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

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.