English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

We investigate the coalescence of two DNA-bubbles initially located at weakdomains and separated by a more stable barrier region in a designed constructof double-stranded DNA. In a continuum Fokker-Planck approach, thecharacteristic time for bubble coalescence and the corresponding distributionare derived, as well as the distribution of coalescence positions along thebarrier. Below the melting temperature, we find a Kramers-type barrier crossingbehavior, while at high temperatures, the bubble corners performdrift-diffusion towards coalescence. In the calculations, we map the bubbledynamics on the problem of two vicious walkers in opposite potentials. We alsopresent a discrete master equation approach to the bubble coalescence problem.Numerical evaluation and stochastic simulation of the master equation showexcellent agreement with the results from the continuum approach. Given thatthe coalesced state is thermodynamically stabilized against a state where onlyone or a few base pairs of the barrier region are re-established, it appearslikely that this type of setup could be useful for the quantitativeinvestigation of thermodynamic DNA stability data as well as the rate constantsinvolved in the unzipping and zipping dynamics of DNA, in single moleculefluorescence experiments.

Bubble merging in breathing DNA as a vicious walker problem in opposite potentials