How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model.
Reiter-Schad, Michaela LU ; Werner, Erik ; Tegenfeldt, Jonas LU
; Mehlig, Bernhard
and Ambjörnsson, Tobias
LU
(2015)
In Journal of Chemical Physics
143(11).
- 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... (More)
- 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. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/8035240
- author
- Reiter-Schad, Michaela
LU
; Werner, Erik
; Tegenfeldt, Jonas
LU
; Mehlig, Bernhard
and Ambjörnsson, Tobias
LU
- organization
- publishing date
- 2015
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Physics
- volume
- 143
- issue
- 11
- article number
- 115101
- publisher
- American Institute of Physics (AIP)
- external identifiers
-
- pmid:26395739
- scopus:84942023370
- pmid:26395739
- wos:000361843900064
- ISSN
- 0021-9606
- DOI
- 10.1063/1.4930220
- language
- English
- LU publication?
- yes
- id
- d070ef1c-db17-48d9-98c6-923b78813756 (old id 8035240)
- date added to LUP
- 2016-04-01 10:21:41
- date last changed
- 2024-01-06 14:41:37
@article{d070ef1c-db17-48d9-98c6-923b78813756,
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.}},
author = {{Reiter-Schad, Michaela and Werner, Erik and Tegenfeldt, Jonas and Mehlig, Bernhard and Ambjörnsson, Tobias}},
issn = {{0021-9606}},
language = {{eng}},
number = {{11}},
publisher = {{American Institute of Physics (AIP)}},
series = {{Journal of Chemical Physics}},
title = {{How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model.}},
url = {{http://dx.doi.org/10.1063/1.4930220}},
doi = {{10.1063/1.4930220}},
volume = {{143}},
year = {{2015}},
}