Skip to main content
SpringerLink
Log in

Introduction

  • Chapter
  • First Online:
Coarse-Grained Modelling of DNA and DNA Self-Assembly

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

  • 771 Accesses

Abstract

In this book I introduce a coarse-grained model of deoxyribonucleic acid (DNA) which is optimized for reproducing the thermodynamic and mechanical changes accompanying the formation of B-DNA duplexes from single strands. This process, known as hybridization, is a vital component of the fast-growing field of DNA nanotechnology, as well as being relevant to a wide range of biological systems.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

Notes

  1. 1.

    Chargaff et al. had shown that of the four base types in DNA, the pair adenine and thymine always occur in equal amounts, as do guanine and cytosine [11]. Gulland et al. had also suggested that bases were linked by hydrogen-bonding [12].

  2. 2.

    Ribonucleic acid is a similar to DNA, but possesses a modified sugar and thymine groups are replaced by uracil [10].

  3. 3.

    In this context a dynamical model is one that makes predictions for the kinetics of processes, as opposed to a statistical model which does not directly give kinetic information.

References

  1. R. Dahm. Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Hum. Genet., 122(6):565–581, 2008.

    Google Scholar 

  2. G. K. Hunter. Phoebus Levene and the tetranucleotide structure of nucleic acids. Ambix, 46(2):73–103, 1999.

    Google Scholar 

  3. P. A. Levene. The structure of yeast nucleic acid: IV. ammonia hydrolysis. J. Biol. Chem., 40(2):415–424, 1919.

    Google Scholar 

  4. F. Griffith. The significance of pneumococcal types. J. Hyg., 27(2):113–159, 1928.

    Google Scholar 

  5. M. P. Ball. http://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg

  6. R. Wheeler. http://en.wikipedia.org/wiki/File:A-DNA,_B-DNA_and_Z-DNA.png

  7. O. T. Avery, C. M. MacCleod, and M. McCarty. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. J. Exp. Med., 79(2):137–158, 1944.

    Google Scholar 

  8. S. Neidle. Oxford Handbook of Nucleic Acid Structure. Oxford University Press, Oxford, 1999.

    Google Scholar 

  9. R. Franklin and R. G. Gosling. Molecular configuration in sodium thymonucleate. Nature, 171:738–740, 1953.

    Google Scholar 

  10. W. Saenger. Principles of Nucleic Acid Structure. Springer-Verlag, New York, 1984.

    Google Scholar 

  11. E. Chargaff et al. The composition of the desoxyribonucleic acid of salmon sperm. J. Biol. Chem., 192(1):223–230, 1951.

    Google Scholar 

  12. J. M. Creeth, J. M. Gulland, and D. O. Jordan. Deoxypentose nucleic acids; viscosity and streaming birefringence of solutions of the sodium salt of the deoxypentose nucleic acid of calf thymus. J. Chem. Soc., 25:1141–1145, 1947.

    Google Scholar 

  13. B. Alberts et al. Molecular Biology of the Cell, 4th ed. Garland Science, New York, 2002.

    Google Scholar 

  14. P. J. Hagerman. Flexibility of DNA. Ann. Rev. Biophys. Biophys. Chem., 17:265–286, 1988.

    Google Scholar 

  15. T. Kato et al. High-resolution structural analysis of a DNA nanostructure by cryoEM. Nano Letters, 9(7):2747–2750, 2009.

    Google Scholar 

  16. N. R. Kallenbach, R-I. Ma, and N. C. Seeman. An immobile nucleic acid junction constructed from oligonucleotides. Nature, 305(5937):829–831, 1983.

    Google Scholar 

  17. T. J. Fu and N. C. Seeman. DNA double-crossover molecules. Biochemistry, 32(13):3211, 1993.

    Google Scholar 

  18. H. Yan, et al. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science, 301(5641):1882–1884, 2003.

    Google Scholar 

  19. E. Winfree et al. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539, 1998.

    Google Scholar 

  20. J. Malo et al. Engineering a 2D protein-DNA crystal. Angew. Chem. Int. Ed., 44:3057–3061, 2005.

    Google Scholar 

  21. J. Zheng et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature, 461:74, 77, 2009.

    Google Scholar 

  22. D. N. Selmi et al. DNA-templated protein arrays for single-molecule imaging. Nano Lett., 11(2):657–660, 2011.

    Google Scholar 

  23. J. Chen and N. C. Seeman. Synthesis from DNA of a molecule with the connectivity of a cube. Nature, 350(6319):631–633, 1991.

    Google Scholar 

  24. Y. Zhang and N. C. Seeman. Construction of a DNA-truncated octahedron. J. Am. Chem. Soc., 116(5):1661, 1994.

    Google Scholar 

  25. R. P. Goodman et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science, 310:1661–1665, 2005.

    Google Scholar 

  26. C. M. Erben, R. P. Goodman, and A. J. Turberfield. A self-assembled DNA bipyramid. J. Am. Chem. Soc., 129(22):6992–6993, 2007.

    Google Scholar 

  27. W. M. Shih, J. D. Quispe, and G. F. Joyce. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature, 427(6975):618–621, 2004.

    Google Scholar 

  28. F. F. Andersen et al. Assembly and structural analysis of a covalently closed nano-scale DNA cage. Nucl. Acids Res., 36(4):1113–1119, 2008.

    Google Scholar 

  29. Y. He et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature, 452:198–201, 2008.

    Google Scholar 

  30. Z. Li et al. A replicable tetrahedral nanostructure self-assembled from a single DNA strand. J. Am. Chem. Soc., 131(36):13093–13098, 2009.

    Google Scholar 

  31. P. W. K. Rothemund. Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082):297–302, 2006.

    Google Scholar 

  32. E. S. Andersen et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459:73–76, 2009.

    Google Scholar 

  33. Y. Ke et al. Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano Lett., 9(6):2445–2447, 2009.

    Google Scholar 

  34. S. M. Douglas et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459:414–418, 2009.

    Google Scholar 

  35. H. Dietz, S. M. Douglas, and W. M. Shih. Folding DNA into twisted and curved nanoscale shapes. Science, 325(5941):725–730, 2009.

    Google Scholar 

  36. D. Han et al. DNA origami with complex curvatures in three-dimensional space. Science, 332(6027):342–346, 2011.

    Google Scholar 

  37. S. F. J. Wickham et al. Direct observation of stepwise movement of a synthetic molecular transporter. Nat. Nanotechnol., 6:166–169, 2011.

    Google Scholar 

  38. M. J. Berardi et al. Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature, Published online, 2011.

    Google Scholar 

  39. M. Endo et al. DNA prism structures constructed by folding of multiple rectangular arms. J. Am. Chem. Soc., 131(43):15570–15571, 2009.

    Google Scholar 

  40. Z. Li et al. Molecular behavior of DNA origami in higher-order self-assembly. J. Am. Chem. Soc., 132(38):13545–13552, 2010.

    Google Scholar 

  41. S. Woo and P. W. K. Rothemund. Programmable molecular recognition based on the geometry of DNA nanostructures. Nat. Chem., 3:620–627, 2011.

    Google Scholar 

  42. T. Liedl et al. Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat. Nanotechnol., 5(7):520–524, 2010.

    Google Scholar 

  43. F. A. Aldaye and H. F. Sleiman. Modular acces to structurally switchable 3D discrete DNA assemblies. J. Am. Chem. Soc., 129:13376–13377, 2007.

    Google Scholar 

  44. J. Zimmermann et al. Self-assembly of a DNA dodecahedron from 20 trisoligonucleotides with C(3h) linkers. Angew. Chem. Int. Ed., 47(19):3626–3630, 2008.

    Google Scholar 

  45. A. J. Kim, P. L. Biancaniello, and J. C. Crocker. Engineering DNA-mediated colloidal crystallization. Langmuir, 22(5):1991–2001, 2006.

    Google Scholar 

  46. S. H. Ko et al. Synergistic self-assembly of RNA and DNA molecules. Nat. Chem., 2:1050–1055, 2010.

    Google Scholar 

  47. P. Guo. The emerging field of RNA nanotechnology. Nat. Nanotechnol., 5:833–842, 2010.

    Google Scholar 

  48. A. V. Pinhiero et al. Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotechnol., 6:763–772, 2011.

    Google Scholar 

  49. M. F. Hagan and D. Chandler. Dynamic pathways for viral capsid assembly. Biophys. J., 91:42–54, 2006.

    Google Scholar 

  50. A. W. Wilber et al. Reversible self-assembly of patchy particles into monodisperse icosahedral clusters. J. Chem. Phys., 127(8):085106, 2007.

    Google Scholar 

  51. T. E. Ouldridge et al. The self-assembly of DNA Holliday junctions studied with a minimal model. J. Chem. Phys., 130:065101, 2009.

    Google Scholar 

  52. J. Bath and A. J. Turberfield. DNA nanomachines. Nat. Nanotechnol., 2:275–284, 2007.

    Google Scholar 

  53. B. Yurke and A. Mills. Using DNA to power nanostructures. Gen. Program. Evol. Mach., 4:111–122, 2003.

    Google Scholar 

  54. B. Yurke et al. A DNA-fueled molecular machine made of DNA. Nature, 406:605–608, 2000.

    Google Scholar 

  55. R. P. Goodman et al. Reconfigurable, braced, three-dimensional DNA nanostructures. Nat. Nanotechnol., 3:93–96, 2008.

    Google Scholar 

  56. P. K. Lo et al. Loading and selective release of cargo in DNA nanotubes with longitudinal variation. Nat. Chem., 2:319–328, 2010.

    Google Scholar 

  57. D. Han et al. Folding and cutting DNA into reconfigurable topological nanostructures. Nat. Nanotechnol., 5:712–717, 2010.

    Google Scholar 

  58. S. M. Douglas, I. Bachelet and G. M. Church. A logic-gated nanorobot for targeted transport of molecular payloads. Science, 335:831–824, 2012.

    Google Scholar 

  59. W. B. Sherman and N. C. Seeman. A precisely controlled DNA biped walking device. Nano Lett., 4(7):1203–1207, 2004.

    Google Scholar 

  60. J.-S. Shin and N. A. Pierce. A synthetic DNA walker for molecular transport. J. Am. Chem. Soc., 126(35):10834–10835, 2004.

    Google Scholar 

  61. J. Bath, S. J. Green, and A. J. Turberfield. A free-running DNA motor powered by a nicking enzyme. Angew. Chem. Int. Ed., 117(28):4432–4435, 2005.

    Google Scholar 

  62. Y. Tian et al. A DNAzyme that walks processively and autonomously along a one-dimensional track. Angew. Chem. Int. Ed., 44(28):4355–4358, 2005.

    Google Scholar 

  63. A. J. Turberfield et al. DNA fuel for free-running nanomachines. Phys. Rev. Lett., 90(11):118102–118105, 2003.

    Google Scholar 

  64. T. Omabegho, R. Sha, and N. C. Seeman. A bipedal DNA brownian motor with coordinated legs. Science, 324:67–71, 2009.

    Google Scholar 

  65. J. Bath et al. Mechanism for a directional, processive and reversible DNA motor. Small, 5:1513–1516, 2009.

    Google Scholar 

  66. S. J. Green, J. Bath, and A. J. Turberfield. Coordinated chemoechanical cycles: a mechanism for autonomous molecular motion. Phys. Rev. Lett., 101(23):238101, 2008.

    Google Scholar 

  67. S. Venkataraman et al. An autonomous polymerization motor powered by DNA hybridization. Nat. Nanotechnol., 2:490–494, 2007.

    Google Scholar 

  68. R. A. Muscat, J. Bath, and A. J. Turberfield. A programmable molecular robot. Nano Lett., 11(3):982–987, 2011.

    Google Scholar 

  69. M. L. McKee et al. Multistep DNA-templated reactions for the synthesis of functional sequence controlled oligomers. Angew. Chem. Int. Ed., 49(43):7948–7951, 2010.

    Google Scholar 

  70. H. Gu et al. A proximity-based programmable DNA nanoscale assembly line. Nature, 465:202–205, 2010.

    Google Scholar 

  71. H. Liu and D. Liu. DNA nanomachines and their functional evolution. Chem. Commun. 19:2625–2636, 2009.

    Google Scholar 

  72. L. M. Adleman. Molecular computation of solutions to combinatorial problems. Science, 266(5187):1021–1024, 1994.

    Google Scholar 

  73. S. Tagore et al. DNA computation: application and perspectives. J. Proteomics Bioinform., 3:234–343, 2010.

    Google Scholar 

  74. G. Seelig et al. Enzyme-free nucleic acid logic circuits. Science, 314(5805):1585–1588, 2006.

    Google Scholar 

  75. S. Venkataraman et al. Selective cell death mediated by small conditional RNAs. Proc. Natl. Acad. Sci. U.S.A., 107(39):16777–16782, 2010.

    Google Scholar 

  76. T. Liedl and F. C. Simmel. Switching the conformation of a DNA molecule with a chemical oscillator. Nano Lett., 5(10):1894–1898, 2005.

    Google Scholar 

  77. R. R. Sinden. DNA structure and function. Academic Press Inc., London, 1994.

    Google Scholar 

  78. M. Orozco et al. Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev., 32:350–364, 2003.

    Google Scholar 

  79. R. Lavery et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucl. Acids Res., 38:299–313, 2010.

    Google Scholar 

  80. A. Pérez, F. J. Luque, and M. Orozco. Dynamics of B-DNA on the microsecond time scale. J. Am. Chem. Soc., 129(47):14739–14745, 2007.

    Google Scholar 

  81. C. Mura and A. J. McCammon. Molecular dynamics of a \(\kappa \) B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucl. Acids Res., 36(15):4941–4955, 2008.

    Google Scholar 

  82. S. Kannan and M. Zacharias. Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations. Phys. Chem. Chem. Phys., 11:10589–10595, 2009.

    Google Scholar 

  83. E. J. Sorin et al. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys. J., 85:790–803, 2003.

    Google Scholar 

  84. S. Kannan and M. Zacharias. Folding a DNA hairpin loop structurre in explicit solvent using replica-exchange molecular dynaics simulations. Biophys. J., 93(9):3218–3228, 2007.

    Google Scholar 

  85. D. Swigon. Mathematics of DNA structure, function and interactions, volume 150 of The IMA volumes on mathematics and its applications, chapter 13, pages 293–320. Springer, New York, 2009.

    Google Scholar 

  86. W. B. Sherman and N. C. Seeman. Design of minimally strained nucleic acid nanotubes. Biophys. J., 90(12):4546–4557, 2006.

    Google Scholar 

  87. C. E. Castro, M. Bathe, and H. Dietz. A primer to scaffolded DNA origami. Nat. Meth., 8:221–229, 2011.

    Google Scholar 

  88. S. Khalid et al. DNA and lipid bilayers: self-assembly and insertion. J. R. Soc. Interface, 5:241–250, 2008.

    Google Scholar 

  89. J. Corsi et al. DNA lipoplexes: Formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation. Langmuir, 26(14):12119–12125, 2010.

    Google Scholar 

  90. D. Poland and H. A. Scheraga. Occurrence of a phase transition in nucleic acid models. J. Chem. Phys., 45:1464, 1966.

    Google Scholar 

  91. J. SantaLucia, Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A., 17(95(4)):1460–1465, 1998.

    Google Scholar 

  92. J. SantaLucia, Jr. and D. Hicks. The thermodynamics of DNA structural motifs. Ann. Rev. Biophys. Biomol. Struct., 33:415–440, 2004.

    Google Scholar 

  93. R. Everaers, S. Kumar, and C. Simm. Unified description of poly- and oligonucleotide DNA melting: nearest-neighbor, poland-sheraga, and lattice models. Phys. Rev. E, 75:041918, 2007.

    Google Scholar 

  94. T. Dauxois, M. Peyrard, and A. R. Bishop. Dynamics and thermodynamics of a nonlinear model for dna denaturation. Phys. Rev. E, 47(1):684–695, 1993.

    Google Scholar 

  95. M. Barbi et al. A twist opening model for DNA. J. Biol. Phys., 24:97–114, 1999.

    Google Scholar 

  96. C. Nisoli and A. R. Bishop. Thermomechanics of, DNA: theory of thermal stability under load. Phys. Rev. Lett., 107, 068102, 2011

    Google Scholar 

  97. N. B. Becker and R. Everaers. DNA nanomechanics: how proteins deform the double helix. J. Chem. Phys., 130:135102, 2009.

    Google Scholar 

  98. F. Lankaš et al. On the parameterization of rigid basepair models of DNA from molecular dynamics simulations. Phys. Chem. Chem. Phys., 11:10565–10588, 2009.

    Google Scholar 

  99. M. Paliy, R. Melnik, and B. A. Shapiro. Coarse graining RNA nanostructures for molecular dynamics simulations. Phys. Biol., 7(3):03601, 2010

    Google Scholar 

  100. F. Trovato and V. Tozzini. Supercoiling and local denaturation of plasmids with a minimalist DNA model. J. Phys. Chem. B, 112(42):13197–13200, 2008.

    Google Scholar 

  101. M. Sayar, B. Avşarolu, and A. Kabakçolu. Twist-writhe partitioning in a coarse-grained DNA minicircle model. Phys. Rev. E, 81:041916, 2010.

    Google Scholar 

  102. A. Savelyev and G. A. Papoian. Chemically accurate coarse graining of double-stranded DNA. Proc. Natl. Acad. Sci. U.S.A., 107(47):20340–20345, 2010.

    Google Scholar 

  103. P. D. Dans et al. A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. J. Chem. Theory Comput., 6(5):1711–1725, 2010.

    Google Scholar 

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

    Google Scholar 

  105. K. Voltz et al. Coarse-grained force field for the nucleosome from self-consistent multiscaling. J. Comput. Chem., 29(9):1429–1439, 2008.

    Google Scholar 

  106. A. A. Louis. Beware of density dependent pair potentials. J. Phys. Condens. Matter, 14:9187, 2002.

    Google Scholar 

  107. M. E. Johnson, T. Head-Gordon, and A. A. Louis. Representability problems for coarse-grained water potentials. J. Chem. Phys., 126:144509, 2007.

    Google Scholar 

  108. C. Hyeon and D. Thirumalai. Mechanical unfolding of RNA hairpins. Proc. Natl. Acad. Sci. U.S.A., 102(19):6789–6794, 2005.

    Google Scholar 

  109. C. Hyeon and D. Thirumulai. Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys. J., 92(3):731–743, 2007.

    Google Scholar 

  110. F. Ding et al. Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms. RNA, 14:1164–1173, 2008.

    Google Scholar 

  111. S. Pasquali and P. Derreumaux. HiRE-RNA: A high resolution coarse-grained energy model for RNA. J. Phys. Chem. B, 114(37):11957–11966, 2010.

    Google Scholar 

  112. A. Dickson et al. Flow-dependent unfolding and refolding of an RNA by nonequilibrium umbrella sampling. J. Chem. Theory. Compur

    Google Scholar 

  113. K. Drukker, G. Wu, and G. C. Schatz. Model simulations of DNA denaturation dynamics. J. Chem. Phys., 114(1):579–590, 2001.

    Google Scholar 

  114. M. Sales-Pardo et al. Mesoscopic modelling fo nucleic acid chain dynamics. Phys. Rev. E, 71:051902, 2005.

    Google Scholar 

  115. F. W. Starr and F. Sciortino. Model for assembly and gelation of four-armed DNA dendrimers. J. Phys. Condens. Matter, 18:L347–L353, 2006.

    Google Scholar 

  116. M. Kenward and K. D. Dorfman. Brownian dynamics simulations of single-stranded DNA hairpins. J. Chem. Phys., 130:095101, 2009.

    Google Scholar 

  117. M. C. Linak and K. Dorfman. Analysis of a DNA simulation model through hairpin melting experiments. J. Chem. Phys., 133(12):125101–125112, 2010.

    Google Scholar 

  118. S. Niewieczerzał and M. Cieplak. Stretching and twisting of the DNA duplexes in coarse-grained dynamical models. J. Phys. Condens. Matter, 21(47):474221, 2009.

    Google Scholar 

  119. T. A. Knotts et al. A coarse grain model for DNA. J. Chem. Phys., 126, 084901, 2007.

    Google Scholar 

  120. F. B. Bombelli et al. DNA closed nanostructures: a structural and Monte Carlo simulation study. J. Phys. Chem. B, 112(48):15283, 15294, 2008.

    Google Scholar 

  121. E. J. Sambriski, V. Ortiz, and J. J. de Pablo. Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways. J. Phys. Condens. Matter, 21, 034105, 2009.

    Google Scholar 

  122. E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo. A mesoscal model of DNA and its renaturation. Biophys. J., 96:1675–1690, 2009.

    Google Scholar 

  123. T. R. Prytkova et al. DNA melting in small-molecule-DNA-hybrid dimer structures: experimental characterization and coarse-grained molecular dynamics simulations. J. Phys. Chem. B, 114(8):2627–2634, 2010.

    Google Scholar 

  124. R. C. DeMille, T. E. Cheatham III, and V. Molinero. A coarse-grained model of DNA with explicit solvation by water and ions. J. Phys. Chem. B, 115(1):132–142, 2011.

    Google Scholar 

  125. V. Ortiz and J. J. de Pablo. Molecular origins of DNA flexibility: sequence effects on conformational and mechanical properties. Phys. Rev. Lett., 106(23):238107–238110, 2011.

    Google Scholar 

  126. J. C. Araque, A. Z. Panagiotopoulos, and M. A. Robert. Lattice model of oligonucleotide hybridization in solution. i. Model and thermodynamics. J. Chem. Phys., 134(16):165103–165116, 2011.

    Google Scholar 

  127. T. J. Schmitt and T. A. Knotts IV. Thermodynamics of DNA hybridization on surfaces. J. Chem. Phys., 134, 205105–205113, 2011.

    Google Scholar 

  128. M. J. Hoefert, E. J. Sambriski, and J. J. de Pablo. Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides. Soft Matter, 7:560–566, 2011.

    Google Scholar 

  129. S. Pitchiaya and Y. Krishnan. First blueprint, now bricks: DNA as construction material on the nanoscale. Chem. Soc. Rev., 35:1111–1121, 2006.

    Google Scholar 

  130. M. C. Murphy et al. Probing single-stranded DNA conformational flexibility using flourescence spectroscopy. Biophys. J., 86:2530–2537, 2004.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. University of Oxford, Oxford, UK

    Dr. Thomas E. Ouldridge

Authors
  1. Dr. Thomas E. Ouldridge
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Ouldridge, T.E. (2012). Introduction. In: Coarse-Grained Modelling of DNA and DNA Self-Assembly. Springer Theses. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30517-7_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-30517-7_1

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30516-0

  • Online ISBN: 978-3-642-30517-7

  • eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)

Publish with us

Policies and ethics

Search

Navigation