The Transfer Integral Operator Method in the Study of DNA Unzipping and Bubble Formation

DOI

10.1142/S1402925111001581How to use a DOI?

Keywords

DNA; Peyrard–Bishop–Dauxois model; transfer integral operator method

Abstract

In this work we reexamine the unzipping and bubble formation of DNA in the context of the Peyrard–Bishop–Dauxois DNA model using the transfer integral operator method. After a brief overview of the method, we use it to calculate the probabilities that consecutive base-pairs are stretched beyond a threshold amplitude. We compare the continuous Peyrard–Bishop–Dauxois model with an Ising-type model and demonstrate their similarities. For the Peyrard–Bishop–Dauxois model, we derive an expression for the force that is required to open a double-stranded sequence at one end while the other end is kept closed. In the thermodynamic limit, we use this expression to study the dependence of the unzipping force on the temperature. We also calculate the opening probabilities in the case of zero force and in the case where a force is applied in the middle of the sequence. Analytically, the case where the force is applied in the middle is similar to the case of a homogeneous DNA sequence of strong GC pairs with a defect, in the form of a weaker AT base pair, in the middle. Numerical results verify this similarity.

Copyright

© 2011 The Authors. Published by Atlantis Press and Taylor & Francis

Open Access

This is an open access article distributed under the CC BY-NC 4.0 license (http://creativecommons.org/licenses/by-nc/4.0/).

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TY  - JOUR
AU  - Z. Rapti
AU  - K. Ø. Rasmussen
AU  - A. R. Bishop
PY  - 2021
DA  - 2021/01/07
TI  - The Transfer Integral Operator Method in the Study of DNA Unzipping and Bubble Formation
JO  - Journal of Nonlinear Mathematical Physics
SP  - 381
EP  - 396
VL  - 18
IS  - Supplement 2
SN  - 1776-0852
UR  - https://doi.org/10.1142/S1402925111001581
DO  - 10.1142/S1402925111001581
ID  - Rapti2021
ER  -