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

dc.contributor.utaustinauthorNam, Gi Moonen_US
dc.creatorKwon, Ah Youngen_US
dc.creatorNam, Gi Moonen_US
dc.creatorJohner, Alberten_US
dc.creatorKim, Seyongen_US
dc.creatorHong, Seok Cheolen_US
dc.creatorLee, Nam Kyungen_US
dc.date.accessioned2017-07-18T20:11:22Z
dc.date.available2017-07-18T20:11:22Z
dc.date.issued2016-02en_US
dc.description.abstractUnder 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.en_US
dc.description.departmentChemistryen_US
dc.description.sponsorshipNational Research Foundation NRF-2012 R1A1A3013044 NRF-2014R1A1A2055681en_US
dc.description.sponsorshipNRF-2012R1A1A2021736en_US
dc.description.sponsorshipIBS-R023-D1en_US
dc.description.sponsorshipNRF-2015R1A2A2A01005916en_US
dc.identifierdoi:10.15781/T2NP1X07S
dc.identifier.citationKwon, Ah-Young, Gi-Moon Nam, Albert Johner, Seyong Kim, Seok-Cheol Hong, and Nam-Kyung Lee. "Competition between BZ and BL transitions in a single DNA molecule: Computational studies." Physical Review E 93, no. 2 (2016): 022411.en_US
dc.identifier.doi10.1103/PhysRevE.93.022411en_US
dc.identifier.issn2470-0045en_US
dc.identifier.urihttp://hdl.handle.net/2152/61173
dc.language.isoEnglishen_US
dc.relation.ispartofUT Faculty/Researcher Worksen_US
dc.relation.ispartofserialPhysical Review Een_US
dc.rightsAdministrative deposit of works to Texas ScholarWorks: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access or the publisher allows a PDF version of the article to be freely posted online. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en_US
dc.rights.restrictionopenen_US
dc.subjecttorque measurementsen_US
dc.subjectsupercoiled dnaen_US
dc.subjectfree-energyen_US
dc.subjectelasticityen_US
dc.subjectdynamicsen_US
dc.subjectsequenceen_US
dc.subjecttensionen_US
dc.subjectdomainen_US
dc.titleCompetition between B-Z and B-L transitions in a single DNA molecule: Computational studiesen_US
dc.typeArticleen_US
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