Melting of confined DNA: static and dynamic properties

We study dsDNA (double strand DNA) melting in detail within varying strip-like confinement in a two-dimensional lattice model. The interplay between reduced configurational entropy and attractive base-pairing energy results in a non-monotonic melting profile of DNA. Structural transitions associated with confined DNA melting reveal a stretched or extended state for very strong confinement. By using the exact enumeration method, we investigate the emergence of a local denatured zone e.g. bubbles during DNA melting. The survival time of a single bubble within varying strip width is studied from the Fokker-Planck formalism by considering the bubble size as a reaction co-ordinate. We show that a simple lattice model can capture the sequence heterogeneity effect on DNA melting and bubble dynamics within the strip. Different time scales of bubble zipping for different DNA sequences are found, which may have potential applications in denaturation mapping.

Automated summary

In this study, we investigated the melting process of dsDNA under varying confinement and found structural transitions and the emergence of local denatured zones. By using enumeration and Fokker-Planck formalism, we determined the survival time of single bubbles and the effect of DNA sequences on the melting process.