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Introduction

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DNA Systems Under Internal and External Forcing

Part of the book series: Springer Theses ((Springer Theses))

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Abstract

At least as deep-rooted in humanity as the curiosity that drove the ancients to study the heavens is the inward-facing, existential questioning that seeks to understand ourselves: life, and its unyielding forward motion. In this chapter, we survey DNA, a molecule critical to the propagation of life, examining its interaction with forces and the myriad modelling strategies that have been employed in studying it to date.

The Word is living, being, spirit, all verdant greening, all creativity. This Word manifests itself in every creature.

—St Hildegard von Bingen

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Notes

  1. 1.

    Backbone, stacking, and hydrogen-bonding interactions are localized to distinct sites.

References

  1. Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239

    Article  ADS  Google Scholar 

  2. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2008) Molecular biology of the cell. Garland Science, 5th edn. ISBN 0815341067

    Google Scholar 

  3. Reich D (2018) Who we are and how we got here: ancient DNA and the new science of the human past, 1st edn. Oxford University Press. ISBN 9780198821250

    Google Scholar 

  4. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737

    Article  ADS  Google Scholar 

  5. Crick F (1970) Central dogma of molecular biology. Nature 227:561

    Article  ADS  Google Scholar 

  6. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T et al (2012) Landscape of transcription in human cells. Nature 489:101

    Article  ADS  Google Scholar 

  7. Commons W (2015) File: A-DNA, B-DNA and Z-DNA.png—Wikimedia Commons, the free media repository. Last accessed 18 Apr 2018

    Google Scholar 

  8. Seeman N (1982) Nucleic acid junctions and lattices. J Theor Biol 99:237–247

    Article  Google Scholar 

  9. Fu TJ, Seeman NC (1993) DNA double-crossover molecules. Biochemistry 32:3211–3220

    Article  Google Scholar 

  10. Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539

    Article  ADS  Google Scholar 

  11. Wei B, Dai M, Yin P (2012a) Complex shapes self-assembled from single-stranded DNA tiles. Nature 485:623

    Article  ADS  Google Scholar 

  12. Ke Y, Ong LL, Shih WM, Yin P (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338:1177–1183

    Article  ADS  Google Scholar 

  13. He Y, Ye T, Su M, Zhang C, Ribbe AE, Jiang W, Mao C (2008) Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452:198

    Article  ADS  Google Scholar 

  14. Liedl T, Hogberg B, Tytell J, Ingber DE, Shih WM (2010) Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat Nanotechnol 5:520–524

    Article  ADS  Google Scholar 

  15. Mathieu F, Liao S, Kopatsch J, Wang T, Mao C, Seeman NC (2005) Six-Helix bundles designed from DNA. Nano Lett 5:661–665

    Article  ADS  Google Scholar 

  16. Zhang DY, Turberfield AJ, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–1125

    Article  ADS  Google Scholar 

  17. Bath J, Green SJ, Turberfield AJ (2005) A free-running DNA motor powered by a nicking enzyme. Angew Chem Int Ed 44:4358–4361

    Article  Google Scholar 

  18. Wickham SFJ, Bath J, Katsuda Y, Endo M, Hidaka K, Sugiyama H, Turberfield AJ (2012) A DNA-based molecular motor that can navigate a network of tracks. Nat Nanotechnol 7:169

    Article  ADS  Google Scholar 

  19. Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335:831–834

    Article  ADS  Google Scholar 

  20. Tay CY, Yuan L, Leong DT (2015) Nature-inspired DNA nanosensor for real-time in situ detection of mRNA in living cells. ACS Nano 9:5609–5617

    Article  Google Scholar 

  21. Seeman NC, Sleiman HF (2017) DNA nanotechnology. Nat Rev Mater 3:17068

    Article  ADS  Google Scholar 

  22. Pinheiro AV, Han D, Shih WM, Yan H (2011) Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol 6:763–772

    Article  ADS  Google Scholar 

  23. Genot AJ, Bath J, Turberfield AJ (2011) Reversible logic circuits made of DNA. J Am Chem Soc 133:20080–20083

    Article  Google Scholar 

  24. Seeman NC (2016) Structural DNA nanotechnology. Cambridge University Press

    Google Scholar 

  25. Gupta AN, Vincent A, Neupane K, Yu H, Wang F, Woodside MT (2011) Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements. Nat Phys 7:631

    Article  Google Scholar 

  26. Engel MC, Ritchie DB, Foster DAN, Beach KSD, Woodside MT (2014) Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse weierstrass integral transform. Phys Rev Lett 113:238104

    Article  ADS  Google Scholar 

  27. Yu H, Gupta AN, Liu X, Neupane K, Brigley AM, Sosova I, Woodside MT (2012) Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates. Proc Natl Acad Sci USA 109:14452–14457

    Article  ADS  Google Scholar 

  28. Pfitzner E, Wachauf C, Kilchherr F, Pelz B, Shih WM, Rief M, Dietz H (2013) Rigid DNA beams for high-resolution single-molecule mechanics. Angew Chem Int Ed 52:7766–7771

    Article  Google Scholar 

  29. Dill KA, MacCallum JL (2012) The protein-folding problem, 50 years on. Science 338:1042–1046

    Article  ADS  Google Scholar 

  30. Bustamante C, Liphardt J, Ritort F (2005) The nonequilibrium thermodynamics of small systems. Phys Today 58(7):43–48

    Article  Google Scholar 

  31. Ritort F (2007) The nonequilibrium thermodynamics of small systems. Comptes Rendus Physique 8(5):528–539. Work, dissipation, and fluctuations in nonequilibrium physics

    Article  ADS  Google Scholar 

  32. Uhler C, Shivashankar GV (2017) Regulation of genome organization and gene expression by nuclear mechanotransduction. Nat Rev Mol Cell Biol 18:717

    Article  Google Scholar 

  33. Simmel SS, Nickels PC, Liedl T (2014) Wireframe and tensegrity DNA nanostructures. Acc Chem Res 47:1691–1699

    Article  Google Scholar 

  34. Grashoff C, Hoffman BD, Brenner MD, Zhou R, Parsons M, Yang MT, McLean MA, Sligar SG, Chen CS, Ha T, Schwartz MA (2010) Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics. Nature 466:263

    Article  ADS  Google Scholar 

  35. Gu H, Yang W, Seeman NC (2010) DNA scissors device used to measure MutS binding to DNA mis-pairs. J Am Chem Soc 132:4352–4357 PMID: 20205420

    Article  Google Scholar 

  36. Nickels PC, Wünsch B, Holzmeister P, Bae W, Kneer LM, Grohmann D, Tinnefeld P, Liedl T (2016) Molecular force spectroscopy with a DNA origami–based nanoscopic force clamp. Science 354:305–307

    Article  ADS  Google Scholar 

  37. Šponer J, Šponer JE, Mládek A, Banáš P, Jurecka P, Otyepka M (2013) How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods 64(1):3–11 Nucleic Acid Structure

    Article  Google Scholar 

  38. Mládek A, Krepl M, Svozil D, Čech P, Otyepka M, Banáš P, Zgarbová M, Jurecká P, Šponer J (2013) Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory. Phys Chem Chem Phys 15:7295–7310

    Article  Google Scholar 

  39. Šponer J, Šponer JE, Mládek A, Banáš P, Jurecka P, Otyepka M (2013) Nature and magnitude of aromatic base stacking in DNA and RNA: quantum chemistry, molecular mechanics, and experiment. Biopolymers 99(12):978–988

    Google Scholar 

  40. Gkionis K, Kruse H, Platts JA, Mládek A, Koča J, Šponer J (2014) Ion binding to quadruplex DNA stems. Comparison of MM and QM descriptions reveals sizable polarization effects not included in contemporary simulations. J Chem Theory Comput 10(3):1326–1340

    Article  Google Scholar 

  41. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179–5197

    Article  Google Scholar 

  42. Brooks B, Brooks C, MacKerell A, Nilsson L, Petrella R et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614

    Article  Google Scholar 

  43. Laughton CA, Harris SA (2011) The atomistic simulation of DNA. Wiley Interdiscip Rev Comput Mol Sci 1:590–600

    Article  Google Scholar 

  44. Maffeo C, Aksimentiev A (2017) Molecular mechanism of DNA association with single-stranded DNA binding protein. Nucleic Acids Res 45:12125–12139

    Article  Google Scholar 

  45. Harris SA, Sands ZA, Laughton CA (2005) Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys J 88:1684–1691

    Article  Google Scholar 

  46. Severin PMD, Zou X, Gaub HE, Schulten K (2011) Cytosine methylation alters DNA mechanical properties. Nucleic Acids Res. 39:8740–8751

    Article  Google Scholar 

  47. Randall GL, Zechiedrich L, Pettitt BM (2009) In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form. Nucleic Acids Res 37:5568–5577

    Article  Google Scholar 

  48. Mitchell JS, Laughton CA, Harris SA (2011) Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 39:3928–3938

    Article  Google Scholar 

  49. Sutthibutpong T, Matek C, Benham C, Slade GG, Noy A, Laughton C, Doye, JKP, Louis AA, Harris SA (2016) Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Res 44:9121–9130

    Google Scholar 

  50. Yoo J, Aksimentiev A (2013) In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proc Natl Acad Sci USA 110:20099–20104

    Article  ADS  Google Scholar 

  51. Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A (2014). Close encounters with DNA. J Phys Condens Matter 26:413101

    Google Scholar 

  52. Rubinstein M, Colby R (2003) Polymer physics. OUP Oxford, ISBN 9780198520597

    Google Scholar 

  53. Odijk T (1995) Stiff chains and filaments under tension. Macromolecules 28(20):7016–7018

    Article  ADS  Google Scholar 

  54. Neukirch S, Marko JF (2011) Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA. Phys Rev Lett 106:138104

    Article  ADS  Google Scholar 

  55. Gross P, Laurens N, Oddershede LB, Bockelmann U, Peterman EJG, Wuite GJL (2011) Quantifying how DNA stretches, melts and changes twist under tension. Nat Phys 7:731–736

    Article  Google Scholar 

  56. Smith SB, Cui Y, Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double-stranded and sinle-stranded DNA molecules. Science 271:795–799

    Article  ADS  Google Scholar 

  57. Marko JF, Siggia ED (1995) Stretching DNA. Macromolecules 28:8759–8770

    Article  ADS  Google Scholar 

  58. SantaLucia J, Hicks D (2004) The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct 33:415–440

    Article  Google Scholar 

  59. Louis AA (2002) Beware of density dependent pair potentials. J Phys Condens Matter 14:9187

    ADS  Google Scholar 

  60. Kim D-N, Kilchherr F, Dietz H, Bathe M (2012) Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res 40:2862–2868

    Article  Google Scholar 

  61. Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302

    Article  ADS  Google Scholar 

  62. Dannenberg F, Dunn KE, Bath J, Kwiatkowska M, Turberfield AJ, Ouldridge TE (2015) Modelling DNA origami self-assembly at the domain level. J Chem Phys 143:165102

    Article  ADS  Google Scholar 

  63. Dunn KE, Dannenberg F, Ouldridge TE, Kwiatkowska M, Turberfield AJ, Bath J (2015) Guiding the folding pathway of DNA origami. Nature 525:82

    Article  ADS  Google Scholar 

  64. Reshetnikov RV, Stolyarova AV, Zalevsky AO, Panteleev DY, Pavlova GV, Klinov DV, Golovin AV, Protopopova AD (2018) A coarse-grained model for DNA origami. Nucleic Acids Res 46:1102–1112

    Article  Google Scholar 

  65. Mergell B, Ejtehadi MR, Everaers R (2003) Modeling DNA structure, elasticity, and deformations at the base-pair level. Phys Rev E 68:021911

    Article  ADS  Google Scholar 

  66. Arbona JM, Aimé J-P, Elezgaray J (2012) Modeling the mechanical properties of DNA nanostructures. Phys Rev E 86:051912

    Article  ADS  Google Scholar 

  67. Dans PD, Walther J, Gómez H, Orozco M (2016) Multiscale simulation of DNA. Curr Opin Struct Biol 37:29–45

    Article  Google Scholar 

  68. Doye JPK, Ouldridge TE, Louis AA, Romano F, Šulc P, Matek C, Snodin BEK, Rovigatti L, Schreck JS, Harrison RM, Smith WPJ (2013) Coarse-graining DNA for simulations of DNA nanotechnology. Phys Chem Chem Phys 15:20395–20414

    Article  Google Scholar 

  69. Savelyev A, Papoian GA (2010) Chemically accurate coarse graining of double-stranded DNA. Proc Natl Acad Sci USA 107:20340–20345

    Article  ADS  Google Scholar 

  70. Savelyev A (2012) Do monovalent mobile ions affect DNA’s flexibility at high salt content? Phys Chem Chem Phys 14(7):2250–2254

    Article  Google Scholar 

  71. Cao Q, Zuo C, Ma Y, Li L, Zhang Z (2011) Interaction of double-stranded DNA with a nanosphere: a coarse-grained molecular dynamics simulation study. Soft Matter 7(2):506–514

    Article  ADS  Google Scholar 

  72. Naômé A, Laaksonen A, Vercauteren DP (2014) A solvent-mediated coarse-grained model of DNA derived with the systematic newton inversion method. J Chem Theory Comput 10(8):3541–3549

    Article  Google Scholar 

  73. Naômé A, Laaksonen A, Vercauteren DP (2015) A coarse-grained simulation study of the structures, energetics, and dynamics of linear and circular DNA with its ions. J Chem Theory Comput 11(6):2813–2826

    Article  Google Scholar 

  74. Yagyu H, Lee J-Y, Kim D-N, Tabata O (2017) Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design. J Phys Chem B 121(19):5033–5039

    Article  Google Scholar 

  75. Araque JC, Panagiotopoulos AZ, Robert MA (2011) Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics. J Chem Phys 134(16):165103

    Article  ADS  Google Scholar 

  76. Araque JC, Robert MA (2016) Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity. J Chem Phys 144(12):125101

    Google Scholar 

  77. Maffeo C, Ngo TTM, Ha T, Aksimentiev A (2014a) A coarse-grained model of unstructured single-stranded DNA derived from atomistic simulation and single-molecule experiment. J Chem Theory Comput 10:2891–2896

    Article  Google Scholar 

  78. Belkin M, Chao S-H, Jonsson MP, Dekker C, Aksimentiev A (2015) Plasmonic nanopores for trapping, controlling displacement, and sequencing of DNA. ACS Nano 9(11):10598–10611

    Article  Google Scholar 

  79. Pud S, Chao S-H, Belkin M, Verschueren D, Huijben T, van Engelenburg C, Dekker C, Aksimentiev A (2016) Mechanical trapping of DNA in a double-nanopore system. Nano Lett 16(12):8021–8028 PMID: 27960493

    Article  ADS  Google Scholar 

  80. Ouldridge TE, Louis AA, Doye JPK (2011) Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Comput Phys 134:085101

    Google Scholar 

  81. Šulc P, Romano F, Ouldridge TE, Rovigatti L, Doye JPK, Louis AA (2012) Sequence-dependent thermodynamics of a coarse-grained DNA model. J Comput Phys 137:135101

    Google Scholar 

  82. Snodin BEK, Randisi F, Mosayebi M, Šulc P, Schreck JS, Romano F, Ouldridge TE, Tsukanov R, Nir E, Louis AA, Doye JPK (2015) Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. J Chem Phys 142:234901

    Article  ADS  Google Scholar 

  83. Romano F, Chakraborty D, Doye JPK, Ouldridge TE, Louis AA (2013) Coarse-grained simulations of DNA overstretching. J Chem Phys 138:085101

    Article  ADS  Google Scholar 

  84. Mosayebi M, Louis AA, Doye JPK, Ouldridge TE (2015) Force-induced rupture of a DNA duplex: from fundamentals to force sensors. ACS Nano 9:11993–12003

    Article  Google Scholar 

  85. Snodin BEK, Romano F, Rovigatti L, Ouldridge TE, Louis AA, Doye JPK (2016) Direct simulation of the self-assembly of a small DNA origami. ACS Nano 10:1724–1737

    Article  Google Scholar 

  86. Ouldridge TE, Hoare RL, Louis AA, Doye JPK, Bath J, Turberfield AJ (2013) Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. ACS Nano 7:2479–2490

    Article  Google Scholar 

  87. Khara DC, Schreck JS, Tomov TE, Berger Y, Ouldridge TE, Doye JPK, Nir E (2018) DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size. Nucleic Acids Res 46:1553–1561

    Article  Google Scholar 

  88. Morriss-Andrews A, Rottler J, Plotkin SS (2010) A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality. J Chem Phys 132:035105

    Article  ADS  Google Scholar 

  89. Linak MC, Tourdot R, Dorfman KD (2011) Moving beyond Watson-Crick models of coarse grained DNA dynamics. J Chem Phys 135(20):205102

    Article  ADS  Google Scholar 

  90. Markegard CB, Fu IW, Reddy KA, Nguyen HD (2015) Coarse-grained simulation study of sequence effects on DNA hybridization in a concentrated environment. J Phys Chem B 119(5):1823–1834

    Article  Google Scholar 

  91. Markegard CB, Gallivan CP, Cheng DD, Nguyen HD (2016) Effects of concentration and temperature on DNA hybridization by two closely related sequences via large-scale coarse-grained simulations. J Phys Chem B 120(32):7795–7806

    Article  Google Scholar 

  92. Knotts TA, Rathore N, Schwartz DC, de Pablo JJ (2007) A coarse grain model for DNA. J Chem Phys 126(8):084901

    Article  ADS  Google Scholar 

  93. Sambriski E, Schwartz D, de Pablo J (2009) A mesoscale model of DNA and its renaturation. Biophys J 96:1675–1690

    Article  Google Scholar 

  94. Hinckley DM, Freeman GS, Whitmer JK, de Pablo JJ (2013) An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization. J Chem Phys 139:144903

    Article  ADS  Google Scholar 

  95. Freeman GS, Hinckley DM, Lequieu JP, Whitmer JK, de Pablo JJ (2014a) Coarse-grained modeling of DNA curvature. J Chem Phys 141(16):165103

    Article  ADS  Google Scholar 

  96. Freeman GS, Lequieu JP, Hinckley DM, Whitmer JK, de Pablo JJ (2014b) DNA shape dominates sequence affinity in nucleosome formation. Phys Rev Lett 113:168101

    Article  ADS  Google Scholar 

  97. Lequieu J, Córdoba A, Schwartz DC, de Pablo JJ (2016) Tension-dependent free energies of nucleosome unwrapping. ACS Cent Sci 2(9):660–666

    Article  Google Scholar 

  98. Hinckley DM, Lequieu JP, de Pablo JJ (2014) Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects. J Chem Phys 141(3):035102

    Article  ADS  Google Scholar 

  99. Dey P, Bhattacherjee A (2018) Role of macromolecular crowding on the intracellular diffusion of DNA binding proteins. Sci Rep 8(1):844

    Article  ADS  Google Scholar 

  100. Lequieu JP, Hinckley DM, de Pablo JJ (2015) A molecular view of DNA-conjugated nanoparticle association energies. Soft Matter 11(10):1919–1929

    Article  ADS  Google Scholar 

  101. Chakraborty D, Hori N, Thirumalai D (2018) Sequence-dependent Three Interaction Site (TIS) model for single and double-stranded DNA. ArXiv e-prints

    Google Scholar 

  102. Korolev N, Luo D, Lyubartsev AP, Nordenskild L (2014) A coarse-grained DNA model parameterized from atomistic simulations by inverse Monte Carlo. Polymers 6:1655–1675

    Article  Google Scholar 

  103. Korolev N, Nordenskiöld L, Lyubartsev AP (2016) Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome. Adv Colloid Interface Sci 232:36–48

    Article  Google Scholar 

  104. Uusitalo JJ, Ingólfsson HI, Akhshi P, Tieleman DP, Marrink SJ (2015) Martini coarse-grained force field: extension to DNA. J Chem Theory Comput 11(8):3932–3945

    Article  Google Scholar 

  105. He Y, Maciejczyk M, Ołdziej S, Scheraga HA, Liwo A (2013) Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Phys Rev Lett 110:098101

    Article  ADS  Google Scholar 

  106. Dans PD, Zeida A, Machado MR, Pantano S (2010) A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. J Chem Theory Comput 6(5):1711–1725

    Article  Google Scholar 

  107. Dans PD, Darré L, Machado MR, Zeida A, Brandner AF, Pantano S (2013) Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level. In: Setubal JC, Almeida NF (eds) Advances in bioinformatics and computational biology. Springer International Publishing, Cham, pp 71–81. ISBN 978-3-319-02624-4

    Chapter  Google Scholar 

  108. Machado MR, Pantano S (2015) Exploring lacI-DNA dynamics by multiscale simulations using the SIRAH force field. J Chem Theory Comput 11(10):5012–5023

    Article  Google Scholar 

  109. Brandner A, Schüller A, Melo F, Pantano S (2018) Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes. Biochem Biophys Res Commun 498(2):319–326

    Article  Google Scholar 

  110. Cragnolini T, Derreumaux P, Pasquali S (2013) Coarse-grained simulations of RNA and DNA duplexes. J Phys Chem B 117(27):8047–8060

    Article  Google Scholar 

  111. Cragnolini T, Chakraborty D, Šponer J, Derreumaux P, Pasquali S, Wales DJ (2017) Multifunctional energy landscape for a DNA G-quadruplex: an evolved molecular switch. J Chem Phys 147(15):152715

    Article  ADS  Google Scholar 

  112. Henrich O, Gutiérrez Fosado YA, Curk T, Ouldridge TE (2018) Coarse-grained simulation of DNA using LAMMPS. Eur Phys J E 41(5):57

    Article  Google Scholar 

  113. Snodin BEK (2016) Simulating large DNA nanostructures with a coarse-grained model. PhD thesis, University of Oxford, UK

    Google Scholar 

  114. Sharma R, Schreck JS, Romano F, Louis AA, Doye JPK (2017) Characterizing the motion of jointed DNA nanostructures using a coarse-grained model. ACS Nano 11:12426–12435

    Article  Google Scholar 

  115. Schreck JS, Romano F, Zimmer MH, Louis AA, Doye JPK (2016) Characterizing DNA star-tile-based nanostructures using a coarse-grained model. ACS Nano 10:4236–4247

    Article  Google Scholar 

  116. Castro CE, Kilchherr F, Kim D-N, Shiao EL, Wauer T, Wortmann P, Bathe M, Dietz H (2011) A primer to scaffolded DNA origami. Nat Methods 8:221

    Article  Google Scholar 

  117. Pan K, Kim D-N, Zhang F, Adendorff MR, Yan H, Bathe M (2014) Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nat Commun 5:5578

    Article  ADS  Google Scholar 

  118. Sun W, Boulais E, Hakobyan Y, Wang WL, Guan A, Bathe M, Yin P (2014) Casting inorganic structures with DNA molds. Science 346(6210):1258361

    Article  Google Scholar 

  119. Sedeh RS, Pan K, Adendorff MR, Hallatschek O, Bathe K-J, Bathe M (2016) Computing nonequilibrium conformational dynamics of structured nucleic acid assemblies. J Chem Theory Comput 12(1):261–273

    Article  Google Scholar 

  120. Pan K, Bricker WP, Ratanalert S, Bathe M (2017) Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Res 45(11):6284–6298

    Article  Google Scholar 

  121. Klaus M, Prokoph N, Girbig M, Wang X, Huang Y-H, Srivastava Y, Hou L, Narasimhan K, Kolatkar PR, Francois M, Jauch R (2016) Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction. Nucleic Acids Res 44(8):3922–3935

    Article  Google Scholar 

  122. Li C-Y, Hemmig EA, Kong J, Yoo J, Hernández-Ainsa S, Keyser UF, Aksimentiev A (2015) Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field. ACS Nano 9(2):1420–1433

    Article  Google Scholar 

  123. Göpfrich K, Li C-Y, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF (2016a) Ion channels made from a single membrane-spanning DNA duplex. Nano Lett 16(7):4665–4669

    Article  ADS  Google Scholar 

  124. Göpfrich K, Li C-Y, Ricci M, Bhamidimarri SP, Yoo J, Gyenes B, Ohmann A, Winterhalter M, Aksimentiev A, Keyser UF (2016b) Large-conductance transmembrane porin made from DNA origami. ACS Nano 10(9):8207–8214

    Article  Google Scholar 

  125. Slone SM, Li C-Y, Yoo J, Aksimentiev A (2016a) Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity. New J Phys 18(5):055012

    Article  Google Scholar 

  126. Reinhardt A, Frenkel D (2016) DNA brick self-assembly with an off-lattice potential. Soft Matter 12(29):6253–6260

    Article  ADS  Google Scholar 

  127. Reinhardt A, Frenkel D (2014) Numerical evidence for nucleated self-assembly of DNA brick structures. Phys Rev Lett 112:238103

    Article  ADS  Google Scholar 

  128. Fonseca P, Romano F, Schreck JS, Ouldridge TE, Doye JPK, Louis AA (2018) Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly. J Chem Phys 148(13):134910

    Article  ADS  Google Scholar 

  129. Shi Z, Castro CE, Arya G (2017) Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations. ACS Nano 11(5):4617–4630

    Article  Google Scholar 

  130. Srinivas N, Ouldridge TE, Šulc P, Schaeffer JM, Yurke B, Louis AA, Doye JPK, Winfree E (2013) On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res 41:10641–10658

    Article  Google Scholar 

  131. Šulc P, Ouldridge TE, Romano F, Doye JPK, Louis AA (2014) Simulating a burnt-bridges DNA motor with a coarse-grained DNA model. Nat Comput 13(4):535–547

    Article  MathSciNet  Google Scholar 

  132. Kočar V, Schreck JS, Čeru S, Gradišar H, Bašić N, Pisanski T, Doye JPK, Jerala R (2016) Design principles for rapid folding of knotted DNA nanostructures. Nat Commun 7:10803

    Google Scholar 

  133. Ouldridge TE (2011) Coarse-grained modelling of DNA and DNA self-assembly. PhD thesis, University of Oxford, UK

    Google Scholar 

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  1. John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA

    Dr. Megan Clare Engel

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Engel, M.C. (2019). Introduction. In: DNA Systems Under Internal and External Forcing. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-030-25413-1_1

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