Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis

  • Thana SutthibutpongEmail author
  • Agnes Noy
  • Sarah Harris
Part of the Methods in Molecular Biology book series (MIMB, volume 1431)


While DNA supercoiling is ubiquitous in vivo, the structure of supercoiled DNA is more challenging to study experimentally than simple linear sequences because the DNA must have a closed topology in order to sustain superhelical stress. DNA minicircles, which are closed circular double-stranded DNA sequences typically containing between 60 and 500 base pairs, have proven to be useful biochemical tools for the study of supercoiled DNA mechanics. We present detailed protocols for constructing models of DNA minicircles in silico, for performing atomistic molecular dynamics (MD) simulations of supercoiled minicircle DNA, and for analyzing the results of the calculations. These simulations are computationally challenging due to the large system sizes. However, improvements in parallel computing software and hardware promise access to improve conformational sampling and simulation timescales. Given the concurrent improvements in the resolution of experimental techniques such as atomic force microscopy (AFM) and cryo-electron microscopy, the study of DNA minicircles will provide a more complete understanding of both the structure and the mechanics of supercoiled DNA.

Key words

Atomistic molecular dynamics DNA supercoiling 


  1. 1.
    Bates AD, Maxwell A (2005) DNA topology. Oxford University Press, OxfordGoogle Scholar
  2. 2.
    Dekker J, Marti-Renom M, Mirny L (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 14:390–403CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Williamson I, Berlivet S, Eskeland R et al (2014) Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev 28:2778–2791CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Benedetti F, Japaridze A, Dorier J et al (2015) Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling. Nucleic Acids Res 43:2390–2399CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Drew HR, Weeks JR, Travers AA (1985) Negative supercoiling induces spontaneous unwinding of a bacterial promoter. EMBO J 4:1025–1032PubMedPubMedCentralGoogle Scholar
  6. 6.
    Kouzine F, Levens D, Baranello L (2014) DNA topology and transcription. Nucleus 5:195–202CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Pemberton IK, Muskhelishvili G, Travers AA et al (2002) FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter. J Mol Biol 318:651–663CrossRefPubMedGoogle Scholar
  8. 8.
    Fogg JM, Randall GL, Pettitt BM et al (2012) Bullied no more: when and how DNA shoves proteins around. Q Rev Biophys 45:257–299CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Olson WK, Gorin AA, Lu X-J et al (1998) DNA sequence-dependent deformability deduced from protein–DNA crystal complexes. Proc Natl Acad Sci U S A 95:11163–11168CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Luscombe NM, Austin SE, Berman HM et al (2000) An overview of the structures of protein-DNA complexes. Genome Biol 1:1CrossRefGoogle Scholar
  11. 11.
    Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423:145–150CrossRefPubMedGoogle Scholar
  12. 12.
    Du Q, Kotlyar A, Vologodskii A (2008) Kinking the double helix by bending deformation. Nucleic Acids Res 36:1120–1128CrossRefPubMedGoogle Scholar
  13. 13.
    Lionberger TA, Demurtas D, Witz G et al (2011) Cooperative kinking at distant sites in mechanically stressed DNA. Nucleic Acids Res 39:9820–9832CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Fogg JM, Kolmakova N, Rees I et al (2006) Exploring writhe in supercoiled minicircle DNA. J Phys Condens Matter 18:S145–S159CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Shlyakhtenko LS, Potaman VN, Sinden RR et al (1998) Structure and dynamics of supercoil-stabilized DNA cruciforms. J Mol Biol 280:61–72CrossRefPubMedGoogle Scholar
  16. 16.
    Schmatko T, Muller P, Maaloum M (2014) Surface charge effects on the 2D conformation of supercoiled DNA. Soft Matter 10:2520–2529CrossRefPubMedGoogle Scholar
  17. 17.
    Bednar J, Furrer P, Stasiak A et al (1994) The Twist Writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. J Mol Biol 235:825–847CrossRefPubMedGoogle Scholar
  18. 18.
    Amzallag A, Vaillant C, Jacob M et al (2006) 3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy. Nucleic Acids Res 34:e125CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Irobalieva RN, Fogg JM, Catanese DJ et al (2015) Structural diversity of supercoiled DNA. Nat Commun 6:8440CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Beveridge DL, Cheatham TE, Mezei M (2012) The ABCs of molecular dynamics simulations on B-DNA, circa 2012. J Biosci 37:379–397CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Mitchell JS, Laughton CA, Harris SA (2011) Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 39:3928–3938CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Harris SA, Laughton CA, Liverpool TB (2008) Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Res 36:21–29CrossRefPubMedGoogle Scholar
  23. 23.
    Liverpool TB, Harris SA, Laughton CA (2008) Supercoiling and denaturation of DNA loops. Phys Rev Lett 100:238103CrossRefPubMedGoogle Scholar
  24. 24.
    Gray A, Harlen OG, Harris SA et al (2015) In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation. Acta Crystallogr D D71:162–172CrossRefGoogle Scholar
  25. 25.
    Pronk S, Páll S, Schulz R et al (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29:845–854CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Case DA, Cheatham TE, Darden T et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Phillips JC, Braun R, Wang W et al (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Pérez A, Marchán I, Svozil D et al (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 92:3817–3829CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Krepl M, Zgarbová M, Stadlbauer P et al (2012) Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER forcefield: quadruplex DNA, quadruplex RNA, and Z-DNA. J Chem Theor Comput 8:2506–2520CrossRefGoogle Scholar
  30. 30.
    Zgarbova M, Luque FJ, Jir S et al (2013) Toward improved description of DNA backbone: revisiting epsilon and zeta torsion force field parameters. J Chem Theor Comput 9:2339–2354CrossRefGoogle Scholar
  31. 31.
    Vanommeslaeghe K, Hatcher E, Acharya C et al (2009) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31:671–690Google Scholar
  32. 32.
    Pérez A, Luque FJ, Orozco M (2007) Dynamics of B-DNA on the microsecond time scale. J Am Chem Soc 129:14739–14745CrossRefPubMedGoogle Scholar
  33. 33.
    Hart K, Foloppe N, Baker CM et al (2012) Optimization of the CHARMM additive force field for DNA: improved treatment of the BI/BII conformational equilibrium. J Chem Theor Comput 8:348–362CrossRefGoogle Scholar
  34. 34.
    Yoo J, Aksimentiev A (2013) In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proc Natl Acad Sci U S A 110:20099–20104CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Crick FHC, Klug A (1975) Kinky helix. Nature 255:530–533CrossRefPubMedGoogle Scholar
  36. 36.
    Lankas F, Lavery R, Maddocks JH (2006) Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure (London 1993) 14:1527–1534CrossRefGoogle Scholar
  37. 37.
    Ackermann D, Rasched G, Verma S et al (2010) Assembly of dsDNA nanocircles into dimeric and oligomeric aggregates. Chem Commun (Camb) 46:4154–4156CrossRefGoogle Scholar
  38. 38.
    Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38CrossRefPubMedGoogle Scholar
  39. 39.
    Lavery R, Moakher M, Maddocks JH et al (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res 37:5917–5929CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Lu X-J, Olson WK (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc 3:1213–1227CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Sutthibutpong T, Harris SA, Noy A (2015) Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA. J Chem Theor Comput 11(6):2768–2775CrossRefGoogle Scholar
  42. 42.
    Dror RO, Dirks RM, Grossman JP et al (2012) Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys 41:429–452CrossRefPubMedGoogle Scholar
  43. 43.
    Goetz AW, Williamson MJ, Xu D et al (2012) Routine microsecond molecular dynamics simulations with amber – part I: generalized born. J Chem Theor Comput 8:1542–1555CrossRefGoogle Scholar
  44. 44.
    Mukhopadhyay A, Fenley AT, Tolokh IS et al (2012) Charge hydration asymmetry : the basic principle and how to use it to test and improve water models charge hydration asymmetry: the basic principle and how to use it to test and improve water models. J Phys Chem B 116:9776–9783CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Mukhopadhyay A, Aguilar BH, Tolokh IS et al (2014) Introducing charge hydration asymmetry into the generalized born model. J Chem Theor Comput 10:1788–1794CrossRefGoogle Scholar
  46. 46.
    Shaw DE, Deneroff MM, Dror RO et al (2008) Anton, a special-purpose machine for molecular dynamics simulation. Commun ACM 51:91–97CrossRefGoogle Scholar
  47. 47.
    Piana S, Lindorff-Larsen K, Shaw DE (2012) Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci 109:17845–17850CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Shaw DE, Grossman JP, Bank JA et al (2014) Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer, SC14: international conference for high performance computing, networking, storage and analysis, pp 41–53Google Scholar
  49. 49.
    Zhao N, Fogg JM, Zechiedrich L et al (2011) Transfection of shRNA-encoding Minivector DNA of a few hundred base pairs to regulate gene expression in lymphoma cells. Gene Ther 18:220–224CrossRefPubMedGoogle Scholar
  50. 50.
    Catanese DJ, Fogg JM, Schrock DE et al (2012) Supercoiled Minivector DNA resists shear forces associated with gene therapy delivery. Gene Ther 19:94–100CrossRefPubMedGoogle Scholar
  51. 51.
    Shibata Y, Kumar P, Layer R et al (2012) Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science (New York) 336:82–86CrossRefGoogle Scholar
  52. 52.
    Tsui V, Case DA (2000) Theory and applications of the generalized born solvation model in. Biopolymers 56:275–291CrossRefPubMedGoogle Scholar
  53. 53.
    Case DA, Darden TA, Cheatham TE III et al (2010) Amber 11. University of California, San Francisco, CAGoogle Scholar
  54. 54.
    Smith DE, Dang LX (1994) Computer simulations of NaCl association in polarizable water. J Chem Phys 100:3757CrossRefGoogle Scholar
  55. 55.
    Shields GC, Laughton CA, Orozco M (1997) Molecular dynamics simulations of the d(T · A · T) triple helix. J Am Chem Soc 119:7463–7469CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Theoretical and Computational Science Center (TaCS)Science Laboratory Building, Faculty of Science, King Mongkut University of Technology ThonburiBang Mod, Thung Khru, BangkokThailand
  2. 2.School of Physics and AstronomyUniversity of LeedsLeedsUK
  3. 3.Astbury Centre for Structural and Molecular BiologyUniversity of LeedsLeedsUK

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