Skip to main content
SpringerLink
Log in

Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation

  • Protocol
  • First Online:
Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 924))

Abstract

The structure and dynamics of the B-DNA double helix involves subtle sequence-dependent effects which are decisive for its function, but difficult to characterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics simulations with the major force fields in use today. We explain why a critical analysis of the MD trajectories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Perez A, Luque FJ, Orozco M (2007) Dynamics of B-DNA on the microsecond time scale. J Am Chem Soc 129:14739–14745

    Article  PubMed  CAS  Google Scholar 

  2. Banavali NK, Mackerell AD Jr (2009) Characterizing structural transitions using localized free energy landscape analysis. PLoS One 4:e5525

    Article  PubMed  CAS  Google Scholar 

  3. Banavali NK, Roux B (2005) Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J Am Chem Soc 127:6866–6876

    Article  PubMed  CAS  Google Scholar 

  4. Cheatham TE 3rd, Kollman PA (1996) Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J Mol Biol 259:434–444

    Article  PubMed  CAS  Google Scholar 

  5. Knee KM, Dixit SB, Aitken CE, Ponomarev S, Beveridge DL, Mukerji I (2008) Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA. Biophys J 95:257–272

    Article  PubMed  CAS  Google Scholar 

  6. Langley DR (1998) Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results. J Biomol Struct Dyn 16:487–509

    Article  PubMed  CAS  Google Scholar 

  7. Noy A, Perez A, Laughton CA, Orozco M (2007) Theoretical study of large conformational transitions in DNA: the B ↔ A conformational change in water and ethanol/water. Nucleic Acids Res 35:3330–3338

    Article  PubMed  CAS  Google Scholar 

  8. Foloppe N, MacKerell AD (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 21:86–104

    Article  CAS  Google Scholar 

  9. Cheatham TE 3rd, Cieplak P, Kollman PA (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

    Article  PubMed  CAS  Google Scholar 

  10. Wang J, Cieplak P, Kollman P (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21:1049–1074

    Article  CAS  Google Scholar 

  11. Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE 3rd, Laughton CA, Orozco M (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 92:3817–3829

    Article  PubMed  CAS  Google Scholar 

  12. Cheatham TE 3rd (2004) Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr Opin Struct Biol 14:360–367

    Article  PubMed  CAS  Google Scholar 

  13. Mackerell AD Jr (2004) Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25:1584–1604

    Article  PubMed  CAS  Google Scholar 

  14. Orozco M, Perez A, Noy A, Luque FJ (2003) Theoretical methods for the simulation of nucleic acids. Chem Soc Rev 32:350–364

    Article  PubMed  CAS  Google Scholar 

  15. Ponomarev SY, Thayer KM, Beveridge DL (2004) Ion motions in molecular dynamics simulations on DNA. Proc Natl Acad Sci U S A 101:14771–14775

    Article  PubMed  CAS  Google Scholar 

  16. Varnai P, Zakrzewska K (2004) DNA and its counterions: a molecular dynamics study. Nucleic Acids Res 32:4269–4280

    Article  PubMed  CAS  Google Scholar 

  17. Heddi B, Foloppe N, Oguey C, Hartmann B (2008) Importance of accurate DNA structures in solution: the Jun-Fos model. J Mol Biol 382:956–970

    Article  PubMed  CAS  Google Scholar 

  18. Perez A, Lankas F, Luque FJ, Orozco M (2008) Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res 36(7):2379–2394

    Article  PubMed  CAS  Google Scholar 

  19. Arthanari H, McConnell KJ, Beger R, Young MA, Beveridge DL, Bolton PH (2003) Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. Biopolymers 68:3–15

    Article  PubMed  CAS  Google Scholar 

  20. Foloppe N, Nilsson L (2005) Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides. J Phys Chem B 109:9119–9131

    Article  PubMed  CAS  Google Scholar 

  21. Konerding DE, Cheatham TE 3rd, Kollman PA, James TL (1999) Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. J Biomol NMR 13:119–131

    Article  PubMed  CAS  Google Scholar 

  22. Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE 3rd, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, Varnai P, Young MA (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys J 87:3799–3813

    Article  PubMed  CAS  Google Scholar 

  23. Dixit SB, Beveridge DL, Case DA, Cheatham TE 3rd, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P (2005) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J 89:3721–3740

    Article  PubMed  CAS  Google Scholar 

  24. Isaacs RJ, Spielmann HP (2004) Insight into G[bond]T mismatch recognition using molecular dynamics with time-averaged restraints derived from NMR spectroscopy. J Am Chem Soc 126:583–590

    Article  PubMed  CAS  Google Scholar 

  25. Zuo X, Cui G, Merz KM Jr, Zhang L, Lewis FD, Tiede DM (2006) X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc Natl Acad Sci U S A 103:3534–3539

    Article  PubMed  CAS  Google Scholar 

  26. Heddi B, Foloppe N, Bouchemal N, Hantz E, Hartmann B (2006) Quantification of DNA BI/BII backbone states in solution implications for DNA overall structure and recognition. J Am Chem Soc 128:9170–9177

    Article  PubMed  CAS  Google Scholar 

  27. Heddi B, Foloppe N, Hantz E, Hartmann B (2007) The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J Mol Biol 368:1403–1411

    Article  PubMed  CAS  Google Scholar 

  28. Djuranovic D, Hartmann B (2003) Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: evidence for sub-states. J Biomol Struct Dyn 20:771–788

    Article  PubMed  CAS  Google Scholar 

  29. Djuranovic D, Hartmann B (2004) DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations. Biopolymers 73:356–368

    Article  PubMed  CAS  Google Scholar 

  30. Heddi B, Abi-Ghanem J, Lavigne M, Hartmann B (2010) Sequence-dependent DNA flexibility mediates DNase I cleavage. J Mol Biol 395:123–133

    Article  PubMed  CAS  Google Scholar 

  31. Isaacs RJ, Spielmann HP (2001) NMR evidence for mechanical coupling of phosphate B(I)–B(II) transitions with deoxyribose conformational exchange in DNA. J Mol Biol 311:149–160

    Article  PubMed  CAS  Google Scholar 

  32. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci U S A 95:11163–11168

    Article  PubMed  CAS  Google Scholar 

  33. van Dam L, Levitt MH (2000) BII nucleotides in the B and C forms of natural-sequence polymeric DNA: a new model for the C form of DNA. J Mol Biol 304:541–561

    Article  PubMed  CAS  Google Scholar 

  34. Winger RH, Liedl KR, Pichler A, Hallbrucker A, Mayer E (1999) Helix morphology changes in B-DNA induced by spontaneous B(I) ↔ B(II) substrate interconversion. J Biomol Struct Dyn 17:223–235

    Article  PubMed  CAS  Google Scholar 

  35. Wu Z, Maderia M, Barchi JJ Jr, Marquez VE, Bax A (2005) Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy. Proc Natl Acad Sci U S A 102:24–28

    Article  PubMed  CAS  Google Scholar 

  36. Heddi B, Oguey C, Lavelle C, Foloppe N, Hartmann B (2010) Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res 38:1034–1047

    Article  PubMed  CAS  Google Scholar 

  37. Hart K, Nilsson L (2008) Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study. Proteins 73:325–337

    Article  PubMed  CAS  Google Scholar 

  38. Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T 3rd, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, Singh T, Spackova N, Sponer J (2010) A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res 38:299–313

    Article  PubMed  CAS  Google Scholar 

  39. Lankas F, Spackova N, Moakher M, Enkhbayar P, Sponer J (2010) A measure of bending in nucleic acids structures applied to A-tract DNA. Nucleic Acids Res 38:3414–3422

    Article  PubMed  CAS  Google Scholar 

  40. Abi-Ghanem J, Heddi B, Foloppe N, Hartmann B (2010) DNA structures from phosphate chemical shifts. Nucleic Acids Res 38:e18

    Article  PubMed  CAS  Google Scholar 

  41. Hashem Y, Auffinger P (2009) A short guide for molecular dynamics simulations of RNA systems. Methods 47:187–197

    Article  PubMed  CAS  Google Scholar 

  42. Mackerell AD Jr, Nilsson L (2008) Molecular dynamics simulations of nucleic acid–protein complexes. Curr Opin Struct Biol 18:194–199

    Article  PubMed  CAS  Google Scholar 

  43. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688

    Article  PubMed  CAS  Google Scholar 

  44. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614

    Article  PubMed  CAS  Google Scholar 

  45. Phillips J, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802

    Article  PubMed  CAS  Google Scholar 

  46. Macke T, Case D (1998) Modeling unusual nucleic acid structures. ACS Publications, Washington, DC, pp 379–393

    Google Scholar 

  47. Bansal M, Bhattacharyya D, Ravi B (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Bioinformatics 11:281

    Article  CAS  Google Scholar 

  48. de Souza ON, Ornstein RL (1997) Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method. Biophys J 72:2395–2397

    Article  PubMed  Google Scholar 

  49. Aaqvist J (1990) Ion–water interaction potentials derived from free energy perturbation simulations. J Phys Chem 94:8021–8024

    Article  CAS  Google Scholar 

  50. Noy A, Soteras I, Luque FJ, Orozco M (2009) The impact of monovalent ion force field model in nucleic acids simulations. Phys Chem Chem Phys 11:10596–10607

    Article  PubMed  CAS  Google Scholar 

  51. Joung IS, Cheatham TE 3rd (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 112:9020–9041

    Article  PubMed  CAS  Google Scholar 

  52. Auffinger P, Cheatham TE 3rd, Vaiana AC (2007) Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue? J Chem Theor Comput 3:1851–1859

    Article  CAS  Google Scholar 

  53. Beglov D, Roux B (1994) Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J Chem Phys 100:9050–9063

    Article  CAS  Google Scholar 

  54. Dang L (1995) Mechanism and thermodynamics of ion selectivity in aqueous solutions of 18-crown-6 ether: a molecular dynamics study. J Am Chem Soc 117:6954–6960

    Article  CAS  Google Scholar 

  55. Jensen K, Jorgensen W (2006) Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions. J Chem Theor Comput 2:1499–1509

    Article  CAS  Google Scholar 

  56. Auffinger P, Westhof E (2000) Water and ion binding around RNA and DNA (C, G) oligomers. J Mol Biol 300:1113–1131

    Article  PubMed  CAS  Google Scholar 

  57. Jorgensen WL, Chandrasekhar J, Madura JD (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  58. Berendsen H, Grigera J, Straatsma T (1987) The missing term in effective pair potentials. J Phys Chem 91:6269–6271

    Article  CAS  Google Scholar 

  59. Glättli A, Daura X, Van Gunsteren W (2003) A novel approach for designing simple point charge models for liquid water with three interaction sites. J Comput Chem 24:1087–1096

    Article  PubMed  CAS  Google Scholar 

  60. Cheatham TE 3rd, Kollman PA (1998) Structure, motion, interaction and expression of biological macromolecules: proceedings of the Tenth Conversation in the Discipline Biomolecular Stereodynamics, held at the University of Albany. Adenine Press, Schenectady

    Google Scholar 

  61. Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, Hura GL, Head-Gordon T (2004) Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J Chem Phys 120:9665–9678

    Article  PubMed  CAS  Google Scholar 

  62. Darden T, Perera L, Li L, Pedersen L (1999) New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure 7:R55–R60

    Article  PubMed  CAS  Google Scholar 

  63. Norberg J, Nilsson L (2000) On the truncation of long-range electrostatic interactions in DNA. Biophys J 79:1537–1553

    Article  PubMed  CAS  Google Scholar 

  64. Cheatham TE 3rd, Kollman PA (2000) Molecular dynamics simulation of nucleic acids. Annu Rev Phys Chem 51:435–471

    Article  PubMed  CAS  Google Scholar 

  65. Cheatham T, Miller J, Fox T, Darden T, Kollman P (1995) Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA RNA, and proteins. J Am Chem Soc 117:4193–4194

    Article  CAS  Google Scholar 

  66. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  67. Beck DA, Armen RS, Daggett V (2005) Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry 44:609–616

    Article  PubMed  CAS  Google Scholar 

  68. Hünenberger P (2005) Thermostat algorithms for molecular dynamics simulations. Adv Comp Simul 173:105–149

    Google Scholar 

  69. Ryckaert J, Ciccotti G, Berendsen H (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

    Article  CAS  Google Scholar 

  70. Harvey S, Robert K, Cheatham T III (1998) The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J Comput Chem 19:726–740

    Article  CAS  Google Scholar 

  71. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690

    Article  CAS  Google Scholar 

  72. Varnai P, Djuranovic D, Lavery R, Hartmann B (2002) Alpha/gamma transitions in the B-DNA backbone. Nucleic Acids Res 30:5398–5406

    Article  PubMed  CAS  Google Scholar 

  73. Grest G, Kremer K (1986) Molecular dynamics simulation for polymers in the presence of a heat bath. Phys Rev A 33:3628–3631

    Article  PubMed  CAS  Google Scholar 

  74. Nose J (1984) J Chem Phys 81:511

    Article  CAS  Google Scholar 

  75. Hoover W (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev A 31:1695–1697

    Article  PubMed  Google Scholar 

  76. Luan B, Aksimentiev A (2008) Strain softening in stretched DNA. Phys Rev Lett 101:118101

    Article  PubMed  CAS  Google Scholar 

  77. Cerutti DS, Duke R, Freddolino PL, Fan H, Lybrand TP (2008) Vulnerability in popular molecular dynamics packages concerning Langevin and Andersen dynamics. J Chem Theor Comput 4:1669–1680

    Article  CAS  Google Scholar 

  78. Khalili M, Liwo A, Jagielska A, Scheraga HA (2005) Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems. J Phys Chem B 109:13798–13810

    Article  PubMed  CAS  Google Scholar 

  79. Foloppe N, Hartmann B, Nilsson L, MacKerell AD Jr (2002) Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J 82:1554–1569

    Article  PubMed  CAS  Google Scholar 

  80. Dickerson RE (1989) Definitions and nomenclature of nucleic acid structure components. Nucleic Acids Res 17:1797–1803

    Article  PubMed  CAS  Google Scholar 

  81. Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu XJ, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung CS, Westhof E, Wolberger C, Berman HM (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol 313:229–237

    Article  PubMed  CAS  Google Scholar 

  82. Lavery R, Sklenar H (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J Biomol Struct Dyn 6:63–91

    Article  PubMed  CAS  Google Scholar 

  83. Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res 37:5917–5929

    Article  PubMed  CAS  Google Scholar 

  84. Lu XJ, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108–5121

    Article  PubMed  CAS  Google Scholar 

  85. Peters JP 3rd, Maher LJ (2010) DNA curvature and flexibility in vitro and in vivo. Quart Rev Biophys 43:23–63

    Article  CAS  Google Scholar 

  86. Subirana JA, Faria T (1997) Influence of sequence on the conformation of the B-DNA helix. Biophys J 73:333–338

    Article  PubMed  CAS  Google Scholar 

  87. Dickerson RE, Goodsell DS, Neidle S (1994) …the tyranny of the lattice…. Proc Natl Acad Sci U S A 91:3579–3583

    Article  PubMed  CAS  Google Scholar 

  88. Hahn M, Heinemann U (1993) DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR. Acta Crystallogr 49:468–477

    Article  CAS  Google Scholar 

  89. Heinemann U, Alings C, Hahn M (1994) Crystallographic studies of DNA helix structure. Biophys Chem 50:157–167

    Article  PubMed  CAS  Google Scholar 

  90. Lankas F (2004) DNA sequence-dependent deformability—insights from computer simulations. Biopolymers 73:327–339

    Article  PubMed  CAS  Google Scholar 

  91. Valls N, Wright G, Steiner RA, Murshudov GN, Subirana JA (2004) DNA variability in five crystal structures of d(CGCAATTGCG). Acta Crystallogr Section D: Biol Crystallogr 60:680–685

    Article  CAS  Google Scholar 

  92. Tonelli M, James TL (1998) Insights into the dynamic nature of DNA duplex structure via analysis of nuclear Overhauser effect intensities. Biochemistry 37:11478–11487

    Article  PubMed  CAS  Google Scholar 

  93. van Wijk J, Huckriede BD, Ippel JH, Altona C (1992) Furanose sugar conformations in DNA from NMR coupling constants. Methods Enzymol 211:286–306

    Article  PubMed  Google Scholar 

  94. Wu Z, Delaglio F, Tjandra N, Zhurkin VB, Bax A (2003) Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy. J Biomol NMR 26:297–315

    Article  PubMed  CAS  Google Scholar 

  95. Wijmenga SS, van Buuren BNM (1998) The use of NMR methods for conformational studies of nucleic acids. Prog Nucl Magn Reson Spectrosc 32:287–387

    Article  CAS  Google Scholar 

  96. Foloppe N, MacKerell AD Jr (1999) Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A B, and Z forms of DNA. Biophys J 76:3206–3218

    Article  PubMed  CAS  Google Scholar 

  97. Bosch D, Foloppe N, Pastor N, Pardo L, Campillo M (2001) Calibrating nucleic acids torsional energetics in force field: insights from model compounds. J Mol Struct: Theochem 537:283–305

    Article  CAS  Google Scholar 

  98. Foloppe N, MacKerell AD (1999) Contribution of the phosphodiester backbone and glycosyl linkage intrinsic torsional energetics to DNA structure and dynamics. J Phys Chem B 103:10955–10964

    Article  CAS  Google Scholar 

  99. Hartmann B, Lavery R (1996) DNA structural forms. Quart Rev Biophys 29:309–368

    Article  CAS  Google Scholar 

  100. Oguey C, Foloppe N, Hartmann B (2010) Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions. PLoS One 5:e15931

    Article  PubMed  CAS  Google Scholar 

  101. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New York, NY

    Google Scholar 

  102. Lefebvre A, Fermandjian S, Hartmann B (1997) Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics. Nucleic Acids Res 25:3855–3862

    Article  PubMed  CAS  Google Scholar 

  103. Mauffret O, Tevanian G, Fermandjian S (2002) Residual dipolar coupling constants and structure determination of large DNA duplexes. J Biomol NMR 24:317–328

    Article  PubMed  CAS  Google Scholar 

  104. Tian Y, Kayatta M, Shultis K, Gonzalez A, Mueller LJ, Hatcher ME (2009) (31)P NMR investigation of backbone dynamics in DNA binding sites (dagger). J Phys Chem B 113:2596–2603

    Article  PubMed  CAS  Google Scholar 

  105. Nose J (1984) Mol Phys 52:255

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Cambridge, UK

    Nicolas Foloppe

  2. INSERM, Paris, France

    Marc Guéroult

  3. FranceInstitut de Biologie Physico-Chimique, CNRS, Paris, France

    Marc Guéroult

  4. Laboratoire de biologie et pharmacologie appliquée (LBPA), CNRS, Paris, France

    Brigitte Hartmann

Authors
  1. Nicolas Foloppe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marc Guéroult
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Brigitte Hartmann
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Brigitte Hartmann .

Editor information

Editors and Affiliations

  1. DSIMB, UMR-S 665, INSERM, rue Alexandre Cabanel 6, Paris, 75015, France

    Luca Monticelli

  2. , Department of Applied Physics, Aalto University, Otakaari, AALTO, FI-00076, Finland

    Emppu Salonen

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this protocol

Cite this protocol

Foloppe, N., Guéroult, M., Hartmann, B. (2013). Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation. In: Monticelli, L., Salonen, E. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 924. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-017-5_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-017-5_17

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-016-8

  • Online ISBN: 978-1-62703-017-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation