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Volumn 85, Issue 3, 2003, Pages 1787-1804

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates

Author keywords

[No Author keywords available]

Indexed keywords

CATION; DNA; DNA G; GUANINE DERIVATIVE; UNCLASSIFIED DRUG;

EID: 0042823487     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74608-6     Document Type: Article
Times cited : (117)

References (118)
  • 1
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of the entropy from covariance matrices on the atomic fluctuations
    • Andricioaei, I., and M. Karplus. 2001. On the calculation of the entropy from covariance matrices on the atomic fluctuations. J. Chem. Phys. 115:6289-6292.
    • (2001) J. Chem. Phys. , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 2
    • 0344796204 scopus 로고
    • Ion-water interaction potentials derived from free energy perturbation simulations
    • Aqvist, J. 1990. Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 94:8021-8024.
    • (1990) J. Phys. Chem. , vol.94 , pp. 8021-8024
    • Aqvist, J.1
  • 5
    • 0032719066 scopus 로고    scopus 로고
    • Porphyrins can catalyze the interconversion of DNA quadruplex structural types
    • Arthanari, H., and P. H. Bolton. 1999. Porphyrins can catalyze the interconversion of DNA quadruplex structural types. Anticancer Drug Des. 14:317-326.
    • (1999) Anticancer Drug Des. , vol.14 , pp. 317-326
    • Arthanari, H.1    Bolton, P.H.2
  • 6
    • 0034722885 scopus 로고    scopus 로고
    • Telomere maintenance mechanisms as a target for drug development
    • Bearss, D. J., L. H. Hurley, and D. D. Von Hoff. 2000. Telomere maintenance mechanisms as a target for drug development. Oncogene. 19:6632-6641.
    • (2000) Oncogene , vol.19 , pp. 6632-6641
    • Bearss, D.J.1    Hurley, L.H.2    Von Hoff, D.D.3
  • 9
    • 0034036078 scopus 로고    scopus 로고
    • Nucleic acids: Theory and computer simulation, Y2K
    • Beveridge, D. L., and K. J. McConnell. 2000. Nucleic acids: theory and computer simulation, Y2K. Cur. Op. Struct. Biol. 10:182-196.
    • (2000) Cur. Op. Struct. Biol. , vol.10 , pp. 182-196
    • Beveridge, D.L.1    McConnell, K.J.2
  • 10
    • 0032566709 scopus 로고    scopus 로고
    • A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats
    • Bouaziz, S., A. Kettani, and D. J. Patel. 1998. A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats. J. Mol. Biol. 282: 637-652.
    • (1998) J. Mol. Biol. , vol.282 , pp. 637-652
    • Bouaziz, S.1    Kettani, A.2    Patel, D.J.3
  • 11
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
    • Cheatham 3rd, T. E., P. Cieplak, and P. A. Kollman. 1999. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16:845-862.
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-862
    • Cheatham T.E. III1    Cieplak, P.2    Kollman, P.A.3
  • 12
    • 0033654654 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids
    • Cheatham 3rd, T. E., and P. A. Kollman. 2000. Molecular dynamics simulation of nucleic acids. Annu. Rev. Phys. Chem. 51: 435-471.
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 435-471
    • Cheatham T.E. III1    Kollman, P.A.2
  • 13
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids: Successes, limitations and promise
    • Cheatham 3rd, T. E., and M. A. Young. 2001. Molecular dynamics simulations of nucleic acids: Successes, limitations and promise. Biopol. (Nuc. Acid Sci.). 56:232-256.
    • (2001) Biopol. (Nuc. Acid Sci.) , vol.56 , pp. 232-256
    • Cheatham T.E. III1    Young, M.A.2
  • 14
    • 0000094135 scopus 로고    scopus 로고
    • Collective motion artifacts arising in long-duration molecular dynamics simulations
    • Chiu, S.-W., M. Clark, S. Subramaniam, and E. Jakobsson. 2000. Collective motion artifacts arising in long-duration molecular dynamics simulations. J. Comput. Chem. 21:121-131.
    • (2000) J. Comput. Chem. , vol.21 , pp. 121-131
    • Chiu, S.-W.1    Clark, M.2    Subramaniam, S.3    Jakobsson, E.4
  • 15
    • 0033805466 scopus 로고    scopus 로고
    • Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study
    • Chowdhury, S., and M. Bansal. 2000. Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: a molecular dynamics study. J. Biomol. Struct. Dyn. 18:11-28.
    • (2000) J. Biomol. Struct. Dyn. , vol.18 , pp. 11-28
    • Chowdhury, S.1    Bansal, M.2
  • 16
    • 0035833785 scopus 로고    scopus 로고
    • G-quadruplex structure can be stable with only some coordination sites being occupied by cations: A sixnanosecond molecular dynamics study
    • Chowdhury, S., and M. Bansal. 2001a. G-quadruplex structure can be stable with only some coordination sites being occupied by cations: a sixnanosecond molecular dynamics study. J. Phys. Chem. B. 105:7572-7578.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 7572-7578
    • Chowdhury, S.1    Bansal, M.2
  • 17
    • 0035028460 scopus 로고    scopus 로고
    • A nanosecond molecular dynamics study of antiparallel d(G)(7) quadruplex structures: Effect of the coordinated cations
    • Chowdhury, S., and M. Bansal. 2001b. A nanosecond molecular dynamics study of antiparallel d(G)(7) quadruplex structures: effect of the coordinated cations. J. Biomol. Struct. Dyn. 18:647-669.
    • (2001) J. Biomol. Struct. Dyn. , vol.18 , pp. 647-669
    • Chowdhury, S.1    Bansal, M.2
  • 20
    • 0035814387 scopus 로고    scopus 로고
    • Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes
    • Cubero, E., F. J. Luque, and M. Orozco. 2001. Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes. J. Am. Chem. Soc. 123:12018-12025.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 12018-12025
    • Cubero, E.1    Luque, F.J.2    Orozco, M.3
  • 22
    • 0027220845 scopus 로고
    • The β-subunit of Oxytricha telomere-binding protein promotes G-quartet formation by telomeric DNA
    • Fang, G., and T. R. Cech. 1993. The β-subunit of Oxytricha telomere-binding protein promotes G-quartet formation by telomeric DNA. Cell. 74:875-885.
    • (1993) Cell , vol.74 , pp. 875-885
    • Fang, G.1    Cech, T.R.2
  • 23
    • 0031808069 scopus 로고    scopus 로고
    • Structural equilibrium of DNA represented with different force fields
    • Feig, M., and B. M. Pettitt. 1998. Structural equilibrium of DNA represented with different force fields. Biophys. J. 75:134-149.
    • (1998) Biophys. J. , vol.75 , pp. 134-149
    • Feig, M.1    Pettitt, B.M.2
  • 26
    • 0031008575 scopus 로고    scopus 로고
    • On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
    • Froloff, N., A. Windemuth, and B. Honig. 1997. On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions. Protein Sci. 6:1293-1301.
    • (1997) Protein Sci. , vol.6 , pp. 1293-1301
    • Froloff, N.1    Windemuth, A.2    Honig, B.3
  • 28
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • Gilson, M. K., J. A. Given, B. L. Bush, and J. A. McCammon. 1997. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 72:1047-1069.
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 29
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson, M. K., K. A. Sharp, and B. H. Honig. 1987. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 9:327-335.
    • (1987) J. Comput. Chem. , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.H.3
  • 30
    • 0034251465 scopus 로고    scopus 로고
    • Structures and properties of the planar G-C-G-C tetrads: Ab initio HF and DFT studies
    • Gu, J. D., and J. Leszczynski. 2000. Structures and properties of the planar G-C-G-C tetrads: Ab initio HF and DFT studies. J. Phys. Chem. A. 104:7353-7358.
    • (2000) J. Phys. Chem. A , vol.104 , pp. 7353-7358
    • Gu, J.D.1    Leszczynski, J.2
  • 32
    • 0036290781 scopus 로고    scopus 로고
    • Crystal structure of the potassium form of an Oxytricha nova G-quadruplex
    • Haider, S., G. N. Parkinson, and S. Neidle. 2002. Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. J. Mol. Biol. 320:189-200.
    • (2002) J. Mol. Biol. , vol.320 , pp. 189-200
    • Haider, S.1    Parkinson, G.N.2    Neidle, S.3
  • 33
    • 0027503236 scopus 로고
    • The human insulin gene-linked polymorphic region adopts a G-quartet structure in chromatin assembled in vitro
    • Hammond-Kosack, M. C., M. W. Kilpatrick, and K. Docherty. 1993. The human insulin gene-linked polymorphic region adopts a G-quartet structure in chromatin assembled in vitro. J. Mol. Endo. 10:121-126.
    • (1993) J. Mol. Endo. , vol.10 , pp. 121-126
    • Hammond-Kosack, M.C.1    Kilpatrick, M.W.2    Docherty, K.3
  • 34
    • 0039129145 scopus 로고    scopus 로고
    • Accelerated assembly of G-quadruplex structures by a small molecule
    • Han, H. Y., C. L. Cliff, and L. H. Hurley. 1999. Accelerated assembly of G-quadruplex structures by a small molecule. Biochemistry. 38:6981-6986.
    • (1999) Biochemistry , vol.38 , pp. 6981-6986
    • Han, H.Y.1    Cliff, C.L.2    Hurley, L.H.3
  • 35
    • 0034176194 scopus 로고    scopus 로고
    • G-quadruplex DNA: A potential target for anti-cancer drug design
    • Han, H. Y., and L. H. Hurley. 2000. G-quadruplex DNA: a potential target for anti-cancer drug design. Trends Pharmacol. Sci. 21:136-142.
    • (2000) Trends Pharmacol. Sci. , vol.21 , pp. 136-142
    • Han, H.Y.1    Hurley, L.H.2
  • 36
    • 0035913742 scopus 로고    scopus 로고
    • Selective interactions of cationic porphyrins with G-quadruplex structures
    • Han, H. Y., D. R. Langley, A. Rangan, and L. H. Hurley. 2001. Selective interactions of cationic porphyrins with G-quadruplex structures. J. Am. Chem. Soc. 123:8902-8913.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 8902-8913
    • Han, H.Y.1    Langley, D.R.2    Rangan, A.3    Hurley, L.H.4
  • 37
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson, T., J. Marelius, and J. Aqvist. 1998. Ligand binding affinity prediction by linear interaction energy methods. J. Comp.-Aided Mol. Des. 12:27-35.
    • (1998) J. Comp.-Aided Mol. Des. , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Aqvist, J.3
  • 38
    • 0030687511 scopus 로고    scopus 로고
    • Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: Thermodynamic evidence for three linked association pathways
    • Hardin, C. C., M. J. Corregan, D. V. Lieberman, and B. A. Brown 2nd. 1997. Allosteric interactions between DNA strands and monovalent cations in DNA quadruplex assembly: thermodynamic evidence for three linked association pathways. Biochemistry, 36:15428-15450.
    • (1997) Biochemistry , vol.36 , pp. 15428-15450
    • Hardin, C.C.1    Corregan, M.J.2    Lieberman, D.V.3    Brown B.A. II4
  • 39
    • 0025896273 scopus 로고
    • Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates
    • Hardin, C. C., E. Henderson, T. Watson, and J. K. Prosser. 1991. Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates. Biochemistry. 30:4460-4472.
    • (1991) Biochemistry , vol.30 , pp. 4460-4472
    • Hardin, C.C.1    Henderson, E.2    Watson, T.3    Prosser, J.K.4
  • 40
    • 0001505226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids
    • Hardin, C. C., A. G. Perry, and K. White. 2000. Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids. Biopolymers. 56:147-194.
    • (2000) Biopolymers , vol.56 , pp. 147-194
    • Hardin, C.C.1    Perry, A.G.2    White, K.3
  • 42
    • 0001430231 scopus 로고    scopus 로고
    • The flying ice cube: Velocity rescaling in molecular dynamics simulations leads to violation of equipartition
    • Harvey, S. C., R. K.-Z. Tan, and T. E. Cheatham 3rd. 1998. The flying ice cube: velocity rescaling in molecular dynamics simulations leads to violation of equipartition. J. Comput. Chem. 19:726-740.
    • (1998) J. Comput. Chem. , vol.19 , pp. 726-740
    • Harvey, S.C.1    Tan, R.K.-Z.2    Cheatham T.E. III3
  • 43
    • 0023663911 scopus 로고
    • Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs
    • Henderson, E., C. C. Hardin, S. K. Walk, I. J. Tinoco, and E. H. Blackburn. 1987. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell. 51:899-908.
    • (1987) Cell , vol.51 , pp. 899-908
    • Henderson, E.1    Hardin, C.C.2    Walk, S.K.3    Tinoco, I.J.4    Blackburn, E.H.5
  • 44
    • 0030887944 scopus 로고    scopus 로고
    • Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
    • Hermans, J., and L. Wang. 1997. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme. J. Am. Chem. Soc. 119:2707-2714.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 2707-2714
    • Hermans, J.1    Wang, L.2
  • 45
    • 0343213055 scopus 로고    scopus 로고
    • Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results
    • Hobza, P., M. Kabelac, J. Sponer, P. Mejzlik, and J. Vondrasek. 1997. Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: comparison with nonempirical beyond Hartree-Fock results. J. Comput. Chem. 18:1136-1150.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1136-1150
    • Hobza, P.1    Kabelac, M.2    Sponer, J.3    Mejzlik, P.4    Vondrasek, J.5
  • 46
    • 0000965687 scopus 로고    scopus 로고
    • Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
    • Hobza, P., and J. Sponer. 1999. Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem. Rev. 99:3247-3276.
    • (1999) Chem. Rev. , vol.99 , pp. 3247-3276
    • Hobza, P.1    Sponer, J.2
  • 47
    • 0035816210 scopus 로고    scopus 로고
    • DNA G-quartets in a 1.86 Å resolution structure of an Oxytricha nova telomeric protein-DNA complex
    • Horvath, M. P., and S. C. Schultz. 2001. DNA G-quartets in a 1.86 Å resolution structure of an Oxytricha nova telomeric protein-DNA complex. J. Mol. Biol. 310:367-377.
    • (2001) J. Mol. Biol. , vol.310 , pp. 367-377
    • Horvath, M.P.1    Schultz, S.C.2
  • 48
    • 0033534681 scopus 로고    scopus 로고
    • Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex
    • Hud, N. V., P. Schultze, V. Sklenar, and J. Feigon. 1999. Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex. J. Mol. Biol. 285:233-243.
    • (1999) J. Mol. Biol. , vol.285 , pp. 233-243
    • Hud, N.V.1    Schultze, P.2    Sklenar, V.3    Feigon, J.4
  • 49
    • 0029908928 scopus 로고    scopus 로고
    • The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: A thermodynamic analysis by IH NMR
    • Hud, N. V., F. W. Smith, F. A. L. Anet, and J. Feigon. 1996. The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by IH NMR. Biochemistry. 35:15383-15390.
    • (1996) Biochemistry , vol.35 , pp. 15383-15390
    • Hud, N.V.1    Smith, F.W.2    Anet, F.A.L.3    Feigon, J.4
  • 50
  • 54
    • 0032556243 scopus 로고    scopus 로고
    • Free energy analysis of the confonnational preferences of A and B forms of DNA in solution
    • Jayaram, B., D. Sprous, M. A. Young, and D. L. Beveridge. 1998. Free energy analysis of the confonnational preferences of A and B forms of DNA in solution. J. Am. Chem. Soc. 120:10629-10633.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 10629-10633
    • Jayaram, B.1    Sprous, D.2    Young, M.A.3    Beveridge, D.L.4
  • 56
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus, M., and J. N. Kushick. 1981. Method for estimating the configurational entropy of macromolecules. Macromol. 14:325-332.
    • (1981) Macromol. , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 57
    • 0032566629 scopus 로고    scopus 로고
    • Solution structure of a Na cation stabilized DNA quadruplex containing G-G-G-G and G-C-G-C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA
    • Kettani, A., S. Bouaziz, A. Gorin, H. Zhao, R. A. Jones, and D. J. Patel. 1998. Solution structure of a Na cation stabilized DNA quadruplex containing G-G-G-G and G-C-G-C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA. J. Mol. Biol. 282:619-636.
    • (1998) J. Mol. Biol. , vol.282 , pp. 619-636
    • Kettani, A.1    Bouaziz, S.2    Gorin, A.3    Zhao, H.4    Jones, R.A.5    Patel, D.J.6
  • 59
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., M. Billeter, and K. Wuthrich. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14: 51-55, 29-32.
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 61
    • 0034866080 scopus 로고    scopus 로고
    • Structures and properties of multistranded nucleic acids
    • Lane, A. N., and T. C. Jenkins. 2001. Structures and properties of multistranded nucleic acids. Current Organic Chemistry. 5:845-869.
    • (2001) Current Organic Chemistry , vol.5 , pp. 845-869
    • Lane, A.N.1    Jenkins, T.C.2
  • 63
    • 0036568354 scopus 로고    scopus 로고
    • Contributions to the binding free energy of ligands to avidin and streptavidin
    • Lazaridis, T., A. Masunov, and F. Gandolfo. 2002. Contributions to the binding free energy of ligands to avidin and streptavidin. Proteins. 47:194-208.
    • (2002) Proteins , vol.47 , pp. 194-208
    • Lazaridis, T.1    Masunov, A.2    Gandolfo, F.3
  • 64
    • 0034728563 scopus 로고    scopus 로고
    • Synthetic adenine receptors: Direct calculation of binding affinity and entropy
    • Luo, R., and M. K. Gilson. 2000. Synthetic adenine receptors: direct calculation of binding affinity and entropy. J. Am. Chem. Soc. 122:2934-2937.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2934-2937
    • Luo, R.1    Gilson, M.K.2
  • 65
    • 0027467617 scopus 로고
    • Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution
    • Macaya, R. F., P. Schulze, F. W. Smith, J. A. Roe, and J. Feigon. 1993. Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc. Natl. Acad. Sci. USA. 90:3745-3749.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 3745-3749
    • Macaya, R.F.1    Schulze, P.2    Smith, F.W.3    Roe, J.A.4    Feigon, J.5
  • 66
    • 0028133296 scopus 로고
    • A simple empirical model describing the thermodynamics of hydration of ions of widely varying charges, sizes, and shapes
    • Marcus, Y. 1994. A simple empirical model describing the thermodynamics of hydration of ions of widely varying charges, sizes, and shapes. Biophys. Chem. 51:111-127.
    • (1994) Biophys. Chem. , vol.51 , pp. 111-127
    • Marcus, Y.1
  • 67
    • 0002496235 scopus 로고    scopus 로고
    • Calculation of ligand binding free energies from molecular dynamics simulations
    • Marelius, J., T, Hansson, and J. Aqvist. 1998. Calculation of ligand binding free energies from molecular dynamics simulations. Int. J. Quant. Chem. 69:77-88.
    • (1998) Int. J. Quant. Chem. , vol.69 , pp. 77-88
    • Marelius, J.1    Hansson, T.2    Aqvist, J.3
  • 71
    • 0035818135 scopus 로고    scopus 로고
    • Are guanine tetrads stabilized by bifurcated hydrogen bonds?
    • Meyer, M., M. Brandl, and J. Suhnel. 2001a. Are guanine tetrads stabilized by bifurcated hydrogen bonds? J. Phys. Chem. A. 105:8223-8225.
    • (2001) J. Phys. Chem. A , vol.105 , pp. 8223-8225
    • Meyer, M.1    Brandl, M.2    Suhnel, J.3
  • 72
    • 0345893810 scopus 로고    scopus 로고
    • Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes
    • Meyer, M., T. Steinke, M. Brandl, and J. Suhnel. 2001b. Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. J. Comput. Chem. 22:109-124.
    • (2001) J. Comput. Chem. , vol.22 , pp. 109-124
    • Meyer, M.1    Steinke, T.2    Brandl, M.3    Suhnel, J.4
  • 73
    • 0030032805 scopus 로고    scopus 로고
    • The electrostatic contribution to the B to Z transition of DNA
    • Misra, V. K., and B. Honig. 1996. The electrostatic contribution to the B to Z transition of DNA. Biochemistry. 35:1115-1124.
    • (1996) Biochemistry , vol.35 , pp. 1115-1124
    • Misra, V.K.1    Honig, B.2
  • 74
    • 0028246710 scopus 로고
    • Salt effects on ligand-DNA binding. Minor groove binding antibiotics
    • Misra, V. K., K. A. Sharp, R. A. Friedman, and B. Honig. 1994. Salt effects on ligand-DNA binding. Minor groove binding antibiotics. J. Mol. Biol. 238:245-263.
    • (1994) J. Mol. Biol. , vol.238 , pp. 245-263
    • Misra, V.K.1    Sharp, K.A.2    Friedman, R.A.3    Honig, B.4
  • 75
    • 0028860737 scopus 로고
    • The fragile X syndrome single strand d(CGG)n nucleotide repeats readily fold back to form unimolecular hairpin structures
    • Nadel, Y., P. Weisman-Shomer, and M. Fry. 1995. The fragile X syndrome single strand d(CGG)n nucleotide repeats readily fold back to form unimolecular hairpin structures. J. Biol. Chem. 270:28970-28977.
    • (1995) J. Biol. Chem. , vol.270 , pp. 28970-28977
    • Nadel, Y.1    Weisman-Shomer, P.2    Fry, M.3
  • 76
    • 0034018083 scopus 로고    scopus 로고
    • Structure-activity relationships among guanine-quadruplex telomerase inhibitors
    • Neidle, S., R. J. Harrison, A. P. Reszka, and M. A. Read. 2000. Structure-activity relationships among guanine-quadruplex telomerase inhibitors. Pharmacol. Ther. 85:133-139.
    • (2000) Pharmacol. Ther. , vol.85 , pp. 133-139
    • Neidle, S.1    Harrison, R.J.2    Reszka, A.P.3    Read, M.A.4
  • 77
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls, A., and B. Honig. 1991. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem. 12:435-445.
    • (1991) J. Comput. Chem. , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 78
    • 0015101706 scopus 로고
    • Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect
    • Page, M. I., and W. P. Jencks. 1971. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. Proc. Natl. Acad. Sci. USA. 68:1678-1683.
    • (1971) Proc. Natl. Acad. Sci. USA , vol.68 , pp. 1678-1683
    • Page, M.I.1    Jencks, W.P.2
  • 79
    • 0037142071 scopus 로고    scopus 로고
    • Crystal structure of parallel quadruplexes from human telomeric DNA
    • Parkinson, G. N., M. P. Lee, and S. Neidle. 2002. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature. 417:876-880.
    • (2002) Nature , vol.417 , pp. 876-880
    • Parkinson, G.N.1    Lee, M.P.2    Neidle, S.3
  • 80
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules
    • Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules. Comp. Phys. Commun. 91: 141.
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 141
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 81
    • 0031576353 scopus 로고    scopus 로고
    • The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution
    • Phillips, K., Z. Dauter, A. I. H. Murchie, D. M. J. Lilley, and B. Luisi. 1997. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution. J. Mol. Biol. 273:171-182.
    • (1997) J. Mol. Biol. , vol.273 , pp. 171-182
    • Phillips, K.1    Dauter, Z.2    Murchie, A.I.H.3    Lilley, D.M.J.4    Luisi, B.5
  • 83
    • 0033524027 scopus 로고    scopus 로고
    • Molecular modeling studies on G-quadruplex complexes of telomerase inhibitors: Structure-activity relationships
    • Read, M. A., A. A. Wood, J. R. Harrison, S. M. Gowan, L. R. Kelland, H. S. Dosanjh, and S. Neidle. 1999. Molecular modeling studies on G-quadruplex complexes of telomerase inhibitors: structure-activity relationships. J. Med. Chem. 42:4538-4546.
    • (1999) J. Med. Chem. , vol.42 , pp. 4538-4546
    • Read, M.A.1    Wood, A.A.2    Harrison, J.R.3    Gowan, S.M.4    Kelland, L.R.5    Dosanjh, H.S.6    Neidle, S.7
  • 84
    • 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
  • 86
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner, M. F., A. J. Olson, and J,-C. Spehner. 1996. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 38:305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.-C.3
  • 87
    • 0034323089 scopus 로고    scopus 로고
    • Absolute entropies from molecular dynamics simulation trajectories
    • Schafer, H., A. E. Mark, and W. F. van Gunsteren. 2000. Absolute entropies from molecular dynamics simulation trajectories. J. Chem. Phys. 113:7809-7817.
    • (2000) J. Chem. Phys. , vol.113 , pp. 7809-7817
    • Schafer, H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 88
    • 0035902465 scopus 로고    scopus 로고
    • In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei
    • Schaffitzel, C., I. Berger, J. Postberg, J. Hanes, H. J. Lipps, and A. Pluckthun. 2001. In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl. Acad. Sci. USA. 98:8572-8577.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 8572-8577
    • Schaffitzel, C.1    Berger, I.2    Postberg, J.3    Hanes, J.4    Lipps, H.J.5    Pluckthun, A.6
  • 89
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • Schlitter, J. 1993. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem. Phys. Lett. 215: 617-621.
    • (1993) Chem. Phys. Lett. , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 90
    • 0036722785 scopus 로고    scopus 로고
    • Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
    • Schwarzl, S. M., T. B. Tschopp, J. C. Smith, and S. Fischer. 2002. Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J. Comput. Chem. 23:1143-1149.
    • (2002) J. Comput. Chem. , vol.23 , pp. 1143-1149
    • Schwarzl, S.M.1    Tschopp, T.B.2    Smith, J.C.3    Fischer, S.4
  • 91
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and applications
    • Sharp, K. A., and B. Honig. 1990. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301-332.
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301-332
    • Sharp, K.A.1    Honig, B.2
  • 92
    • 0030873459 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the d(TAT) triplex helix
    • Shields, G. C., C. A. Laughton, and M. Orozco. 1997. Molecular dynamics simulations of the d(TAT) triplex helix. J. Am. Chem. Soc. 119:7463-7469.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 7463-7469
    • Shields, G.C.1    Laughton, C.A.2    Orozco, M.3
  • 93
    • 0031749571 scopus 로고    scopus 로고
    • Molecular dynamics simulation of a PNA-DNA-PNA triple helix in aqueous solution
    • Shields, G. C., C. A. Laughton, and M. Orozco. 1998. Molecular dynamics simulation of a PNA-DNA-PNA triple helix in aqueous solution. J. Am. Chem. Soc. 120:5895-5904.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 5895-5904
    • Shields, G.C.1    Laughton, C.A.2    Orozco, M.3
  • 94
    • 0032030327 scopus 로고    scopus 로고
    • DNA tetraplex formation in the control region of c-myc
    • Simonsson, T., P. Pecinka, and M. Kubista. 1998. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 26:1167-1172.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1167-1172
    • Simonsson, T.1    Pecinka, P.2    Kubista, M.3
  • 95
    • 0026554887 scopus 로고
    • Quadruplex structure of Oxytricha telomeric DNA oligonucleotides
    • Smith, F. W., and J. Feigon. 1992. Quadruplex structure of Oxytricha telomeric DNA oligonucleotides. Nature. 356:164-168.
    • (1992) Nature , vol.356 , pp. 164-168
    • Smith, F.W.1    Feigon, J.2
  • 96
    • 0027240171 scopus 로고
    • Strand orientation in the DNA quadruplex formed from the Oxytricha telomere repeat nucleotide d(G4T4G4-quadruplex) in solution
    • Smith, F. W., and J. Feigon. 1993. Strand orientation in the DNA quadruplex formed from the Oxytricha telomere repeat nucleotide d(G4T4G4-quadruplex) in solution. Biochemistry. 32:8682-8692.
    • (1993) Biochemistry , vol.32 , pp. 8682-8692
    • Smith, F.W.1    Feigon, J.2
  • 97
    • 0031749572 scopus 로고    scopus 로고
    • Molecular dynamics of a hemiprotonated intercalated four-stranded i-DNA: Stable trajectories on a nanosecond time scale
    • Spackova, N., I. Berger, M. Egli, and J. Sponer. 1998. Molecular dynamics of a hemiprotonated intercalated four-stranded i-DNA: Stable trajectories on a nanosecond time scale. J. Am. Chem. Soc. 120:6147-6151.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 6147-6151
    • Spackova, N.1    Berger, I.2    Egli, M.3    Sponer, J.4
  • 98
    • 0040164390 scopus 로고    scopus 로고
    • Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules
    • Spackova, N., I. Berger, and J. Sponer. 1999. Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. J. Am. Chem. Soc. 121:5519-5534.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 5519-5534
    • Spackova, N.1    Berger, I.2    Sponer, J.3
  • 99
    • 0034625886 scopus 로고    scopus 로고
    • Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G-A mismatch pairs
    • Spackova, N., I. Berger, and J. Sponer. 2000. Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G-A mismatch pairs. J. Am. Chem. Soc. 122:7564-7572.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 7564-7572
    • Spackova, N.1    Berger, I.2    Sponer, J.3
  • 100
    • 0034836422 scopus 로고    scopus 로고
    • Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
    • Spackova, N., I. Berger, and J. Sponer. 2001. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. J. Am. Chem. Soc. 123:3295-3307.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 3295-3307
    • Spackova, N.1    Berger, I.2    Sponer, J.3
  • 101
    • 0037442584 scopus 로고    scopus 로고
    • Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. I. Minor groove binding between 4·,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution
    • Spackova, N., T. E. Cheatham 3rd, F. Ryjacek, F. Lankas, L. van Meervelt, P. Hobza, and J. Sponer. 2003. Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. I. Minor groove binding between 4·,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution. J. Am. Chem. Soc. 125:1759-1769.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1759-1769
    • Spackova, N.1    Cheatham T.E. III2    Ryjacek, F.3    Lankas, F.4    Van Meervelt, L.5    Hobza, P.6    Sponer, J.7
  • 103
    • 0028589540 scopus 로고
    • G-C base pair in parallel-stranded DNA - A novel type of base pairing: An ab initio quantum chemical study
    • Sponer, J., and P. Hobza. 1994. G-C base pair in parallel-stranded DNA - a novel type of base pairing: an ab initio quantum chemical study. J. Biomol. Struct. Dyn. 12:671-680.
    • (1994) J. Biomol. Struct. Dyn. , vol.12 , pp. 671-680
    • Sponer, J.1    Hobza, P.2
  • 104
    • 0011824888 scopus 로고    scopus 로고
    • Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation
    • Sponer, J., J. Leszczynski, and P. Hobza. 1996. Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. J. Phys. Chem. 100:1965-1974.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1965-1974
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 105
    • 0000115258 scopus 로고    scopus 로고
    • Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture: Theoretical considerations of the A ⇔ B transition
    • Sprous, D., M. A. Young, and D. L. Beveridge. 1998. Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture: theoretical considerations of the A ⇔ B transition. J. Phys. Chem. B. 102:4658-4667.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 4658-4667
    • Sprous, D.1    Young, M.A.2    Beveridge, D.L.3
  • 106
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA and phosphoramidate helices
    • Srinivasan, J., T. E. Cheatham 3rd, P. Cieplak, P. A. Kollman, and D. A. Case. 1998. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate helices. J. Am. Chem. Soc. 120:9401-9409.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham T.E. III2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 107
    • 0035134733 scopus 로고    scopus 로고
    • Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thio-guanine, and 6-thiopurine
    • Stefl, R., N. Spackova, I. Berger, J. Koca, and J. Sponer. 2001a. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thio-guanine, and 6-thiopurine. Biophys. J. 80:455-468.
    • (2001) Biophys. J. , vol.80 , pp. 455-468
    • Stefl, R.1    Spackova, N.2    Berger, I.3    Koca, J.4    Sponer, J.5
  • 108
  • 109
    • 0031823992 scopus 로고    scopus 로고
    • 2 quadruplex via particle mesh Ewald molecular dynamics simulations
    • 2 quadruplex via particle mesh Ewald molecular dynamics simulations. Biophys. J. 75: 968-981.
    • (1998) Biophys. J. , vol.75 , pp. 968-981
    • Strahan, G.D.1    Keniry, M.A.2    Shafer, R.H.3
  • 110
    • 0034885641 scopus 로고    scopus 로고
    • Targeting telomeres and telomerase
    • Sun, D., and L. H. Hurley. 2001. Targeting telomeres and telomerase. Methods Enzymol. 340:573-592.
    • (2001) Methods Enzymol. , vol.340 , pp. 573-592
    • Sun, D.1    Hurley, L.H.2
  • 111
    • 0028360307 scopus 로고
    • The contribution of vibrational entropy to molecular association
    • Tidor, B., and M. Karplus. 1994. The contribution of vibrational entropy to molecular association. J. Mol. Biol. 238:405-414.
    • (1994) J. Mol. Biol. , vol.238 , pp. 405-414
    • Tidor, B.1    Karplus, M.2
  • 112
    • 0034615785 scopus 로고    scopus 로고
    • An A-type double helix of DNA having B-type puckering of the deoxyribose rings
    • Trantirek, L., R. Stefl, M. Vorlickova, J. Koca, V. Sklenar, and J. Kypr. 2000. An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J. Mol. Biol. 297:907-922.
    • (2000) J. Mol. Biol. , vol.297 , pp. 907-922
    • Trantirek, L.1    Stefl, R.2    Vorlickova, M.3    Koca, J.4    Sklenar, V.5    Kypr, J.6
  • 113
    • 0035892161 scopus 로고    scopus 로고
    • Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics
    • Tsui, V., and D. A. Case. 2001. Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics. J. Phys. Chem. B. 105: 11314-11325.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 11314-11325
    • Tsui, V.1    Case, D.A.2
  • 114
    • 0033746537 scopus 로고    scopus 로고
    • The chemical meaning of the standard free energy of transfer: Use of van der Waals' equation of state to unravel the interplay between free volume, volume entropy, and the role of standard states
    • Vitha, M. F., and P. W. Carr. 2000. The chemical meaning of the standard free energy of transfer: use of van der Waals' equation of state to unravel the interplay between free volume, volume entropy, and the role of standard states. J. Phys. Chem. B. 104:5343-5349.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 5343-5349
    • Vitha, M.F.1    Carr, P.W.2
  • 115
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • Vorobjev, Y. N., J. C. Almagro, and J. Hermans. 1998. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins. 32:399-413.
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 117
    • 0027918585 scopus 로고
    • Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex
    • Wang, Y., and D. J. Patel. 1993. Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure. 1:263-282.
    • (1993) Structure , vol.1 , pp. 263-282
    • Wang, Y.1    Patel, D.J.2
  • 118
    • 0034870959 scopus 로고    scopus 로고
    • Contribution of translational and rotational motions to molecular association in aqueous solution
    • Yu, Y. B., P. L. Privalov, and R. S. Hodges. 2001. Contribution of translational and rotational motions to molecular association in aqueous solution. Biophys. J. 81:1632-1642.
    • (2001) Biophys. J. , vol.81 , pp. 1632-1642
    • Yu, Y.B.1    Privalov, P.L.2    Hodges, R.S.3


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