Laboratoire de Physique Théorique
Toulouse - UMR 5152

In a recent letter, A.K. Dasanna, N. Destainville, J. Palmeri and M. Manghi from the LPT have studied theoretically the mechanism of DNA denaturation bubbles closure and shown that chain bending and strand diffusion are at the origin of the long closure times measured experimentally.

In the course of DNA transcription, denaturation bubbles (DNA segments where base-pairs are broken) are nucleated in DNA and an important issue concerns the closure time of such DNA « bubbles ». Experiments have measured suprisingly long closure times in the range of 20 to 100 microseconds for small bubbles of length around 20 base-pairs.

Using Brownian dynamics simulations and analytical arguments, it is shown that the closure of a pre-equilibrated bubble (a) occurs in two steps. The first step consists in a fast zipping of the initial bubble until a metastable bubble state of length around 10 base-pairs is reached (b). The driving force for this fast kinetics is the energetic gain in base-pair closure, which becomes forbidden at some point by the large bending stored in the bubble. The closure of this metastable state is then controlled by the rotational diffusion of the two stiff arms (c). For real DNAs, the closure time is found to scale as N^2.4 for DNA lengths N between 20 and 100.

Reference : A.K. Dasanna, N. Destainville, J. Palmeri and M. Manghi, Strand diffusion-limited closure of denaturation bubbles in DNA, Europhysics Letters 98, 38002 (2012)