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How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model | | Michaela Reiter-Schad
; Erik Werner
; Jonas O. Tegenfeldt
; Bernhard Mehlig
; Tobias Ambjornsson
; | | Date: |
8 May 2015 | | Abstract: | When double-stranded DNA molecules are heated, or exposed to denaturing
agents, the two strands get separated. The statistical physics of this process
has a long history, and is commonly described in term of the Poland-Scheraga
(PS) model. Crucial to this model is the configurational entropy for a melted
region (compared to the entropy of an intact region of the same size),
quantified by the loop factor. In this study we investigate how confinement
affects the DNA melting transition, by using the loop factor for an ideal
Gaussian chain. By subsequent numerical solutions of the PS model, we
demonstrate that the melting temperature depends on the persistence lengths of
single-stranded and double-stranded DNA. For realistic values of the
persistence lengths the melting temperature is predicted to decrease with
decreasing channel diameter. We also demonstrate that confinement broadens the
melting transition. These general findings hold for the three scenarios
investigated: namely 1. homo-DNA, i.e. identical basepairs along the DNA
molecule; 2. random sequence DNA, and 3. "real" DNA, here T4 phage DNA. We show
that cases 2 and 3 in general give rise to broader transitions than case 1.
Case 3 exhibits a similar phase transition as case 2 provided the random
sequence DNA has the same ratio of AT to GC basepairs. A simple analytical
estimate for the shift in melting temperature is provided as a function of
nanochannel diameter. For homo-DNA, we also present an analytical prediction of
the melting probability as a function of temperature. | | Source: | arXiv, 1505.1968 | | Services: | Forum | Review | PDF | Favorites | |
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