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RESEARCH PRODUCT

Computer simulations of DNA stretching

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Abstract In this chapter we will give short review of computer modelling/simulations of DNA manipulation as a complementary tool to current single molecule manipulation experiments in order to follow the impact on molecular structure during the manipulation experiments. As an example we report molecular dynamics simulations of a 22 base-pair DNA fragment in an explicit water solution with counter-ions to mimic a torsionally unconstrained single-molecule stretching experiment. Positions of the O5′ and O3′ atoms at one end of the 22-mer were fixed while an external linearly increasing tensile force was applied on the corresponding atoms at the other end. Changes in the intramolecular potential energy components reflect large structural changes during the stretching. Large increase in the specific torsional angles of the elongated double-strand DNA is observed as the angles find new stationary values, quite different from those in the dynamically stable original structure before the stretching. Upon pulling the DNA gradually looses its twist developing a spectacular base-stacked structure with the backbones are stretching out in parallel, and the bases were in a zipper-like stack in the position of the major groove of the original un-stretched structure. The results are discussed in the light of recent experiments and some biological consequences of the simulation results are indicated.