College of Physics, Guizhou University, Guiyang 550025, China.
Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China.
Phys Rev E. 2023 Jul;108(1-1):014406. doi: 10.1103/PhysRevE.108.014406.
Macromolecule crowding has a prominent impact on a series of biochemical processes in the cell. It is also expected to promote macromolecular complexation induced by excluded volume effects, which conflicts with recent advances in the thermodynamic interaction between inert, synthetic polymers, and nucleic acids. Along this line, a method combining high-resolution magnetic tweezers and extended crowder-oxDNA model was applied to resolve these discrepancies by systematically studying the kinetics and thermodynamics of the folding-unfolding transition for an individual DNA hairpin in a crowded environment. More specifically, from the magnetic tweezers-based experiments, the linear dependence of the critical force of the DNA hairpin on the polyethylene glycol (PEG) concentration was demonstrated, which is 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 the DNA hairpin. These consistencies highlight that the excluded volume effects are mainly responsible for the interaction between PEG and the DNA hairpin, which is different from the interaction between dextran and the DNA hairpin. In the meantime, the dependence of the folding rate on the molecule weight of PEG, which was different from fluorescence resonance energy transfer-based results, was identified. The proposed method opens a path to detect the interaction between an inert, synthetic molecule, and the DNA hairpin, which is important to accurately mimic the cytosolic environments using mixtures of different inert molecules.
大分子拥挤对细胞内的一系列生化过程有显著影响。它还有望促进由排除体积效应引起的大分子复合，这与惰性合成聚合物和核酸之间热力学相互作用的最新进展相冲突。沿着这条线，一种结合高分辨率磁镊和扩展拥挤 oxDNA 模型的方法被应用于通过系统地研究单个 DNA 发夹在拥挤环境中的折叠-展开转变的动力学和热力学来解决这些差异。更具体地说，从基于磁镊的实验中，证明了 DNA 发夹的临界力与聚乙二醇（PEG）浓度的线性关系，这与基于拥挤 oxDNA 模型的结果一致，其中采用 Lennard-Jones 势能来表示拥挤剂与 DNA 发夹之间的相互作用。这些一致性突出表明，排除体积效应主要负责 PEG 与 DNA 发夹之间的相互作用，这与葡聚糖与 DNA 发夹之间的相互作用不同。同时，确定了折叠速率对 PEG 分子量的依赖性，这与荧光共振能量转移的结果不同。所提出的方法为检测惰性合成分子与 DNA 发夹之间的相互作用开辟了道路，这对于使用不同惰性分子的混合物准确模拟细胞质环境非常重要。
