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Volumn 8, Issue 1, 2012, Pages 348-362

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium

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EID: 84855661433     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct200723y     Document Type: Article
Times cited : (393)

References (81)
  • 1
    • 4444351490 scopus 로고    scopus 로고
    • Empirical Force Fields for Biological Macromolecules: Overview and Issues
    • MacKerell, A. D., Jr. Empirical Force Fields for Biological Macromolecules: Overview and Issues J. Comput. Chem. 2004, 25, 1584-1604
    • (2004) J. Comput. Chem. , vol.25 , pp. 1584-1604
    • MacKerell, Jr.A.D.1
  • 2
    • 42149084972 scopus 로고    scopus 로고
    • Recent advances in the study of nucleic acid flexibility by molecular dynamics
    • Orozco, M.; Noy, A.; Pérez, A. Recent advances in the study of nucleic acid flexibility by molecular dynamics Curr. Opin. Struct. Biol. 2008, 18, 185-193
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 185-193
    • Orozco, M.1    Noy, A.2    Pérez, A.3
  • 3
  • 4
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe, N.; MacKerell, A. D., Jr. All-atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 2000, 21, 86-104
    • (2000) J. Comput. Chem. , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell, Jr.A.D.2
  • 6
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
    • Cheatham, T. E., III; Cieplak, P.; 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. 1999, 16, 845-861
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-861
    • Cheatham Iii, T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 7
    • 0032459726 scopus 로고    scopus 로고
    • Molecular dynamic simulations of environment and sequence dependent DNA conformations: The development of the BMS nucleic acid force field and comparison with experimental results
    • Langley, D. R. Molecular dynamics simulations of environment and sequence dependent DNA conformation: The development of the BMS nucleic acid force field and comparison with experimental results J. Biomol. Struct. Dyn. 1998, 16, 487-509 (Pubitemid 29100308)
    • (1998) Journal of Biomolecular Structure and Dynamics , vol.16 , Issue.3 , pp. 487-509
    • Langley, D.R.1
  • 11
    • 19944414979 scopus 로고    scopus 로고
    • Toward a full characterization of nucleic acid components in aqueous solution: Simulations of nucleosides
    • DOI 10.1021/jp044513u
    • Foloppe, N.; Nilsson, L. Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides J. Phys. Chem. B 2005, 109, 9119-9131 (Pubitemid 40750949)
    • (2005) Journal of Physical Chemistry B , vol.109 , Issue.18 , pp. 9119-9131
    • Foloppe, N.1    Nilsson, L.2
  • 13
    • 51249090299 scopus 로고    scopus 로고
    • Importance of accurate DNA structures in solution: The Jun-Fos model
    • Heddi, B.; Foloppe, N.; Oguey, C.; Hartmann, B. Importance of accurate DNA structures in solution: the Jun-Fos model J. Mol. Biol. 2008, 382, 956-970
    • (2008) J. Mol. Biol. , vol.382 , pp. 956-970
    • Heddi, B.1    Foloppe, N.2    Oguey, C.3    Hartmann, B.4
  • 14
    • 0347087230 scopus 로고    scopus 로고
    • Insight into G-T Mismatch Recognition Using Molecular Dynamics with Time-Averaged Restraints Derived from NMR Spectroscopy
    • DOI 10.1021/ja037333r
    • Isaacs, R. J.; Spielmann, H. P. Insight into G-T mismatch recognition using molecular dynamics with time-averaged restraints derived from NMR spectroscopy J. Am. Chem. Soc. 2004, 126, 583-590 (Pubitemid 38084639)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.2 , pp. 583-590
    • Isaacs, R.J.1    Spielmann, H.P.2
  • 15
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
    • DOI 10.1529/biophysj.106.097782
    • Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, I.; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of alpha/gamma Conformers Biophys. J. 2007, 92, 3817-3829 (Pubitemid 46910569)
    • (2007) Biophysical Journal , vol.92 , Issue.11 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham III, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 16
    • 49449085241 scopus 로고    scopus 로고
    • Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
    • Joung, I. S.; Cheatham, T. E., 3rd. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations J Phys Chem B 2008, 112, 9020-9041
    • (2008) J Phys Chem B , vol.112 , pp. 9020-9041
    • Joung, I.S.1    Cheatham III, T.E.2
  • 17
    • 77952368283 scopus 로고    scopus 로고
    • Reparameterization of RNA ζ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine
    • Yildirim, I.; Stern, H. A.; Kennedy, S. D.; Tubbs, J. D.; Turner, D. H. Reparameterization of RNA ζ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine J. Chem. Theory Comput. 2010, 6, 1520-1531
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1520-1531
    • Yildirim, I.1    Stern, H.A.2    Kennedy, S.D.3    Tubbs, J.D.4    Turner, D.H.5
  • 19
    • 80052820313 scopus 로고    scopus 로고
    • Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
    • Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T. E., 3rd.; Jurecka, P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles J. Chem. Theory Comput. 2011, 7, 2886-2902
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2886-2902
    • Zgarbova, M.1    Otyepka, M.2    Sponer, J.3    Mladek, A.4    Banas, P.5    Cheatham III, T.E.6    Jurecka, P.7
  • 20
    • 33746074088 scopus 로고    scopus 로고
    • Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition
    • DOI 10.1021/ja061686j
    • Heddi, B.; Foloppe, N.; Bouchemal, N.; Hantz, E.; Hartmann, B. Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition J. Am. Chem. Soc. 2006, 128, 9170-9177 (Pubitemid 44078998)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.28 , pp. 9170-9177
    • Heddi, B.1    Foloppe, N.2    Bouchemal, N.3    Hantz, E.4    Hartmann, B.5
  • 21
    • 52249100539 scopus 로고    scopus 로고
    • Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study
    • Hart, K.; Nilsson, L. Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study Proteins: Struct., Funct., Bioinf. 2008, 73, 325-337
    • (2008) Proteins: Struct., Funct., Bioinf. , vol.73 , pp. 325-337
    • Hart, K.1    Nilsson, L.2
  • 22
    • 0020359857 scopus 로고
    • Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATT(Br)CGCG
    • Fratini, A. V.; Kopka, M. L.; Drew, H. R.; Dickerson, R. E. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG J. Biol. Chem. 1982, 257, 14686-14707 (Pubitemid 13159563)
    • (1982) Journal of Biological Chemistry , vol.257 , Issue.24 , pp. 14686-14707
    • Fratini, A.V.1    Kopka, M.L.2    Drew, H.R.3    Dickerson, R.E.4
  • 26
    • 78650840757 scopus 로고    scopus 로고
    • Understanding the Sequence-Dependence of DNA Groove Dimensions: Implications for DNA Interactions
    • Oguey, C.; Foloppe, N.; Hartmann, B. Understanding the Sequence-Dependence of DNA Groove Dimensions: Implications for DNA Interactions PLoS ONE 2010, 5, e15931
    • (2010) PLoS ONE , vol.5 , pp. 15931
    • Oguey, C.1    Foloppe, N.2    Hartmann, B.3
  • 27
    • 0038118496 scopus 로고    scopus 로고
    • Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: Evidence for sub-states
    • Djuranovic, D.; Hartmann, B. Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states J. Biomol. Struct. Dyn. 2003, 20, 771-788 (Pubitemid 36706123)
    • (2003) Journal of Biomolecular Structure and Dynamics , vol.20 , Issue.6 , pp. 771-788
    • Djuranovic, D.1    Hartmann, B.2
  • 28
    • 0036835785 scopus 로고    scopus 로고
    • Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
    • Lamoureux, J. S.; Stuart, D.; Tsang, R.; Wu, C.; Glover, J. N. M. Structure of the sporulation-specific transcription factor Ndt80 bound to DNA EMBO J. 2002, 21, 5721-5732
    • (2002) EMBO J. , vol.21 , pp. 5721-5732
    • Lamoureux, J.S.1    Stuart, D.2    Tsang, R.3    Wu, C.4    Glover, J.N.M.5
  • 29
    • 34247272005 scopus 로고    scopus 로고
    • +
    • DOI 10.1016/j.jmb.2007.03.010, PII S0022283607003415
    • Heddi, B.; Foloppe, N.; Hantz, E.; Hartmann, B. The DNA structure responds differently to physiological concentrations of K(+) or Na(+) J. Mol. Biol. 2007, 368, 1403-1411 (Pubitemid 46617604)
    • (2007) Journal of Molecular Biology , vol.368 , Issue.5 , pp. 1403-1411
    • Heddi, B.1    Foloppe, N.2    Hantz, E.3    Hartmann, B.4
  • 31
    • 0001549017 scopus 로고    scopus 로고
    • Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics
    • Foloppe, N.; MacKerell, A. D., Jr. Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics J. Phys. Chem. B 1999, 103, 10955-10964
    • (1999) J. Phys. Chem. B , vol.103 , pp. 10955-10964
    • Foloppe, N.1    MacKerell, Jr.A.D.2
  • 32
    • 0346996697 scopus 로고    scopus 로고
    • Recognition of 5′-YpG-3′ Sequences by Coupled Stacking/ Hydrogen Bonding Interactions with Amino Acid Residues
    • DOI 10.1016/j.jmb.2003.10.071
    • Lamoureux, J. S.; Maynes, J. T.; Glover, M. J. N. Recognition of 5′-YpG-3′ Sequences by Coupled Stacking/Hydrogen Bonding Interactions with Amino Acid Residues J. Mol. Biol. 2004, 335, 399-408 (Pubitemid 37532643)
    • (2004) Journal of Molecular Biology , vol.335 , Issue.2 , pp. 399-408
    • Lamoureux, J.S.1    Maynes, J.T.2    Glover, J.N.M.3
  • 33
    • 46349098220 scopus 로고    scopus 로고
    • DNA conformations and their sequence preferences
    • DOI 10.1093/nar/gkn260
    • Svozil, D.; Kalina, J.; Omelka, M.; Schneider, B. DNA conformations and their sequence preferences Nucl. Acid Res. 2008, 36, 3690-3706 (Pubitemid 351917531)
    • (2008) Nucleic Acids Research , vol.36 , Issue.11 , pp. 3690-3706
    • Svozil, D.1    Kalina, J.2    Omelka, M.3    Schneider, B.4
  • 34
    • 79955484353 scopus 로고    scopus 로고
    • Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
    • Denning, E. J.; Priyakumar, U. D.; Nilsson, L.; MacKerell, A. D., Jr. Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA J. Comput. Chem. 2011, 32, 1929-1943
    • (2011) J. Comput. Chem. , vol.32 , pp. 1929-1943
    • Denning, E.J.1    Priyakumar, U.D.2    Nilsson, L.3    MacKerell, Jr.A.D.4
  • 37
    • 65249180756 scopus 로고    scopus 로고
    • Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI and BII forms of duplex DNA
    • MacKerell, A. D., Jr. Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI and BII forms of duplex DNA J. Phys. Chem. B 2009, 113, 3235-3244
    • (2009) J. Phys. Chem. B , vol.113 , pp. 3235-3244
    • MacKerell, Jr.A.D.1
  • 40
    • 0036192864 scopus 로고    scopus 로고
    • Intrinsic conformational energetics associated with the glycosyl torsion in DNA: A quantum mechanical study
    • Foloppe, N.; Hartmann, B.; Nilsson, L.; MacKerell, A. D., Jr. Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: a Quantum Mechanical Study Biophys. J. 2002, 82, 1554-1569 (Pubitemid 34204773)
    • (2002) Biophysical Journal , vol.82 , Issue.3 , pp. 1554-1569
    • Foloppe, N.1    Hartmann, B.2    Nilsson, L.3    MacKerell Jr., A.D.4
  • 43
    • 0000214231 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: 2) Application to solution MD simulations of DNA
    • MacKerell, A. D., Jr.; Banavali, N. K. All-atom empirical force field for nucleic acids: 2) Application to solution MD simulations of DNA J. Comput. Chem. 2000, 21, 105-120
    • (2000) J. Comput. Chem. , vol.21 , pp. 105-120
    • MacKerell, Jr.A.D.1    Banavali, N.K.2
  • 45
    • 0001538909 scopus 로고
    • Canonical Dynamics - Equilibrium Phase-Space Distributions
    • Hoover, W. G. Canonical Dynamics-Equilibrium Phase-Space Distributions Phys. Rev. A 1985, 31, 1695-1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 46
    • 36449007836 scopus 로고
    • Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method
    • Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, R. W. Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method J. Chem. Phys. 1995, 103, 4613-4621
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, R.W.4
  • 47
    • 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.; 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. 1977, 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 48
    • 67650135820 scopus 로고    scopus 로고
    • Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations
    • Nilsson, L. Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations. J. Comput. Chem. 2009, 30, 1490-1498.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1490-1498
    • Nilsson, L.1
  • 49
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems
    • Darden, T. A.; York, D.; Pedersen, L. G. Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.A.1    York, D.2    Pedersen, L.G.3
  • 50
    • 84986534166 scopus 로고
    • New Spherical-Cutoff Methods of Long-Range Forces in Macromolecular Simulations
    • Steinbach, P. J.; Brooks, B. R. New Spherical-Cutoff Methods of Long-Range Forces in Macromolecular Simulations J. Comput. Chem. 1994, 15, 667-683
    • (1994) J. Comput. Chem. , vol.15 , pp. 667-683
    • Steinbach, P.J.1    Brooks, B.R.2
  • 51
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of the axis of curvature for irregular nucleic acids
    • Lavery, R.; Sklenar, H. The definition of generalized helicoidal parameters and of the axis of curvature for irregular nucleic acids J. Biomol. Str. Dyn. 1988, 6, 63-91
    • (1988) J. Biomol. Str. Dyn. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 52
    • 0024556774 scopus 로고
    • Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: 'Curves, dials and windows
    • Ravishanker, G.; Swaminathan, S.; Beveridge, D. L.; Lavery, R.; Sklenar, H. Conformational and Helicoidal Analysis of 30 ps of Molecular Dynamics on the d(CGCGAATTCGCG) Double Helix: Curves', Dials and Windows J. Biomol. Str. Dyn. 1989, 6, 669-699 (Pubitemid 19079753)
    • (1989) Journal of Biomolecular Structure and Dynamics , vol.6 , Issue.4 , pp. 669-699
    • Ravishanker, G.1    Swaminathan, S.2    Beveridge, D.L.3    Lavery, R.4    Sklenar, H.5
  • 53
    • 0036306053 scopus 로고    scopus 로고
    • Free energy and structural pathways of base flipping in a DNA GCGC containing sequence
    • DOI 10.1016/S0022-2836(02)00194-8
    • Banavali, N. K.; MacKerell, A. D., Jr. Free Energy and Structural Pathways of Base Flipping in a DNA GCGC containing sequence J. Mol. Biol. 2002, 319, 141-160 (Pubitemid 34729492)
    • (2002) Journal of Molecular Biology , vol.319 , Issue.1 , pp. 141-160
    • Banavali, N.K.1    MacKerell Jr., A.D.2
  • 54
    • 33745469232 scopus 로고    scopus 로고
    • Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER and BMS
    • Priyakumar, U. D.; MacKerell, A. D., Jr. Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER and BMS J. Chem. Theory Comput. 2005, 2, 187-200
    • (2005) J. Chem. Theory Comput. , vol.2 , pp. 187-200
    • Priyakumar, U.D.1    MacKerell, Jr.A.D.2
  • 55
    • 31444443924 scopus 로고    scopus 로고
    • NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases
    • DOI 10.1021/ja056445a
    • Priyakumar, D.; MacKerell, A. D., Jr. Proton Exchange Experiments on Duplex DNA Primarily Monitor the Opening of Purine Bases. J. Am. Chem. Soc. 2006, 678-679. (Pubitemid 43152995)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.3 , pp. 678-679
    • Priyakumar, U.D.1    MacKerell Jr., A.D.2
  • 56
    • 0033032014 scopus 로고    scopus 로고
    • Intrinsic conformational properties of deoxyribonucleosides: Implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA
    • Foloppe, N.; MacKerell, A. D., Jr. Intrinsic Conformational Properties of Deoxyribonucleosides: Implicated role for cytosine in the equilibrium between the A, B and Z forms of DNA Biophys. J. 1999, 76, 3206-3218 (Pubitemid 29269467)
    • (1999) Biophysical Journal , vol.76 , Issue.6 , pp. 3206-3218
    • Foloppe, N.1    MacKerell Jr., A.D.2
  • 57
    • 0025112951 scopus 로고
    • Molecular dynamics of an in vacuo model of duplex d(CGCGAATTCGCG) in the B-form based on the amber 3.0 force field
    • Srinivasan, J.; Withka, J. M.; Beveridge, D. L. Molecular dynamics of an in vacuo model of duplex d(CGCGAATTCGCG) in the B-form based on the amber 3.0 force field Biophys. J. 1990, 58, 533-547 (Pubitemid 20249679)
    • (1990) Biophysical Journal , vol.58 , Issue.2 , pp. 533-547
    • Srinivasan, J.1    Withka, J.M.2    Beveridge, D.L.3
  • 58
    • 0028052906 scopus 로고
    • A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates
    • McConnell, K. J.; Nirmala, R.; Young, M. A.; Ravishanker, G.; Beveridge, D. L. A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates J. Am. Chem. Soc. 1994, 116, 4461-4462
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 4461-4462
    • McConnell, K.J.1    Nirmala, R.2    Young, M.A.3    Ravishanker, G.4    Beveridge, D.L.5
  • 59
    • 0032846562 scopus 로고    scopus 로고
    • Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation
    • Sen, S.; Nilsson, L. Structure, Interactions, Dynamics and Solvent Effects on the DNA-EcoRI Complex in Aqueous Solution from MD Simulation Biophys. J. 1999, 77, 1782-1800 (Pubitemid 29463144)
    • (1999) Biophysical Journal , vol.77 , Issue.4 , pp. 1782-1800
    • Sen, S.1    Nilsson, L.2
  • 60
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning, G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides Quart. Rev. Biophys. 1978, 11, 179-246 (Pubitemid 8373665)
    • (1978) Quarterly Reviews of Biophysics , vol.11 , Issue.2 , pp. 179-246
    • Manning, G.S.1
  • 61
    • 78751676012 scopus 로고    scopus 로고
    • Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model
    • Baker, C. M.; Anisimov, V. M.; MacKerell, A. D., Jr. Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model J. Phys. Chem. B 2011, 115, 580-596
    • (2011) J. Phys. Chem. B , vol.115 , pp. 580-596
    • Baker, C.M.1    Anisimov, V.M.2    MacKerell, Jr.A.D.3
  • 62
    • 0033568921 scopus 로고    scopus 로고
    • How NF-κB can be attracted by its cognate DNA
    • DOI 10.1006/jmbi.1999.3157
    • Tisne, C.; Delepierre, M.; Hartmann, B. How NF-kappaB can be attracted by its cognate DNA J. Mol. Biol. 1999, 293, 139-150 (Pubitemid 29494876)
    • (1999) Journal of Molecular Biology , vol.293 , Issue.1 , pp. 139-150
    • Tisne, C.1    Delepierre, M.2    Hartmann, B.3
  • 63
    • 47249117197 scopus 로고    scopus 로고
    • 13C spin relaxation and molecular dynamics simulation study
    • DOI 10.1093/nar/gkn375
    • Duchardt, E.; Nilsson, L.; Schleucher, J. Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study Nucleic Acids Res. 2008, 36, 4211-4219 (Pubitemid 351984836)
    • (2008) Nucleic Acids Research , vol.36 , Issue.12 , pp. 4211-4219
    • Duchardt, E.1    Nilsson, L.2    Schleucher, J.3
  • 64
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
    • Record, M. T., Jr.; Anderson, C. F.; Lohman, T. M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity Quart. Rev. Biophys. 1978, 11, 103-178 (Pubitemid 8373664)
    • (1978) Quarterly Reviews of Biophysics , vol.11 , Issue.2 , pp. 103-178
    • Record Jr., M.T.1    Anderson, C.F.2    Lohman, T.M.3
  • 65
    • 58149089147 scopus 로고    scopus 로고
    • Crystallographic analysis of sex-specific enhancer element:sequence- dependent DNA structure, hydration and dynamics
    • Narayana, N.; Weiss, M. A. Crystallographic analysis of sex-specific enhancer element:sequence-dependent DNA structure, hydration and dynamics J. Mol. Biol. 2009, 385, 469-490
    • (2009) J. Mol. Biol. , vol.385 , pp. 469-490
    • Narayana, N.1    Weiss, M.A.2
  • 66
    • 18644368600 scopus 로고    scopus 로고
    • Free energy landscape of A-DNA to B-DNA conversion in aqueous solution
    • DOI 10.1021/ja050482k
    • Banavali, N. K.; Roux, B. Free energy landscape of A-DNA to B-DNA conversion in aqueous solution J. Am. Chem. Soc. 2005, 127, 6866-6876 (Pubitemid 40664194)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.18 , pp. 6866-6876
    • Banavali, N.K.1    Roux, B.2
  • 67
    • 0032522139 scopus 로고    scopus 로고
    • DNA bending: The prevalence of kinkiness and the virtues of normality
    • DOI 10.1093/nar/26.8.1906
    • Dickerson, R. E. DNA bending: the prevalence of kinkiness and the virtures of normality Nucleic Acids Res. 1998, 26, 1906-1926 (Pubitemid 28291723)
    • (1998) Nucleic Acids Research , vol.26 , Issue.8 , pp. 1906-1926
    • Dickerson, R.E.1
  • 68
    • 0037342509 scopus 로고    scopus 로고
    • DNA polymorphism: A comparison of force fields for nucleic acids
    • Reddy, S. Y.; Leclerc, F.; Karplus, M. DNA polymorphism: a comparison of force fields for nucleic acids Biophys. J. 2003, 84, 1421-1449 (Pubitemid 36322913)
    • (2003) Biophysical Journal , vol.84 , Issue.3 , pp. 1421-1449
    • Reddy, S.Y.1    Leclerc, F.2    Karplus, M.3
  • 69
    • 0027155070 scopus 로고
    • Orthorhombic crystal structure of the A-DNA octamer d(GTACGTAC). Comparison with the tetragonal structure
    • Langlois D'Estaintot, B.; Dautant, A.; Courseille, C.; Precigoux, G. Orthorhombic Crystal Structure of the A-DNA Octamer d(GTACGTAC). Comparison with the Tetragonal Structure Eur. J. Biochem. 1993, 213, 673-682 (Pubitemid 23125636)
    • (1993) European Journal of Biochemistry , vol.213 , Issue.2 , pp. 673-682
    • Langlois D'Estaintot, B.1    Dautant, A.2    Courseille, C.3    Precigoux, G.4
  • 70
    • 0025816853 scopus 로고
    • The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G - The effect of base pair reversals
    • Grzeskowiak, K.; Yanagi, K.; Prive, G. G.; Dickerson, R. E. The Structure of B-Helical CGATCGATCG and Comparison with CCAACGTTGG. The Effect of Base Pair Reversals J. Biol. Chem. 1991, 266, 8861-8883 (Pubitemid 21906593)
    • (1991) Journal of Biological Chemistry , vol.266 , Issue.14 , pp. 8861-8883
    • Grzeskowiak, K.1    Yanagi, K.2    Prive, G.G.3    Dickerson, R.E.4
  • 72
    • 0019843568 scopus 로고
    • Structure of a B-DNA dodecamer. III. Geometry of hydration
    • Drew, H. R.; Dickerson, R. E. Structure of a B-DNA Dodecamer III. Geometry of Hydration J. Mol. Biol. 1981, 151, 535-556 (Pubitemid 12252694)
    • (1981) Journal of Molecular Biology , vol.151 , Issue.3 , pp. 535-556
    • Drew, H.R.1    Dickerson, R.E.2
  • 74
    • 84977299328 scopus 로고
    • Anisotropic Thermal-Parameter Refinement of the DNA Dodecamer CGCGAATTCGCG by the Segmented Rigid-Body Method
    • Holbrook, S. R.; Dickerson, R. E.; Kim, S.-H. Anisotropic Thermal-Parameter Refinement of the DNA Dodecamer CGCGAATTCGCG by the Segmented Rigid-Body Method Acta Crystallogr., Sect. B 1985, 41, 255-262
    • (1985) Acta Crystallogr., Sect. B , vol.41 , pp. 255-262
    • Holbrook, S.R.1    Dickerson, R.E.2    Kim, S.-H.3
  • 75
    • 0023459640 scopus 로고
    • Re-Refinement of the B-Dodecamer d(CGCGAATTCGCG) with a Comparative Analysis of the Solvent in it and in the Z-Hexamer d(5BrCG5BrCG5BrCG)
    • Westhof, E. Re-Refinement of the B-Dodecamer d(CGCGAATTCGCG) with a Comparative Analysis of the Solvent in it and in the Z-Hexamer d(5BrCG5BrCG5BrCG) J. Biomol. Struct. Dyn. 1987, 8, 581-600
    • (1987) J. Biomol. Struct. Dyn. , vol.8 , pp. 581-600
    • Westhof, E.1
  • 76
    • 0034647435 scopus 로고    scopus 로고
    • A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: Symmetry effects on sequence-dependent DNA structure
    • Johansson, E.; Parkinson, G.; Neidle, S. A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure J. Mol. Biol. 2000, 300, 551-561
    • (2000) J. Mol. Biol. , vol.300 , pp. 551-561
    • Johansson, E.1    Parkinson, G.2    Neidle, S.3
  • 77
    • 11844289660 scopus 로고    scopus 로고
    • Resolving conflicting crystallographic and NMR models for solution-state DNA with solution X-ray diffraction
    • DOI 10.1021/ja044533+
    • Zuo, X.; Tiede, D. M. Resolving conflicting crystallographic and NMR models for solution-state DNA with solution X-ray diffraction J. Am. Chem. Soc. 2005, 127, 16-17 (Pubitemid 40094342)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.1 , pp. 16-17
    • Zuo, X.1    Tiede, D.M.2
  • 78
    • 0032488608 scopus 로고    scopus 로고
    • Solution structures of DNA·RNA hybrids with purine-rich and pyrimidine- rich strands: Comparison with the homologous DNA and RNA duplexes
    • DOI 10.1021/bi9719713
    • Gyi, J. I.; Lane, A. N.; Conn, G. L.; Brown, T. Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes Biochemistry 1998, 37, 73-80 (Pubitemid 28049109)
    • (1998) Biochemistry , vol.37 , Issue.1 , pp. 73-80
    • Gyi, J.I.1    Lane, A.N.2    Conn, G.L.3    Brown, T.4
  • 81
    • 0015913888 scopus 로고
    • Conformational Analysis of the Sugar Ring in Nucleosides and Nucleotides. Improved Method for the Interpretation of Proton Magnetic Resonance Coupling Constants
    • Altona, C.; Sundaralingam, M. Conformational Analysis of the Sugar Ring in Nucleosides and Nucleotides. Improved Method for the Interpretation of Proton Magnetic Resonance Coupling Constants J. Am. Chem. Soc. 1973, 95, 2333-2344
    • (1973) J. Am. Chem. Soc. , vol.95 , pp. 2333-2344
    • Altona, C.1    Sundaralingam, M.2


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