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The persistence length and length per base of single-stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory

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  • Chi, Qingjia
  • Wang, Guixue
  • Jiang, Jiahuan

Abstract

A dynamical mean field theory is used to predict the end-monomer mean square displacement of single-stranded DNA and finally estimate two important parameters—the persistence length lp and the length per base ld. Both parameters are set free, and finally reach optimum values by fitting the theoretical data to the experimental data of Shusterman et al. [R. Shusterman, S. Alon, T. Gavrinyov, O. Krichevsky, Monomer dynamics in double- and single-stranded DNA polymers, Phys. Rev. Lett. 92 (2004) 048303]. Three optimization methods, global optimization, individual optimization and selected optimization are performed with the Monte Carlo method. All the optimization methods can faithfully reproduce the experimental data. In selected optimization for 2400 and 6700 bases ssDNA, lp=2.223nm and ld=0.676nm are obtained. The theoretical results show a larger persistence length for ssDNA than ordinary synthetic polymers, and the obtained length per base is larger than the reported value obtained from single molecule force measurements. The lp and ld obtained from mean field theory complement the current data previously measured for different salt concentrations in solution.

Suggested Citation

  • Chi, Qingjia & Wang, Guixue & Jiang, Jiahuan, 2013. "The persistence length and length per base of single-stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(5), pages 1072-1079.
    • Handle: RePEc:eee:phsmap:v:392:y:2013:i:5:p:1072-1079
    DOI: 10.1016/j.physa.2012.09.022
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    References listed on IDEAS

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    1. Gijs J.L. Wuite & Steven B. Smith & Mark Young & David Keller & Carlos Bustamante, 2000. "Single-molecule studies of the effect of template tension on T7 DNA polymerase activity," Nature, Nature, vol. 404(6773), pages 103-106, March.
    2. Hinczewski, Michael & Netz, Roland R., 2010. "Dynamics of DNA: Experimental controversies and theoretical insights," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(15), pages 2993-2996.
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    Cited by:

    1. Deepak Karna & Eriko Mano & Jiahao Ji & Ibuki Kawamata & Yuki Suzuki & Hanbin Mao, 2023. "Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Lidice González & Daniel Kolbin & Christian Trahan & Célia Jeronimo & François Robert & Marlene Oeffinger & Kerry Bloom & Stephen W. Michnick, 2023. "Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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