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Structural, mechanical and thermodynamic properties of a coarse-grained DNA modelThomas E. Ouldridge, Ard A. Louis and Jonathan P.K. DoyeJ. Chem. Phys. 134, 085101 (2011)AbstractWe explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Ref. 1. Effective interactions are used to represent chain connectivity, excluded volume, base stacking and hydrogen bonding, naturally reproducing a range of DNA behaviour. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the torsional and stretching stiffness of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.The full paper is available from the Journal of Chemical Physics and arXiv.org. |