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Journal of Fluorescence

, Volume 27, Issue 4, pp 1373–1383 | Cite as

Persistence Length and Cooperativity Estimation of Single Stranded DNA using FCS Combined with HYDRO Program

  • Seokhyun Jung
  • Dongkeun Lee
  • Sok W. Kim
  • Soo Y. Kim
ORIGINAL ARTICLE
  • 439 Downloads

Abstract

Translational diffusion properties of single-stranded DNA (ssDNA) and G-quadruplexes were studied to determine the persistence length and cooperativity of G-quadruplex formation using FCS combined with HYDRO in which wormlike chain (WLC)-based Monte Carlo simulation are implemented. The presence of a guanine instead of a thymine shortened the contour length of nucleic acids and increased the vulnerability to ion screening. For cooperativity estimation, the telomeric sequence HT72 was assumed to undergo 27 intermediate states, which can be classified as ssDNA, single-G-quadruplex, double-G-quadruplex, and three consecutive G-quadruplexes. Each state type was modeled using a series of beads and appropriate bond lengths, which were obtained from the WLC model. Using the HYDRO program, we calculated diffusion times for each species, and these were used to calculate simulated HT72 diffusion times for mixtures of species in arbitrary KCl concentrations. By comparison between simulated and experimental diffusion properties, we obtained a positive cooperativity of C = 200 from FCS combined with HYDRO.

Keywords

Fcs G quadruplex HYDRO program Single stranded DNA Translational diffusion 

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Seokhyun Jung
    • 1
  • Dongkeun Lee
    • 1
  • Sok W. Kim
    • 2
  • Soo Y. Kim
    • 1
  1. 1.Department of PhysicsKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea
  2. 2.Department of PhysicsUniversity of UlsanUlsanSouth Korea

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