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 language | English |
|---|---|
| Article number | 022411 |
| Journal | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics |
| Volume | 93 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 2016 Feb 19 |
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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 journal › Article
}
TY - JOUR
T1 - Competition between B-Z and B-L transitions in a single DNA molecule
T2 - Computational studies
AU - Kwon, Ah Young
AU - Nam, Gi Moon
AU - Johner, Albert
AU - Kim, Seyong
AU - Hong, Seok Cheol
AU - Lee, Nam Kyung
PY - 2016/2/19
Y1 - 2016/2/19
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=84959420547&partnerID=8YFLogxK
U2 - 10.1103/PhysRevE.93.022411
DO - 10.1103/PhysRevE.93.022411
M3 - Article
C2 - 26986366
AN - SCOPUS:84959420547
VL - 93
JO - Physical Review E
JF - Physical Review E
SN - 2470-0045
IS - 2
M1 - 022411
ER -