Annealed random copolymer model of the B-Z transition in DNA: Torsional responses

Ah Young Kwon; Nam Kyung Lee; Seok Cheol Hong; Julien Fierling; Albert Johner

doi:10.1016/j.bpj.2015.03.060

Annealed random copolymer model of the B-Z transition in DNA: Torsional responses

Ah Young Kwon, Nam Kyung Lee, Seok Cheol Hong, Julien Fierling, Albert Johner

Department of Physics

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Abstract

Both in vivo and in vitro, specific sequences in double-stranded DNA can adopt the left-handed Z-form when underwound. Recently, the B-Z transition of DNA has been studied in detail in magnetic tweezers experiments by several groups. We present a theoretical description of this transition, based on an annealed random copolymer model. The transition of a switchable sequence is discussed as a function of energetic and geometric parameters of the B- and Z-forms, of the applied boundary conditions, and of the characteristics of the B-Z interface. We address a possible torsional softening upon the B-Z transition. The model can be also applied to other biofilaments with annealed torsional/flexural degrees of freedom.

Original language	English
Pages (from-to)	2562-2572
Number of pages	11
Journal	Biophysical Journal
Volume	108
Issue number	10
DOIs	https://doi.org/10.1016/j.bpj.2015.03.060
Publication status	Published - 2015 May 19

Bibliographical note

Funding Information:
N.-K.L. acknowledges financial support from the Korean Research Foundation via grants No. 2012R1A1A3013044 and No. 2014R1A1A2055681. N.-K.L. and A.J. acknowledge support from the Star Exchange Program (grant No. NRF-2012K1A3A1A21030441). This work is also supported by Korean Research Foundation grant No. 2012R1A1A2021736 (to S.-C.H.).

Publisher Copyright:
© 2015 Biophysical Society.

ASJC Scopus subject areas

Biophysics

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title = "Annealed random copolymer model of the B-Z transition in DNA: Torsional responses",

abstract = "Both in vivo and in vitro, specific sequences in double-stranded DNA can adopt the left-handed Z-form when underwound. Recently, the B-Z transition of DNA has been studied in detail in magnetic tweezers experiments by several groups. We present a theoretical description of this transition, based on an annealed random copolymer model. The transition of a switchable sequence is discussed as a function of energetic and geometric parameters of the B- and Z-forms, of the applied boundary conditions, and of the characteristics of the B-Z interface. We address a possible torsional softening upon the B-Z transition. The model can be also applied to other biofilaments with annealed torsional/flexural degrees of freedom.",

author = "Kwon, {Ah Young} and Lee, {Nam Kyung} and Hong, {Seok Cheol} and Julien Fierling and Albert Johner",

note = "Funding Information: N.-K.L. acknowledges financial support from the Korean Research Foundation via grants No. 2012R1A1A3013044 and No. 2014R1A1A2055681. N.-K.L. and A.J. acknowledge support from the Star Exchange Program (grant No. NRF-2012K1A3A1A21030441). This work is also supported by Korean Research Foundation grant No. 2012R1A1A2021736 (to S.-C.H.). Publisher Copyright: {\textcopyright} 2015 Biophysical Society.",

year = "2015",

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doi = "10.1016/j.bpj.2015.03.060",

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T1 - Annealed random copolymer model of the B-Z transition in DNA

T2 - Torsional responses

AU - Kwon, Ah Young

AU - Lee, Nam Kyung

AU - Hong, Seok Cheol

AU - Fierling, Julien

AU - Johner, Albert

N1 - Funding Information: N.-K.L. acknowledges financial support from the Korean Research Foundation via grants No. 2012R1A1A3013044 and No. 2014R1A1A2055681. N.-K.L. and A.J. acknowledge support from the Star Exchange Program (grant No. NRF-2012K1A3A1A21030441). This work is also supported by Korean Research Foundation grant No. 2012R1A1A2021736 (to S.-C.H.). Publisher Copyright: © 2015 Biophysical Society.

PY - 2015/5/19

Y1 - 2015/5/19

N2 - Both in vivo and in vitro, specific sequences in double-stranded DNA can adopt the left-handed Z-form when underwound. Recently, the B-Z transition of DNA has been studied in detail in magnetic tweezers experiments by several groups. We present a theoretical description of this transition, based on an annealed random copolymer model. The transition of a switchable sequence is discussed as a function of energetic and geometric parameters of the B- and Z-forms, of the applied boundary conditions, and of the characteristics of the B-Z interface. We address a possible torsional softening upon the B-Z transition. The model can be also applied to other biofilaments with annealed torsional/flexural degrees of freedom.

AB - Both in vivo and in vitro, specific sequences in double-stranded DNA can adopt the left-handed Z-form when underwound. Recently, the B-Z transition of DNA has been studied in detail in magnetic tweezers experiments by several groups. We present a theoretical description of this transition, based on an annealed random copolymer model. The transition of a switchable sequence is discussed as a function of energetic and geometric parameters of the B- and Z-forms, of the applied boundary conditions, and of the characteristics of the B-Z interface. We address a possible torsional softening upon the B-Z transition. The model can be also applied to other biofilaments with annealed torsional/flexural degrees of freedom.

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JO - Biophysical Journal

JF - Biophysical Journal

IS - 10

ER -

Annealed random copolymer model of the B-Z transition in DNA: Torsional responses

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