1. Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation
- Author
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Cynthia Shaheen, Cameron Hastie, Kimberly Metera, Shane Scott, Zhi Zhang, Sitong Chen, Gracia Gu, Lisa Weber, Brian Munsky, Fedor Kouzine, David Levens, Craig Benham, and Sabrina Leslie
- Subjects
Kinetics ,DNA, Superhelical ,Genetics ,Nucleic Acid Conformation ,DNA ,Single Molecule Imaging ,Plasmids - Abstract
Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
- Published
- 2022