05/27 2023 Seminar
- Title题目 Quantification of Macromolecule Crowding and DNA Mismatch at Single Molecule Level
- Speaker报告人 刘艳辉 (贵州大学)
- Date日期 2023年5月27日 10:30
- Venue地点 会议室：北楼322 zoom meeting: https://us02web.zoom.us/j/88015281682?pwd=aGVJazZwZlFEcDBhY2xnMmNyYXZEZz09 会议号: 880 1528 1682 密码: 525646
Defective structures of DNA, such as DNA mismatch, and macromolecule crowding have prominent impacts on a series of biochemical processes in cell. The ox-DNA model was extended to identify the intermediate state caused by DNA mismatch in DNA hairpin structure. DNA mismatch definitely reduced the critical forces of DNA hairpins, and a common rule about the dependence of the intermediate state on the position of DNA mismatch was generalized in a phase diagram constructed in a phase space of a scaled position of DNA mismatch. At the same time, a novel method combining high-resolution magnetic tweezers and extended crowder-oxDNA model was applied to systematically studied the kinetics and thermodynamics of the folding/unfolding transition for an individual DNA hairpin in a crowded environment. The linear dependence of critical force of DNA hairpin on the PEG concentration, demonstrated by the magnetic tweezers experiments, was consistent with the results based on the crowder-oxDNA model in which the Lennard-Jones potential was adopted to express the interaction between the crowders and DNA hairpin. These consistencies highlight that the excluded volume effects are mainly responsible for the interaction between PEG and DNA hairpin, which is different from the interaction between dextran and DNA hairpin. In the meantime, the dependence of the folding rate on the molecule weight of PEG, which was different from FRET-based results, was first identified. The proposed method opens a path to detect the interaction between an inert, and synthetic molecule, and the DNA hairpin, which is important to accurately mimic the cytosolic environments using mixtures of different inert molecules.