Related Experiment Videos
Persistence Length and Cooperativity Estimation of Single Stranded DNA using FCS Combined with HYDRO Program
Seokhyun Jung1, Dongkeun Lee1, Sok W Kim2
1Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea.
Journal of Fluorescence
|April 4, 2017
Summary
This study quantifies G-quadruplex formation cooperativity using fluorescence correlation spectroscopy (FCS) and HYDRO simulations. Results reveal a positive cooperativity of 200, aiding understanding of DNA structure and dynamics.
Area of Science:
- Biophysics
- Molecular Biology
- Computational Chemistry
Background:
- G-quadruplexes are crucial DNA structures with implications in various biological processes.
- Understanding their formation cooperativity is key to elucidating their function.
- Single-stranded DNA (ssDNA) and G-quadruplex diffusion properties are influenced by sequence and ionic conditions.
Purpose of the Study:
- To determine the persistence length and cooperativity of G-quadruplex formation.
- To investigate the impact of guanine versus thymine on nucleic acid properties.
- To model and simulate G-quadruplex formation dynamics.
Main Methods:
- Fluorescence Correlation Spectroscopy (FCS) was employed to measure diffusion properties.
- HYDRO software was used for wormlike chain (WLC)-based Monte Carlo simulations.
- Nucleic acid states were modeled using bead-and-bond representations derived from WLC parameters.
Main Results:
- Guanine-rich sequences exhibited shorter contour lengths and increased susceptibility to ion screening compared to thymine-containing sequences.
- A telomeric sequence (HT72) was modeled with 27 intermediate states, including ssDNA and various G-quadruplex configurations.
- Simulated diffusion times, based on calculated species diffusion, were compared with experimental FCS data.
Conclusions:
- The study successfully combined FCS and HYDRO simulations to quantify G-quadruplex formation.
- A significant positive cooperativity value (C=200) was determined for G-quadruplex formation.
- Findings provide insights into the structural dynamics and stability of G-quadruplex structures.