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Volumn 381, Issue 3, 2008, Pages 692-706

Identification of Intrinsic Dynamics in a DNA Sequence Preferentially Cleaved by Topoisomerase II Enzyme

Author keywords

cleavage site; molecular dynamics; NMR; nucleic acid; topoisomerase II

Indexed keywords

ADENINE NUCLEOTIDE; DNA TOPOISOMERASE (ATP HYDROLYSING); OLIGONUCLEOTIDE;

EID: 47849096960     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.06.024     Document Type: Article
Times cited : (13)

References (69)
  • 1
    • 0030014783 scopus 로고    scopus 로고
    • DNA topoisomerases
    • Wang J.C. DNA topoisomerases. Annu. Rev. Biochem. 65 (1996) 635-692
    • (1996) Annu. Rev. Biochem. , vol.65 , pp. 635-692
    • Wang, J.C.1
  • 2
    • 0036085460 scopus 로고    scopus 로고
    • Cellular roles of DNA topoisomerases: a molecular perspective
    • Wang J.C. Cellular roles of DNA topoisomerases: a molecular perspective. Nat. Rev. Mol. Cell Biol. 3 (2002) 430-440
    • (2002) Nat. Rev. Mol. Cell Biol. , vol.3 , pp. 430-440
    • Wang, J.C.1
  • 3
    • 28844493513 scopus 로고    scopus 로고
    • Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases
    • Maxwell A., Costenaro L., Mitelheiser S., and Bates A.D. Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases. Biochem. Soc. Trans. 33 (2005) 1460-1464
    • (2005) Biochem. Soc. Trans. , vol.33 , pp. 1460-1464
    • Maxwell, A.1    Costenaro, L.2    Mitelheiser, S.3    Bates, A.D.4
  • 4
    • 0025865792 scopus 로고
    • Sequence requirements for mammalian topoisomerase II mediated DNA cleavage stimulated by an ellipticine derivative
    • Fossé P., René B., Le Bret M., Paoletti C., and Saucier J.M. Sequence requirements for mammalian topoisomerase II mediated DNA cleavage stimulated by an ellipticine derivative. Nucleic Acids Res. 19 (1991) 2861-2868
    • (1991) Nucleic Acids Res. , vol.19 , pp. 2861-2868
    • Fossé, P.1    René, B.2    Le Bret, M.3    Paoletti, C.4    Saucier, J.M.5
  • 5
    • 0025037693 scopus 로고
    • Sequence-selective topoisomerase II inhibition by anthracycline derivatives in SV40 DNA: relationship with DNA binding affinity and cytotoxicity
    • Capranico G., Zunino F., Kohn K.W., and Pommier Y. Sequence-selective topoisomerase II inhibition by anthracycline derivatives in SV40 DNA: relationship with DNA binding affinity and cytotoxicity. Biochemistry 29 (1990) 562-569
    • (1990) Biochemistry , vol.29 , pp. 562-569
    • Capranico, G.1    Zunino, F.2    Kohn, K.W.3    Pommier, Y.4
  • 6
    • 0030448769 scopus 로고    scopus 로고
    • Drug sensitivity and sequence specificity of human recombinant DNA topoisomerases IIalpha (p170) and IIbeta (p180)
    • Cornarotti M., Tinelli S., Willmore E., Zunino F., Fisher L.M., Austin C.A., and Capranico G. Drug sensitivity and sequence specificity of human recombinant DNA topoisomerases IIalpha (p170) and IIbeta (p180). Mol. Pharmacol. 50 (1996) 1463-1471
    • (1996) Mol. Pharmacol. , vol.50 , pp. 1463-1471
    • Cornarotti, M.1    Tinelli, S.2    Willmore, E.3    Zunino, F.4    Fisher, L.M.5    Austin, C.A.6    Capranico, G.7
  • 7
    • 0030582837 scopus 로고    scopus 로고
    • Amsacrine-promoted DNA cleavage site determinants for the two human DNA topoisomerase II isoforms alpha and beta
    • Marsh K.L., Willmore E., Tinelli S., Cornarotti M., Meczes E.L., Capranico G., et al. Amsacrine-promoted DNA cleavage site determinants for the two human DNA topoisomerase II isoforms alpha and beta. Biochem. Pharmacol. 52 (1996) 1675-1685
    • (1996) Biochem. Pharmacol. , vol.52 , pp. 1675-1685
    • Marsh, K.L.1    Willmore, E.2    Tinelli, S.3    Cornarotti, M.4    Meczes, E.L.5    Capranico, G.6
  • 8
    • 0026093801 scopus 로고
    • Local base sequence preferences for DNA cleavage by mammalian topoisomerase II in the presence of amsacrine or teniposide
    • Pommier Y., Capranico G., Orr A., and Kohn K.W. Local base sequence preferences for DNA cleavage by mammalian topoisomerase II in the presence of amsacrine or teniposide. Nucleic Acids Res. 19 (1991) 5973-5980
    • (1991) Nucleic Acids Res. , vol.19 , pp. 5973-5980
    • Pommier, Y.1    Capranico, G.2    Orr, A.3    Kohn, K.W.4
  • 9
    • 0023902435 scopus 로고
    • A consensus sequence for cleavage by vertebrate DNA topoisomerase II
    • Spitzner J.R., and Muller M.T. A consensus sequence for cleavage by vertebrate DNA topoisomerase II. Nucleic Acids Res. 16 (1988) 5533-5556
    • (1988) Nucleic Acids Res. , vol.16 , pp. 5533-5556
    • Spitzner, J.R.1    Muller, M.T.2
  • 10
    • 0033214044 scopus 로고    scopus 로고
    • Molecular analysis of yeast and human type II topoisomerases. Enzyme-DNA and drug interactions
    • Strumberg D., Nitiss J.L., Dong J., Kohn K.W., and Pommier Y. Molecular analysis of yeast and human type II topoisomerases. Enzyme-DNA and drug interactions. J. Biol. Chem. 274 (1999) 28246-28255
    • (1999) J. Biol. Chem. , vol.274 , pp. 28246-28255
    • Strumberg, D.1    Nitiss, J.L.2    Dong, J.3    Kohn, K.W.4    Pommier, Y.5
  • 11
    • 0032189945 scopus 로고    scopus 로고
    • DNA sequence selectivity of topoisomerases and topoisomerase poisons
    • Capranico G., and Binaschi M. DNA sequence selectivity of topoisomerases and topoisomerase poisons. Biochim. Biophys. Acta 1400 (1998) 185-194
    • (1998) Biochim. Biophys. Acta , vol.1400 , pp. 185-194
    • Capranico, G.1    Binaschi, M.2
  • 12
    • 0033582466 scopus 로고    scopus 로고
    • In vitro evolution of preferred topoisomerase II DNA cleavage sites
    • Burden D.A., and Osheroff N. In vitro evolution of preferred topoisomerase II DNA cleavage sites. J. Biol. Chem. 274 (1999) 5227-5235
    • (1999) J. Biol. Chem. , vol.274 , pp. 5227-5235
    • Burden, D.A.1    Osheroff, N.2
  • 13
    • 0030741586 scopus 로고    scopus 로고
    • Distribution of topoisomerase II-mediated cleavage sites and relation to structural and functional landmarks in 830 kb of Drosophila DNA
    • Miassod R., Razin S.V., and Hancock R. Distribution of topoisomerase II-mediated cleavage sites and relation to structural and functional landmarks in 830 kb of Drosophila DNA. Nucleic Acids Res. 25 (1997) 2041-2046
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2041-2046
    • Miassod, R.1    Razin, S.V.2    Hancock, R.3
  • 14
    • 0025740443 scopus 로고
    • Nuclear matrix attachment regions and topoisomerase II binding and reaction sites in the vicinity of a chicken DNA replication origin
    • Razin S.V., Vassetzky Y.S., and Hancock R. Nuclear matrix attachment regions and topoisomerase II binding and reaction sites in the vicinity of a chicken DNA replication origin. Biochem. Biophys. Res. Commun. 177 (1991) 265-270
    • (1991) Biochem. Biophys. Res. Commun. , vol.177 , pp. 265-270
    • Razin, S.V.1    Vassetzky, Y.S.2    Hancock, R.3
  • 15
    • 22844436224 scopus 로고    scopus 로고
    • Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix
    • Iarovaia O.V., Akopov S.B., Nikolaev L.G., Sverdlov E.D., and Razin S.V. Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix. Nucleic Acids Res. 33 (2005) 4157-4163
    • (2005) Nucleic Acids Res. , vol.33 , pp. 4157-4163
    • Iarovaia, O.V.1    Akopov, S.B.2    Nikolaev, L.G.3    Sverdlov, E.D.4    Razin, S.V.5
  • 16
    • 1842584772 scopus 로고    scopus 로고
    • Chromatin loops are selectively anchored using scaffold/matrix-attachment regions
    • Heng H.H., Goetze S., Ye C.J., Liu G., Stevens J.B., Bremer S.W., et al. Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J. Cell Sci. 117 (2004) 999-1008
    • (2004) J. Cell Sci. , vol.117 , pp. 999-1008
    • Heng, H.H.1    Goetze, S.2    Ye, C.J.3    Liu, G.4    Stevens, J.B.5    Bremer, S.W.6
  • 17
    • 0021046130 scopus 로고
    • Actively transcribed genes are associated with the nuclear matrix
    • Ciejek E.M., Tsai M.J., and O'Malley B.W. Actively transcribed genes are associated with the nuclear matrix. Nature 306 (1983) 607-609
    • (1983) Nature , vol.306 , pp. 607-609
    • Ciejek, E.M.1    Tsai, M.J.2    O'Malley, B.W.3
  • 18
    • 34247346622 scopus 로고    scopus 로고
    • Does topoisomerase II specifically recognize and cleave hairpins, cruciforms and crossovers of DNA?
    • René B., Fermandjian S., and Mauffret O. Does topoisomerase II specifically recognize and cleave hairpins, cruciforms and crossovers of DNA?. Biochimie 89 (2007) 508-515
    • (2007) Biochimie , vol.89 , pp. 508-515
    • René, B.1    Fermandjian, S.2    Mauffret, O.3
  • 19
    • 33745812359 scopus 로고    scopus 로고
    • Alteration of Escherichia coli topoisomerase IV conformation upon enzyme binding to positively supercoiled DNA
    • Crisona N.J., and Cozzarelli N.R. Alteration of Escherichia coli topoisomerase IV conformation upon enzyme binding to positively supercoiled DNA. J. Biol. Chem. 281 (2006) 18927-18932
    • (2006) J. Biol. Chem. , vol.281 , pp. 18927-18932
    • Crisona, N.J.1    Cozzarelli, N.R.2
  • 21
    • 0043194014 scopus 로고    scopus 로고
    • Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases
    • Charvin G., Bensimon D., and Croquette V. Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases. Proc. Natl Acad. Sci. U. S. A. 100 (2003) 9820-9825
    • (2003) Proc. Natl Acad. Sci. U. S. A. , vol.100 , pp. 9820-9825
    • Charvin, G.1    Bensimon, D.2    Croquette, V.3
  • 22
    • 0032545153 scopus 로고    scopus 로고
    • Symmetry and chirality in topoisomerase II-DNA crossover recognition
    • Timsit Y., Duplantier B., Jannink G., and Sikorav J.L. Symmetry and chirality in topoisomerase II-DNA crossover recognition. J. Mol. Biol. 284 (1998) 1289-1299
    • (1998) J. Mol. Biol. , vol.284 , pp. 1289-1299
    • Timsit, Y.1    Duplantier, B.2    Jannink, G.3    Sikorav, J.L.4
  • 23
    • 28244433817 scopus 로고    scopus 로고
    • Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks
    • McClendon A.K., Rodriguez A.C., and Osheroff N. Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks. J. Biol. Chem. 280 (2005) 39337-39345
    • (2005) J. Biol. Chem. , vol.280 , pp. 39337-39345
    • McClendon, A.K.1    Rodriguez, A.C.2    Osheroff, N.3
  • 24
    • 85047688890 scopus 로고    scopus 로고
    • MIB-1 and DNA topoisomerase II alpha could be helpful for predicting long-term survival of patients with glioblastoma
    • Ho D.M., Hsu C.Y., Ting L.T., and Chiang H. MIB-1 and DNA topoisomerase II alpha could be helpful for predicting long-term survival of patients with glioblastoma. Am. J. Clin. Pathol. 119 (2003) 715-722
    • (2003) Am. J. Clin. Pathol. , vol.119 , pp. 715-722
    • Ho, D.M.1    Hsu, C.Y.2    Ting, L.T.3    Chiang, H.4
  • 25
    • 0034643810 scopus 로고    scopus 로고
    • Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA
    • Redinbo M.R., Champoux J.J., and Hol W.G. Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA. Biochemistry 39 (2000) 6832-6840
    • (2000) Biochemistry , vol.39 , pp. 6832-6840
    • Redinbo, M.R.1    Champoux, J.J.2    Hol, W.G.3
  • 26
  • 27
    • 0032489634 scopus 로고    scopus 로고
    • Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA
    • Redinbo M.R., Stewart L., Kuhn P., Champoux J.J., and Hol W.G. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279 (1998) 1504-1513
    • (1998) Science , vol.279 , pp. 1504-1513
    • Redinbo, M.R.1    Stewart, L.2    Kuhn, P.3    Champoux, J.J.4    Hol, W.G.5
  • 28
    • 34247580761 scopus 로고    scopus 로고
    • Unlocking and opening a DNA gate
    • Wang J.C. Unlocking and opening a DNA gate. Proc. Natl Acad. Sci. U. S. A. 104 (2007) 4773-4774
    • (2007) Proc. Natl Acad. Sci. U. S. A. , vol.104 , pp. 4773-4774
    • Wang, J.C.1
  • 29
    • 37549023863 scopus 로고    scopus 로고
    • Structural basis for gate-DNA recognition and bending by type IIA topoisomerases
    • Dong K.C., and Berger J.M. Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature 450 (2007) 1201-1205
    • (2007) Nature , vol.450 , pp. 1201-1205
    • Dong, K.C.1    Berger, J.M.2
  • 30
    • 34547096540 scopus 로고    scopus 로고
    • DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
    • Mueller-Planitz F., and Herschlag D. DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity. Nucleic Acids Res. 35 (2007) 3764-3773
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3764-3773
    • Mueller-Planitz, F.1    Herschlag, D.2
  • 32
    • 0030589089 scopus 로고    scopus 로고
    • The hairpin structure of a topoisomerase II site DNA strand analyzed by combined NMR and energy minimization methods
    • Amir-Aslani A., Mauffret O., Sourgen F., Neplaz S., Maroun R.G., Lescot E., et al. The hairpin structure of a topoisomerase II site DNA strand analyzed by combined NMR and energy minimization methods. J. Mol. Biol. 263 (1996) 776-788
    • (1996) J. Mol. Biol. , vol.263 , pp. 776-788
    • Amir-Aslani, A.1    Mauffret, O.2    Sourgen, F.3    Neplaz, S.4    Maroun, R.G.5    Lescot, E.6
  • 35
    • 20144368711 scopus 로고    scopus 로고
    • Base pair opening in three DNA-unwinding elements
    • Coman D., and Russu I.M. Base pair opening in three DNA-unwinding elements. J. Biol. Chem. 280 (2005) 20216-20221
    • (2005) J. Biol. Chem. , vol.280 , pp. 20216-20221
    • Coman, D.1    Russu, I.M.2
  • 37
    • 33845686801 scopus 로고    scopus 로고
    • Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA
    • Bochkareva E., Martynowski D., Seitova A., and Bochkarev A. Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA. EMBO J. 25 (2006) 5961-5969
    • (2006) EMBO J. , vol.25 , pp. 5961-5969
    • Bochkareva, E.1    Martynowski, D.2    Seitova, A.3    Bochkarev, A.4
  • 38
    • 33750989070 scopus 로고    scopus 로고
    • General method of preparation of uniformly (13)C, (15)N-labeled DNA fragments for NMR analysis of DNA structures
    • René B., Masliah G., Zargarian L., Mauffret O., and Fermandjian S. General method of preparation of uniformly (13)C, (15)N-labeled DNA fragments for NMR analysis of DNA structures. J. Biomol. NMR 36 (2006) 137-146
    • (2006) J. Biomol. NMR , vol.36 , pp. 137-146
    • René, B.1    Masliah, G.2    Zargarian, L.3    Mauffret, O.4    Fermandjian, S.5
  • 39
    • 0031941596 scopus 로고    scopus 로고
    • Preparation of uniformly isotope-labeled DNA oligonucleotides for NMR spectroscopy
    • Louis J.M., Martin R.G., Clore G.M., and Gronenborn A.M. Preparation of uniformly isotope-labeled DNA oligonucleotides for NMR spectroscopy. J. Biol. Chem. 273 (1998) 2374-2378
    • (1998) J. Biol. Chem. , vol.273 , pp. 2374-2378
    • Louis, J.M.1    Martin, R.G.2    Clore, G.M.3    Gronenborn, A.M.4
  • 41
    • 0242290881 scopus 로고    scopus 로고
    • DNA basepair step deformability inferred from molecular dynamics simulations
    • Lankas F., Sponer J., Langowski J., and Cheatham III T.E. DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J. 85 (2003) 2872-2883
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankas, F.1    Sponer, J.2    Langowski, J.3    Cheatham III, T.E.4
  • 42
    • 11444267252 scopus 로고    scopus 로고
    • The relative flexibility of B-DNA and A-RNA duplexes: database analysis
    • Perez A., Noy A., Lankas F., Luque F.J., and Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Res. 32 (2004) 6144-6151
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6144-6151
    • Perez, A.1    Noy, A.2    Lankas, F.3    Luque, F.J.4    Orozco, M.5
  • 43
    • 28044444099 scopus 로고    scopus 로고
    • Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition
    • Arauzo-Bravo M.J., Fujii S., Kono H., Ahmad S., and Sarai A. Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition. J. Am. Chem. Soc. 127 (2005) 16074-16089
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 16074-16089
    • Arauzo-Bravo, M.J.1    Fujii, S.2    Kono, H.3    Ahmad, S.4    Sarai, A.5
  • 44
    • 33846895418 scopus 로고    scopus 로고
    • Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases
    • Wang Y.T., Yang W.J., Li C.L., Doudeva L.G., and Yuan H.S. Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases. Nucleic Acids Res. 35 (2007) 584-594
    • (2007) Nucleic Acids Res. , vol.35 , pp. 584-594
    • Wang, Y.T.1    Yang, W.J.2    Li, C.L.3    Doudeva, L.G.4    Yuan, H.S.5
  • 45
    • 33745471427 scopus 로고    scopus 로고
    • Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix
    • Banavali N.K., Huang N., and MacKerell Jr. A.D. Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. J. Phys. Chem. B 110 (2006) 10997-11004
    • (2006) J. Phys. Chem. B , vol.110 , pp. 10997-11004
    • Banavali, N.K.1    Huang, N.2    MacKerell Jr., A.D.3
  • 46
    • 0033928295 scopus 로고    scopus 로고
    • NMR evidence for base dynamics at all TpA steps in DNA
    • McAteer K., and Kennedy M.A. NMR evidence for base dynamics at all TpA steps in DNA. J. Biomol. Struct. Dyn. 17 (2000) 1001-1009
    • (2000) J. Biomol. Struct. Dyn. , vol.17 , pp. 1001-1009
    • McAteer, K.1    Kennedy, M.A.2
  • 47
    • 0028804849 scopus 로고
    • The effects of sequence context on base dynamics at TpA steps in DNA studied by NMR
    • McAteer K., Ellis P.D., and Kennedy M.A. The effects of sequence context on base dynamics at TpA steps in DNA studied by NMR. Nucleic Acids Res. 23 (1995) 3962-3966
    • (1995) Nucleic Acids Res. , vol.23 , pp. 3962-3966
    • McAteer, K.1    Ellis, P.D.2    Kennedy, M.A.3
  • 48
    • 34247185394 scopus 로고    scopus 로고
    • 2 + binding: role in the kissing-duplex structural transition
    • 2 + binding: role in the kissing-duplex structural transition. Nucleic Acids Res. 35 (2007) 1698-1713
    • (2007) Nucleic Acids Res. , vol.35 , pp. 1698-1713
    • Sun, X.1    Zhang, Q.2    Al Hashimi, H.M.3
  • 50
    • 25844495843 scopus 로고    scopus 로고
    • Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism
    • Djuranovic D., and Hartmann B. Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism. Biophys. J. 89 (2005) 2542-2551
    • (2005) Biophys. J. , vol.89 , pp. 2542-2551
    • Djuranovic, D.1    Hartmann, B.2
  • 52
    • 34250317372 scopus 로고    scopus 로고
    • Topoisomerase II, scaffold component, promotes chromatin compaction in vitro in a linker-histone H1-dependent manner
    • Hizume K., Araki S., Yoshikawa K., and Takeyasu K. Topoisomerase II, scaffold component, promotes chromatin compaction in vitro in a linker-histone H1-dependent manner. Nucleic Acids Res. 35 (2007) 2787-2799
    • (2007) Nucleic Acids Res. , vol.35 , pp. 2787-2799
    • Hizume, K.1    Araki, S.2    Yoshikawa, K.3    Takeyasu, K.4
  • 53
    • 27744578574 scopus 로고    scopus 로고
    • A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA
    • Coman D., and Russu I.M. A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA. Biophys. J. 89 (2005) 3285-3292
    • (2005) Biophys. J. , vol.89 , pp. 3285-3292
    • Coman, D.1    Russu, I.M.2
  • 54
    • 0033572734 scopus 로고    scopus 로고
    • An NMR and molecular modelling analysis of d(CTACTGCTTTAG). d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove
    • Leporc S., Mauffret O., Tevanian G., Lescot E., Monnot M., and Fermandjian S. An NMR and molecular modelling analysis of d(CTACTGCTTTAG). d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related to edge-to-edge contacts of their base-pairs in the major groove. Nucleic Acids Res. 27 (1999) 4759-4767
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4759-4767
    • Leporc, S.1    Mauffret, O.2    Tevanian, G.3    Lescot, E.4    Monnot, M.5    Fermandjian, S.6
  • 55
    • 32644444430 scopus 로고    scopus 로고
    • Sequence-dependent base pair opening in DNA double helix
    • Krueger A., Protozanova E., and Frank-Kamenetskii M.D. Sequence-dependent base pair opening in DNA double helix. Biophys. J. 90 (2006) 3091-3099
    • (2006) Biophys. J. , vol.90 , pp. 3091-3099
    • Krueger, A.1    Protozanova, E.2    Frank-Kamenetskii, M.D.3
  • 57
    • 0001123057 scopus 로고
    • NMR of nucleic acids: from spectrum to structure
    • Roberts G.C.K. (Ed), Oxford University Press, Oxford, UK
    • Wijmenga S.S., Mooren M.W., and Hilbers C.W. NMR of nucleic acids: from spectrum to structure. In: Roberts G.C.K. (Ed). NMR of Macromolecules: A Practical Approach (1993), Oxford University Press, Oxford, UK 217-283
    • (1993) NMR of Macromolecules: A Practical Approach , pp. 217-283
    • Wijmenga, S.S.1    Mooren, M.W.2    Hilbers, C.W.3
  • 58
    • 0004040543 scopus 로고    scopus 로고
    • University of California, San Francisco
    • Goddard T.D., and Kneller D.G. Sparky 3 (2006), University of California, San Francisco
    • (2006) Sparky 3
    • Goddard, T.D.1    Kneller, D.G.2
  • 59
    • 0000455182 scopus 로고
    • On the evaluation of interproton distances for three-dimensional structure determination by NMR using a relaxation rate matrix analysis
    • Post C.B., Meadows R.P., and Gorenstein D.G. On the evaluation of interproton distances for three-dimensional structure determination by NMR using a relaxation rate matrix analysis. J. Am. Chem. Soc. 112 (1990) 6796-6803
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6796-6803
    • Post, C.B.1    Meadows, R.P.2    Gorenstein, D.G.3
  • 60
    • 0034794444 scopus 로고    scopus 로고
    • Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions
    • Kuszewski J., Schwieters C., and Clore G.M. Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions. J. Am. Chem. Soc. 123 (2001) 3903-3918
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 3903-3918
    • Kuszewski, J.1    Schwieters, C.2    Clore, G.M.3
  • 63
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery R., and Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6 (1988) 63-91
    • (1988) J. Biomol. Struct. Dyn. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 64
    • 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 Olson W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31 (2003) 5108-5121
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2
  • 65
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
    • Cheatham III T.E., Cieplak P., and Kollman P.A. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16 (1999) 845-862
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-862
    • Cheatham III, T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 66
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids and organic molecules
    • Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., et al. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.R.4    Merz, K.M.5    Ferguson, D.M.6
  • 67
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert J.-P., Ciccotti G., and Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 68
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an N·log(N) method for Ewadl sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald: an N·log(N) method for Ewadl sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3


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