Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies

Ah Young Kwon, Gi Moon Nam, Albert Johner, Seyong Kim, Seok Cheol Hong, Nam Kyung Lee

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC)n repeats or (TG)n repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC)n sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG)n sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.

Original languageEnglish
Article number022411
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume93
Issue number2
DOIs
Publication statusPublished - 2016 Feb 19

Fingerprint

Left handed
deoxyribonucleic acid
Molecules
Random Sequence
torsional stress
Convert
molecules
Quenched Disorder
Right handed
Copolymer
Twist
Torsion
Monte Carlo Simulation
Fluctuations
torsion
Form
Dependent
copolymers
monomers
Interaction

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Statistical and Nonlinear Physics
  • Statistics and Probability

Cite this

Competition between B-Z and B-L transitions in a single DNA molecule : Computational studies. / Kwon, Ah Young; Nam, Gi Moon; Johner, Albert; Kim, Seyong; Hong, Seok Cheol; Lee, Nam Kyung.

In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, Vol. 93, No. 2, 022411, 19.02.2016.

Research output: Contribution to journalArticle

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