title: How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model.
abstract: When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands are separated. The statistical physics of this process has a long history and is commonly described in terms 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: 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 - adenine, T - thymine, G - guanine, C - cytosine). 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.
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
authors.forename: Michaela
authors.initials: M
authors.lastname: Reiter-Schad
authors.affiliation: Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Werner
authors.affiliation: Division of Solid State Physics, Department of Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden.
authors.forename: Jonas O
authors.initials: JO
authors.lastname: Tegenfeldt
authors.affiliation: Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Mehlig
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
authors.forename: Tobias
authors.initials: T
authors.lastname: Ambjörnsson
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D019277:Entropy; D006801:Humans; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013816:Thermodynamics; D044366:Transition Temperature
chemical_list: D004247:DNA