Statistical physics of DNA melting in nanochannels

Feb 24, 2011, 9:45 AM
45m
FB42 (AlbaNova Main Building)

FB42

AlbaNova Main Building

Speaker

Tobias Ambjörnsson (Lund University)

Description

The new melting map approach developed in our collaborator Jonas Tegenfeldt's lab at Gothenburg University constitutes a promising ultra-fast alternative to previous DNA sequencing techniques. Fluorescently stained DNA is stretched in nanochannels and subsequently heated. The resulting local melting will reduce the quantum yield of an intercalating fluorescent dye such that black spots will occur along the DNA. Since AT and GC basepairs have different melting propensities the result is essentially a "barcode" that is a function of the sequence of the DNA and that can thus be used to identify the DNA from different organisms.
In this talk issues related to theoretical DNA melting calculations will be discussed. The Poland-Scheraga (PS) model of DNA melting has been proven to well reproduce (macroscopic) melting data. The PS model is an Ising model with a long-range term, expressed in terms of a critical random walk exponent c, due to the entropy associated with the melted single-stranded regions. The solution to two new problems in the DNA melting field will be addressed in the talk:
1) The numerical solution of the PS model is computationally prohibitive for bacterial genomes with 107 basepairs of interest in experiments. We therefore recently developed a coarse-grained approximate scheme for performing DNA melting calculations for heterogeneous DNA sequences, as a function of local fraction of AT and GC basepairs.
2) The problem of DNA melting for infinite homogeneous DNA sequences has been solved previously. In the talk finite-size effects in homoDNA melting will be discussed.

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