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DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model

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DNA Computing and Molecular Programming (DNA 2012)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7433))

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Abstract

We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework [C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012)]. In our model, a single nucleotide or domain is represented by a single interaction site. Complementary sites can reversibly hybridize and dehybridize during a simulation. This bond dynamics induces a dynamics of the angular and dihedral bonds, that model the collective effects of chemical structure on the hybridization dynamics. We use the DNA model to perform simulations of the self-assembly kinetics of DNA tetrahedra, an icosahedron, as well as strand displacement operations used in DNA computation.

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References

  1. Adleman, L.M.: Molecular computation of solutions to combinatorial problem. Science 266, 1021 (1994)

    Article  Google Scholar 

  2. Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H., Oliveira, C.L.P., Pedersen, J.S., Birkedal, V., Besenbacher, F., Gothelf, K.V., Kjems, J.: Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73 (2008)

    Article  Google Scholar 

  3. Bhatia, D., Mehtab, S., Krishnan, R., Indi, S.S., Basu, A., Krishnan, Y.: Icosahedral DNA nanocapsules by modular assembly. Angew. Chem. 121, 4198 (2009)

    Article  Google Scholar 

  4. Brooks, B.R., Brooks III, C.L., Mackerell Jr., A.D., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A.R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R.W., Post, C.B., Pu, J.Z., Schaefer, M., Tidor, B., Venable, R.M., Woodcock, H.L., Wu, X., Yang, W., York, D.M., Karplus, M.: CHARMM: The Biomolecular Simulation Program. J. Comput. Phys. 30, 1545 (2009)

    Google Scholar 

  5. Cardelli, L.: Strand algebras for DNA computing. Nat. Comput. 10, 407 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  6. Case, D.A., Darden, T.A., Cheatham III, T.E., Simmerling, C.L., Wang, J., Duke, R.E., Luo, R., Walker, R.C., Zhang, W., Merz, K.M., et al.: AMBER 11. University of California, San Francisco (2010)

    Google Scholar 

  7. Cheatham III, T.E., Young, M.A.: Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise. Biopolymers 56, 232 (2000)

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  10. Goodman, R.P., Schaap, I.A.T., Tardin, C.F., Erben, C.M., Berry, R.M., Schmidt, C.F., Turberfield, A.J.: Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661 (2005)

    Article  Google Scholar 

  11. Hsu, C.W., Sciortino, F., Starr, F.W.: Theoretical description of a DNA-linked nanoparticle self-assembly. Phys. Rev. Lett. 105, 55502 (2010)

    Article  Google Scholar 

  12. Jost, D., Everaers, R.: A unified description of poly- and oligonucleotide DNA melting: nearest-neighbor, Poland-Sheraga and lattice models. Phys. Rev. E 75, 041918 (2007)

    Article  Google Scholar 

  13. Jost, D., Everaers, R.: A unified Poland-Scheraga model of oligo-and polynucleotide DNA melting: Salt effects and predictive power. Biophys. J. 96, 1056 (2009)

    Article  Google Scholar 

  14. Jost, D., Everaers, R.: Prediction of RNA multi-loop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model. J. Chem. Phys. 132, 095101 (2010)

    Article  Google Scholar 

  15. Lakin, M.R., Youssef, S., Cardelli, L., Phillips, A.: Abstractions for DNA circuit design. J R Soc. Interface 9, 470 (2012)

    Article  Google Scholar 

  16. Langowski, J.: Polymer chain models of DNA and chromatin. Eur. Phys. J. E Soft Matter 19, 241 (2006)

    Article  Google Scholar 

  17. MacKerell Jr., A.D., Banavali, N., Foloppe, N.: Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56, 257 (2000)

    Article  Google Scholar 

  18. Martinez-Veracoechea, F.J., Mladek, B.M., Tkachenko, A.V., Frenkel, D.: Design rule for colloidcal crystals of DNA-functionalized particles. Phys. Rev. Lett. 107, 045902 (2011)

    Article  Google Scholar 

  19. Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: DNA nanotweezers studied with a coarse-grained model of DNA. Phys. Rev. Lett. 104, 178101 (2010)

    Article  Google Scholar 

  20. Ouldridge, T.E., Louis, A.A., Doye, J.P.K.: Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J. Chem. Phys. 134, 085101 (2011)

    Article  Google Scholar 

  21. de Pablo, J.J.: Polymer simulations: From DNA to composites. Annu. Rev. Phys. Chem. 62 (2011)

    Google Scholar 

  22. Peyrard, M., Cuesta-Lopez, S., James, G.: Modelling DNA at the mesoscale: a challenge for nonlinear science? Nonlinearity 21, T91 (2008)

    Article  MathSciNet  Google Scholar 

  23. Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117, 1 (1995), http://lammps.sandia.gov

    Article  MATH  Google Scholar 

  24. Poland, D., Scheraga, H.A.: Phase transitions in one dimension and the helix-coil transition in polyamino acids. J. Chem. Phys. 45, 1456 (1966)

    Article  Google Scholar 

  25. Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196 (2011)

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  29. SantaLucia, J.J., Hicks, D.: The thermodynamics of DNA structural motiefs. Annu. Rev. Biophys. Biomol. Struct. 33, 415 (2004)

    Article  Google Scholar 

  30. Savelyev, A., Papoian, G.A.: Chemically accurate coarse graining of double-stranded DNA. PNAS 107, 20340 (2010)

    Article  Google Scholar 

  31. Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314, 1585 (2006)

    Article  Google Scholar 

  32. Seeman, N.C.: Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237 (1982)

    Article  Google Scholar 

  33. Svaneborg, C.: LAMMPS framework for dynamic bonding an application modeling DNA. Comp. Phys. Comm. 183, 1793 (2012)

    Article  Google Scholar 

  34. Tinlan, B., Pluen, A., Sturm, J., Weill, G.: Persistence length of single-stranded DNA. Macromolecules 30, 5763 (1997)

    Article  Google Scholar 

  35. Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394, 529 (1998)

    Article  Google Scholar 

  36. Xhang, Y., Seeman, N.C.: Construction of a DNA-truncated octahedron. J. Am. Chem. Soc. 116, 1661 (1994)

    Article  Google Scholar 

  37. Zhang, D.Y., Winfree, E.: Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303 (2009)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Center for Fundamental Living Technology, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5320, Odense, Denmark

    Carsten Svaneborg, Harold Fellermann & Steen Rasmussen

  2. Complex Systems Lab., Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Dr. Aiguadé 88, 08003, Barcelona, Spain

    Harold Fellermann

  3. Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA

    Steen Rasmussen

Authors
  1. Carsten Svaneborg
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  2. Harold Fellermann
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  3. Steen Rasmussen
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of New Mexico, MSC01 1130, 1 University of New Mexico, 87131, Albuquerque, NM, USA

    Darko Stefanovic

  2. Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, OX 1 3PU, Oxford, UK

    Andrew Turberfield

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Svaneborg, C., Fellermann, H., Rasmussen, S. (2012). DNA Self-Assembly and Computation Studied with a Coarse-Grained Dynamic Bonded Model. In: Stefanovic, D., Turberfield, A. (eds) DNA Computing and Molecular Programming. DNA 2012. Lecture Notes in Computer Science, vol 7433. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32208-2_10

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  • DOI: https://doi.org/10.1007/978-3-642-32208-2_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-32207-5

  • Online ISBN: 978-3-642-32208-2

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