Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

– We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials. Introduction. – The Watson-Crick double helix is the thermodynamically stable state of double-stranded DNA in a wide range of temperatures and salt conditions [1]. This stability is effected by hydrogen bonds between the bases in individual base-pairs (bps), and the stronger stacking interactions between nearest neighbour pairs of bps. Driven by thermal fluctuations double-stranded DNA can break apart, to form denaturation bubbles of flexible single-stranded DNA [2]. Although rare, bp-opening events expose active groups of DNA bases, that are otherwise buried within the double helix. They are crucial for the interaction with proteins and chemicals, and therefore for the biological function of DNA. Bubble kinetics has been probed in NMR studies [3], and the growth and reannealing dynamics of individual bubbles has been measured in real time in single DNA fluorescence correlation setups [4].