Stochastic nonlinear models of DNA breathing at a defect
Duduială, Ciprian Ionut (2010) Stochastic nonlinear models of DNA breathing at a defect. PhD thesis, University of Nottingham.
Deoxyribonucleic acid (DNA) is a long polymer consisting of two chains of bases, in which the genetic information is stored. A base from one chain has a corresponding base on the other chain which together form a so-called base-pair. Molecular-dynamics simulations of a normal DNA duplex show that breathing events – the temporary opening of one or more base-pairs – typically occur on the microsecond time-scale. Using the molecular dynamics package AMBER, we analyse, for different twist angles in the range 30-40 degrees of twist, a 12 basepair DNA duplex solvated in a water box, which contains the ’rogue’ base difluorotoluene (F) in place of a thymine base (T). This replacement makes breathing occur on the nanosecond time-scale. The time spent simulating such large systems, as well as the variation of breathing length and frequency with helical twist, determined us to create a simplified model, which is capable to predict with accuracy the DNA behaviour.
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