By Thomas E. Ouldridge
This thesis provides a unique coarse-grained version of DNA, within which bases are represented as inflexible nucleotides. The version is proven to quantitatively reproduce many phenomena, together with elastic houses of the double-stranded country, hairpin formation in unmarried strands and hybridization of pairs of strands to shape duplexes, the 1st time this type of wide selection of homes has been captured by way of a coarse-grained version. The scope and power of the version is verified via 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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Extra info for Coarse-Grained Modelling of DNA and DNA Self-Assembly
When implementing Langevin dynamics, one has a degree of choice of the form of the friction and damping terms, although they must always be related by a fluctuationdissipation theorem if the equilibrium distribution is to be the correct one. Given the degree of simplification inherent in the simulation, it seems unlikely that being precise about the damping terms will prove significantly beneficial. This reasoning justified the simplifying assumptions about the form of the noise and damping terms, effectively treating each nucleotide as a sphere for dynamical purposes.
12. J. SantaLucia, Jr. and D. Hicks. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. , 33:415–40, 2004. 13. N. Peyret. Prediction of nucleic acid hybridization: parameters and algorithms. PhD thesis, Wayne State University, 2000. 14. D. V. Pyshnyi and E. M. Ivanova. Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides. Russ. Chem. B+, 51:1145–1155, 2002. 15. D. V. Pyshnyi and E. M. Ivanova. The influence of nearest neighbors on the efficiency of coaxial stacking at contiguous stacking hybridization of oligodeoxyribonucleotides.
When taken in conjunction with stacking, the result is the famous B-DNA double helix. The model reproduces basepairing through the VHB term, which incorporates a radial term dependent on the separation of hydrogen-bonding sites, δrHB . This interaction is modulated by terms that encourage the co-linear alignment of all four backbone and hydrogen-bonding sites (quantified by the angles θ1 , θ2 , and θ3 ). A further factor is included to encourage the planes of bases to be antiparallel (measured by θ4 ).
Coarse-Grained Modelling of DNA and DNA Self-Assembly by Thomas E. Ouldridge