DNA hybridization kinetics: Zippering, internal displacement and sequence dependence

Nucleic Acids Research

Volumn 41, Issue 19, 2013, Pages 8886-8895

  Ouldridge, Thomas E ^a   Šulc, Petr ^a   Romano, Flavio ^a   Doye, Jonathan P K ^a   Louis, Ard A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; OLIGOMER;

ARTICLE; BASE PAIRING; BINDING AFFINITY; DNA BINDING; DNA HYBRIDIZATION; DNA STRUCTURE; ENTHALPY; HYDROGEN BOND; PRIORITY JOURNAL; SIMULATION; TEMPERATURE; TEMPERATURE DEPENDENCE;

BASE PAIRING; BASE SEQUENCE; COMPUTER SIMULATION; DNA; KINETICS; MODELS, MOLECULAR; NUCLEIC ACID HYBRIDIZATION; REPETITIVE SEQUENCES, NUCLEIC ACID; THERMODYNAMICS;

EID: 84886016409     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt687     Document Type: Article

References (53)

1. Watson, J.D. and Crick, F.H.C. (1953) Molecular structure of nucleic acids. Nature, 171, 737-738.
2. Pinheiro, A.V., Han, D., Shih, W.M. and Yan, H. (2011) Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotechnol., 6, 763-772.
3. Bath, J. and Turberfield, A.J. (2007) DNA nanomachines. Nat. Nanotechnol., 2, 275-284.
4. Qian, L. and Winfree, E. (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science, 332, 1196-1201.
5. SantaLucia, J. Jr and Hicks, D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33, 415-440.
6. Dirks, R.M., Bois, J.S., Schaeffer, J.M., Winfree, E. and Pierce, N.A. (2007) Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev., 29, 65-88.
7. Gao, Y., Wolf, L.K. and Georgiadis, R.M. (2006) Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Res., 34, 370-3377.
8. Morrison, L.E. and Stols, L.M. (1993) Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution. Biochemistry, 32, 3095-3104.
9. Zhang, D.Y. and Winfree, E. (2009) Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc., 131, 17303-17314.
10. Craig, M.E., Crothers, D.M. and Doty, P. (1971) Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol., 62, 383-392.
11. Pörschke, D. and Eigen, M. (1971) Co-operative non-enzymatic base recognition. J. Mol. Biol., 62, 361-381.
12. Pörschke, D., Uhlenbeck, O.C. and Martin, F.H. (1973) Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs. Biopolymers, 12, 1313-1335.
13. Lima, W.F., Monia, B.P., Ecker, D.J. and Freier, S.M. (1992) Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry, 31, 12055-12062.
14. Chen, C., Wang, W., Wang, Z., Wei, F. and Zhao, X.S. (2007) Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization. Nucleic Acids Res., 35, 2875-2884.
15. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R. Jr, Merz, K.M., Fergurson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc., 17, 5179-5197.
16. Starr, F.W. and Sciortino, F. (2006) Model for assembly and gelation of four-armed DNA dendrimers. J. Phys. Condens. Matter, 18, 347-353.
17. Ouldridge, T.E., Johnston, I.G., Louis, A.A. and Doye, J.P.K. (2009) The self-assembly of DNA holliday junctions studied with a minimal model. J. Chem. Phys., 130, 065101.
18. Araque, J.C., Panagiotopoulos, A.Z. and Robert, M.A. (2011) Lattice model of oligonucleotide hybridization in solution. i. Model and thermodynamics. J. Chem. Phys., 134, 165103-165116.
19. Linak, M.C., Tourdot, R. and Dorfman, K.D. (2011) Moving beyond Watson-Crick models of coarse grained DNA dynamics. J. Chem. Phys., 135, 205120.
20. Svaneborg, C. (2012) LAMMPS framework for dynamic bonding and an application modeling DNA. Comput. Phys. Commun., 183, 1793-1802.
21. Drukker, K., Wu, G. and Schatz, G.C. (2001) Model simulations of DNA denaturation dynamics. J. Chem. Phys., 114, 579-590.
22. Morriss-Andrews, A., Rottler, J. and Plotkin, S.S. (2010) A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist and chirality. J. Chem. Phys., 132, 035105.
23. Dans, P.D., Zeida, A., Machado, M.R. and Pantano, S. (2010) A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. J. Chem. Theory Comput., 6, 1711-1725.
24. He, Y., Maciejczyk, M., Oldziej, S., Scheraga, H.A. and Liwo, A. (2013) Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Phys. Rev. Lett., 110, 098101.
25. Dasanna, A.K., Destainville, N., Palmeri, J. and Manghi, M. (2013) Slow closure of denaturation bubbles in DNA: Twist matters. Phys. Rev. E., 87, 052703.
26. Sambriski, E.J., Schwartz, D.C. and de Pablo, J.J. (2009) Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis. Proc. Natl Acad. Sci. USA, 106, 18125-18130.
27. Sambriski, E.J., Ortiz, V. and de Pablo, J.J. (2009) Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways. J. Phys. Condens. Matter, 21, 034105.
28. Ouldridge, T.E., Louis, A.A. and Doye, J.P.K. (2011) Structural, mechanical and thermodynamic properties of a coarse-grained model of DNA.J. Chem. Phys., 134, 085101.
29. Ouldridge, T.E. (2011) Coarse-grained modelling of DNA and DNA nanotechnology. Ph.D. Thesis. University of Oxford, 2011 [Published as a book by Springer, Heidelberg, 2012].
30. Š ulc, P., Romano, F., Ouldridge, T.E., Rovigatti, L., Doye, J.P.K. and Louis, A.A. (2012) Sequence-dependent thermodynamics of a coarse-grained DNA model. J. Chem. Phys., 137, 135101.
31. Romano, F., Chakraborty, D., Doye, J.P.K., Ouldridge, T.E. and Louis, A.A. (2013) Coarse-grained simulations of DNA overstretching. J. Chem. Phys., 138, 085101.
32. Romano, F., Hudson, A., Doye, J.P.K., Ouldridge, T.E. and Louis, A.A. (2012) The effect of topology on the structure and free energy landscape of DNA kissing complexes. J. Chem. Phys., 136, 215102.
33. Matek, C., Ouldridge, T.E., Levy, A., Doye, J.P.K. and Louis, A.A. (2012) DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism. J. Phys. Chem. B, 116, 11616-25.
34. De Michele, C., Rovigatti, L., Bellini, T. and Sciortino, F. (2012) Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link. Soft Matter, 8, 8388-8398.
35. Ouldridge, T.E., Louis, A.A. and Doye, J.P.K. (2010) DNA nanotweezers studied with a coarse-grained model of DNA. Phys. Rev. Lett., 104, 178101.
36. Ouldridge, T.E., Hoare, R.L., Louis, A.A., Doye, J.P.K., Bath, J. and Turberfield, A.J. (2013) Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker. ACS Nano, 7, 2479-2490.
37. http://dna.physics.ox.ac.uk/ (25 July 2013, date last accessed).
38. Davidchack, R.L., Handel, R. and Tretyakov, M.V. (2009) Langevin thermostat for rigid body dynamics. J. Chem. Phys., 130, 234101.
39. Murtola, T., Bunkwer, A., Vattulainen, I. and Deserno, M. (2009) Multiscale modeling of emergent materials: biological and soft matter. Phys. Chem. Chem. Phys., 11, 1869-1892.
40. Russo, J., Tartaglia, P. and Sciortino, F. (2009) Reversible gels of patchy particles: role of the valence. J. Chem. Phys., 131, 014504.
41. Allen, R.J., Warren, P.B. and ten Wolde, P.R. (2005) Sampling rare switching events in biochemical networks. Phys. Rev. Lett., 94, 018104.
42. Allen, R.J., Valeriani, C. and ten Wolde, P.R. (2009) Forward flux sampling for rare event simulations. J. Phys. Condens. Matter, 21, 463102.
43. Whitelam, S., Feng, E.H., Hagan, M.F. and Geissler, P.L. (2009) The role of collective motion in examples of coarsening and self-assembly. Soft Matter, 5, 1251-1262.
44. Torrie, G.M. and Valleau, J.P. (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comp. Phys., 23, 187-199.
45. Saenger, W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York.
46. Pörschke, D. (1977) Elementary steps of base recognition and helix-coil transitions in nucleic acids. Mol. Biol. Biochem. Biophys., 24, 191-218.
47. Flamm, W., Fontana, J.M., Hofacker, I.L. and Schuster, P. (2000) RNA folding at elementary step resolution. RNA, 6, 325-338.
48. Schaeffer, J.M. (2013) Stochastic simulation of the kinetics of multiple interacting nucleic acid strands. PhD thesis, California Institute of Technology.
49. Pörschke, D. (1974) Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction. Biophys. Chem., 2, 83-96.
50. Schmitt, T.J. and Knotts, T.A. IV. (2011) Thermodynamics of DNA hybridization on surfaces. J. Chem. Phys., 134, 205105.
51. Hoefert, M.J., Sambriski, E.J. and de Pablo, J.J. (2011) Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides. Soft Matter, 7, 560-566.
52. Schmitt, T.J., Rogers, C. and Knotts, T.A. IV (2013) Exploring the mechanisms of DNA hybridization on a surface. J. Chem. Phys., 138, 035102.
53. Pleij, C.W., Reitveld, K. and Bosch, L. (1985) A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res., 13, 1717-1731.