scopus 로고
    • New [2 1 2]- and [4 +4]-photodimerizations of 2-pyridones in an inclusion complex with a simple carboxylic acid host: A model of DNA damage by photodimerization of its thymine component
    • Hirano, S., S. Toyota, and F. Toda. 2004. New [2 1 2]- and [4 +4]-photodimerizations of 2-pyridones in an inclusion complex with a simple carboxylic acid host: a model of DNA damage by photodimerization of its thymine component. Heterocycles. 64: 383-391.
    • (2004) Heterocycles , vol.64 , pp. 383-391
    • Hirano, S.1    Toyota, S.2    Toda, F.3
  • 69
    • 38349135961 scopus 로고    scopus 로고
    • Structure and dynamics of poly(T) single-strand DNA: Implications toward CPD formation
    • In press
    • Johnson, A. T., and O. Wiest. 2007. Structure and dynamics of poly(T) single-strand DNA: Implications toward CPD formation. J. Phys. Chem. B. In press.
    • (2007) J. Phys. Chem. B
    • Johnson, A.T.1    Wiest, O.2
  • 71
    • 0031195002 scopus 로고    scopus 로고
    • Conformations of the sugar-phosphate backbone in helical DNA crystal structures
    • Schneider, B., S. Neidle, and H. M. Berman. 1997. Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers. 42:113-124.
    • (1997) Biopolymers , vol.42 , pp. 113-124
    • Schneider, B.1    Neidle, S.2    Berman, H.M.3


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