Singh Gundeep, Hong Yifeng, Inman James T, Sethna James P, Wang Michelle D
Biophysics Program, Cornell University, Ithaca, NY 14853, USA.
Department of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853, USA.
bioRxiv. 2024 Oct 10:2024.10.08.617281. doi: 10.1101/2024.10.08.617281.
Circular DNA found in the cell is actively regulated to an underwound state, with their superhelical density close to . While this underwound state is essential to life, how it impacts the torsional mechanical properties of DNA is not fully understood. In this work, we performed simulations to understand the torsional mechanics of circular DNA and validated our results with single-molecule measurements and analytical theory. We found that the torque generated at is near but slightly below that required to melt DNA, significantly decreasing the energy barrier for proteins that interact with melted DNA. Furthermore, supercoiled circular DNA experiences force (tension) and torque that are equally distributed through the DNA contour. We have also extended a previous analytical framework to show how the plectonemic twist persistence length depends on the intrinsic bending persistence length and twist persistence length. Our work establishes a framework for understanding DNA supercoiling and torsional dynamics of circular DNA.
细胞中发现的环状DNA被积极调控至负超螺旋状态，其超螺旋密度接近 。虽然这种负超螺旋状态对生命至关重要，但它如何影响DNA的扭转力学性质尚未完全了解。在这项工作中，我们进行了模拟以了解环状DNA的扭转力学，并通过单分子测量和分析理论验证了我们的结果。我们发现，在 时产生的扭矩接近但略低于使DNA解链所需的值，这显著降低了与解链DNA相互作用的蛋白质的能量屏障。此外，超螺旋环状DNA所经历的力（张力）和扭矩沿DNA轮廓均匀分布。我们还扩展了先前的分析框架，以展示螺旋扭绞持续长度如何取决于内在弯曲持续长度和扭转持续长度。我们的工作建立了一个理解DNA超螺旋和环状DNA扭转动力学的框架。
