Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea.
Department of Physics, University of Ulsan, Ulsan, 680-749, South Korea.
J Fluoresc. 2017 Jul;27(4):1373-1383. doi: 10.1007/s10895-017-2072-8. Epub 2017 Apr 3.
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 HT 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 HT 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.
使用 FCS 结合 HYDRO 研究了单链 DNA（ssDNA）和 G-四链体的平移扩散性质，以确定 G-四链体形成的持久长度和协同性，其中实施了基于蠕虫链（WLC）的蒙特卡罗模拟。与胸腺嘧啶相比，鸟嘌呤的存在缩短了核酸的轮廓长度，并增加了对离子筛选的脆弱性。为了进行协同性估计，假设端粒序列 HT 经历 27 个中间状态，可以将其分类为 ssDNA、单 G-四链体、双 G-四链体和三个连续的 G-四链体。每个状态类型都使用一系列珠子和适当的键长进行建模，这些键长是从 WLC 模型获得的。使用 HYDRO 程序，我们计算了每种物质的扩散时间，并将这些时间用于计算任意 KCl 浓度下物质混合物的模拟 HT 扩散时间。通过比较模拟和实验扩散性质，我们从 FCS 结合 HYDRO 获得了正协同性 C=200。
