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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- 1.
Backbone, stacking, and hydrogen-bonding interactions are localized to distinct sites.
References
Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2008) Molecular biology of the cell. Garland Science, 5th edn. ISBN 0815341067
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
Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737
Crick F (1970) Central dogma of molecular biology. Nature 227:561
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T et al (2012) Landscape of transcription in human cells. Nature 489:101
Commons W (2015) File: A-DNA, B-DNA and Z-DNA.png—Wikimedia Commons, the free media repository. Last accessed 18 Apr 2018
Seeman N (1982) Nucleic acid junctions and lattices. J Theor Biol 99:237–247
Fu TJ, Seeman NC (1993) DNA double-crossover molecules. Biochemistry 32:3211–3220
Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539
Wei B, Dai M, Yin P (2012a) Complex shapes self-assembled from single-stranded DNA tiles. Nature 485:623
Ke Y, Ong LL, Shih WM, Yin P (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338:1177–1183
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
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
Mathieu F, Liao S, Kopatsch J, Wang T, Mao C, Seeman NC (2005) Six-Helix bundles designed from DNA. Nano Lett 5:661–665
Zhang DY, Turberfield AJ, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–1125
Bath J, Green SJ, Turberfield AJ (2005) A free-running DNA motor powered by a nicking enzyme. Angew Chem Int Ed 44:4358–4361
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
Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335:831–834
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
Seeman NC, Sleiman HF (2017) DNA nanotechnology. Nat Rev Mater 3:17068
Pinheiro AV, Han D, Shih WM, Yan H (2011) Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol 6:763–772
Genot AJ, Bath J, Turberfield AJ (2011) Reversible logic circuits made of DNA. J Am Chem Soc 133:20080–20083
Seeman NC (2016) Structural DNA nanotechnology. Cambridge University Press
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
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
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
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
Dill KA, MacCallum JL (2012) The protein-folding problem, 50 years on. Science 338:1042–1046
Bustamante C, Liphardt J, Ritort F (2005) The nonequilibrium thermodynamics of small systems. Phys Today 58(7):43–48
Ritort F (2007) The nonequilibrium thermodynamics of small systems. Comptes Rendus Physique 8(5):528–539. Work, dissipation, and fluctuations in nonequilibrium physics
Uhler C, Shivashankar GV (2017) Regulation of genome organization and gene expression by nuclear mechanotransduction. Nat Rev Mol Cell Biol 18:717
Simmel SS, Nickels PC, Liedl T (2014) Wireframe and tensegrity DNA nanostructures. Acc Chem Res 47:1691–1699
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
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
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
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
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
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
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
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
Brooks B, Brooks C, MacKerell A, Nilsson L, Petrella R et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614
Laughton CA, Harris SA (2011) The atomistic simulation of DNA. Wiley Interdiscip Rev Comput Mol Sci 1:590–600
Maffeo C, Aksimentiev A (2017) Molecular mechanism of DNA association with single-stranded DNA binding protein. Nucleic Acids Res 45:12125–12139
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
Severin PMD, Zou X, Gaub HE, Schulten K (2011) Cytosine methylation alters DNA mechanical properties. Nucleic Acids Res. 39:8740–8751
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
Mitchell JS, Laughton CA, Harris SA (2011) Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 39:3928–3938
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
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
Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A (2014). Close encounters with DNA. J Phys Condens Matter 26:413101
Rubinstein M, Colby R (2003) Polymer physics. OUP Oxford, ISBN 9780198520597
Odijk T (1995) Stiff chains and filaments under tension. Macromolecules 28(20):7016–7018
Neukirch S, Marko JF (2011) Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA. Phys Rev Lett 106:138104
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
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
Marko JF, Siggia ED (1995) Stretching DNA. Macromolecules 28:8759–8770
SantaLucia J, Hicks D (2004) The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct 33:415–440
Louis AA (2002) Beware of density dependent pair potentials. J Phys Condens Matter 14:9187
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
Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302
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
Dunn KE, Dannenberg F, Ouldridge TE, Kwiatkowska M, Turberfield AJ, Bath J (2015) Guiding the folding pathway of DNA origami. Nature 525:82
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
Mergell B, Ejtehadi MR, Everaers R (2003) Modeling DNA structure, elasticity, and deformations at the base-pair level. Phys Rev E 68:021911
Arbona JM, Aimé J-P, Elezgaray J (2012) Modeling the mechanical properties of DNA nanostructures. Phys Rev E 86:051912
Dans PD, Walther J, Gómez H, Orozco M (2016) Multiscale simulation of DNA. Curr Opin Struct Biol 37:29–45
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
Savelyev A, Papoian GA (2010) Chemically accurate coarse graining of double-stranded DNA. Proc Natl Acad Sci USA 107:20340–20345
Savelyev A (2012) Do monovalent mobile ions affect DNA’s flexibility at high salt content? Phys Chem Chem Phys 14(7):2250–2254
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
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
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
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
Araque JC, Panagiotopoulos AZ, Robert MA (2011) Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics. J Chem Phys 134(16):165103
Araque JC, Robert MA (2016) Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity. J Chem Phys 144(12):125101
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
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
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
Ouldridge TE, Louis AA, Doye JPK (2011) Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Comput Phys 134:085101
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
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
Romano F, Chakraborty D, Doye JPK, Ouldridge TE, Louis AA (2013) Coarse-grained simulations of DNA overstretching. J Chem Phys 138:085101
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
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
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
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
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
Linak MC, Tourdot R, Dorfman KD (2011) Moving beyond Watson-Crick models of coarse grained DNA dynamics. J Chem Phys 135(20):205102
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
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
Knotts TA, Rathore N, Schwartz DC, de Pablo JJ (2007) A coarse grain model for DNA. J Chem Phys 126(8):084901
Sambriski E, Schwartz D, de Pablo J (2009) A mesoscale model of DNA and its renaturation. Biophys J 96:1675–1690
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
Freeman GS, Hinckley DM, Lequieu JP, Whitmer JK, de Pablo JJ (2014a) Coarse-grained modeling of DNA curvature. J Chem Phys 141(16):165103
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
Lequieu J, Córdoba A, Schwartz DC, de Pablo JJ (2016) Tension-dependent free energies of nucleosome unwrapping. ACS Cent Sci 2(9):660–666
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
Dey P, Bhattacherjee A (2018) Role of macromolecular crowding on the intracellular diffusion of DNA binding proteins. Sci Rep 8(1):844
Lequieu JP, Hinckley DM, de Pablo JJ (2015) A molecular view of DNA-conjugated nanoparticle association energies. Soft Matter 11(10):1919–1929
Chakraborty D, Hori N, Thirumalai D (2018) Sequence-dependent Three Interaction Site (TIS) model for single and double-stranded DNA. ArXiv e-prints
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
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
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
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
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
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
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
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
Cragnolini T, Derreumaux P, Pasquali S (2013) Coarse-grained simulations of RNA and DNA duplexes. J Phys Chem B 117(27):8047–8060
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
Henrich O, Gutiérrez Fosado YA, Curk T, Ouldridge TE (2018) Coarse-grained simulation of DNA using LAMMPS. Eur Phys J E 41(5):57
Snodin BEK (2016) Simulating large DNA nanostructures with a coarse-grained model. PhD thesis, University of Oxford, UK
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
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
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
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
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
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
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
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
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
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
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
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
Reinhardt A, Frenkel D (2016) DNA brick self-assembly with an off-lattice potential. Soft Matter 12(29):6253–6260
Reinhardt A, Frenkel D (2014) Numerical evidence for nucleated self-assembly of DNA brick structures. Phys Rev Lett 112:238103
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
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
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
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
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
Ouldridge TE (2011) Coarse-grained modelling of DNA and DNA self-assembly. PhD thesis, University of Oxford, UK
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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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