Coarse-Grained Modelling of DNA and DNA Self-Assembly by Thomas E. Ouldridge

By Thomas E. Ouldridge

This thesis offers a unique coarse-grained version of DNA, during which bases are represented as inflexible nucleotides. The version is proven to quantitatively reproduce many phenomena, together with elastic homes of the double-stranded nation, hairpin formation in unmarried strands and hybridization of pairs of strands to shape duplexes, the 1st time this type of wide variety of houses has been captured through a coarse-grained version. The scope and capability of the version is validated through simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker — the 1st time that coarse-grained modelling has been utilized to dynamic DNA nanotechnology.

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Model simulations of DNA denaturation dynamics. J. Chem. , 114(1):579–590, 2001. 114. M. Sales-Pardo et al. Mesoscopic modelling fo nucleic acid chain dynamics. Phys. Rev. E, 71:051902, 2005. 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. 116. M. Kenward and K. D. Dorfman. Brownian dynamics simulations of single-stranded DNA hairpins. J. Chem. , 130:095101, 2009. 117. M. C. Linak and K. Dorfman. Analysis of a DNA simulation model through hairpin melting experiments.

Note that the hydrogen bonding interaction is taken as non-zero only for complementary base pairs A–T and G–C, but beyond this there is no sequence dependence in the model. Also note that the factors b and x c used in the quadratic smoothing parts of each interaction are not explicitly given. For each funtion, these quantities are specified by demanding differentiability and In fact, after the model was implemented it was found that cos(φ3 ) = cos(φ4 ), and so the modulation could be simply calculated as cos2 (φ3 ).

P. Yakovchuk, E. Protozanova, and M. D. Frank-Kamenetskii. Base-stacking and base-pairing contributions into thermal stability of the dna double helix. Nucl. , 34(2):564–574, 2006. 23. 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. 24. W. Saenger. Principles of Nucleic Acid Structure. Springer-Verlag, New York, 1984. 25. K. M. Guckan et al. Factors contributing to aromatic stacking in water: evaluation in the context of DNA.

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