Strand diffusion-limited closure of denaturation bubbles in DNA
Université de Toulouse; UPS; Laboratoire de Physique Théorique (IRSAMC) - F-31062 Toulouse, France, EU and CNRS; LPT (IRSAMC) - F-31062 Toulouse, France, EU
Accepted: 2 April 2012
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a bending modulus which depends on the base-pair state, with double-strand DNA (dsDNA) segments being 50 times stiffer than ssDNA ones. For DNA lengths from N=20 to 100 base-pairs (bp) and initial bubble sizes of N−6 bp, long closure times of 0.1 to 4 μs are found, following a scaling law in N2.4. The bubble starts to close by a fast zipping which stops when the bubble reaches a highly bent metastable state of length around 10 bp. The limiting final step to complete closure is controlled by the dsDNA “arms” rotational diffusion, with closure occurring once they are nearly aligned. The central role of chain bending, which cannot be accounted for in one-dimensional models, is thus illuminated.
PACS: 87.15.H- – Dynamics of biomolecules / 87.15.A- – Theory, modeling, and computer simulation / 82.39.Pj – Nucleic acids, DNA and RNA bases
© EPLA, 2012