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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.
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Cooperative Rheological State‐Switching of Enzymatically‐Driven Composites of Circular DNA And Dextran
Abstract Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non‐equilibrium materials, which exhibit time‐varying rheological properties, are topics of intense investigation. Here, composites of circular DNA and dextran are pushed out‐of‐equilibrium via enzymatic digestion of DNA rings to linear fragments. These time‐resolved rheology measurements reveal discrete state‐switching, with composites undergoing abrupt transitions between dissipative and elastic‐like states. The gating time and lifetime of the elastic‐like states, and the magnitude and sharpness of the transitions, are surprisingly decorrelated from digestion rates and non‐monotonically depend on the DNA fraction. These results are modeled using sigmoidal two‐state functions to show that bulk state‐switching can arise from continuous molecular‐level activity due to the necessity for cooperative percolation of entanglements to support macroscopic stresses. This platform, coupling the tunability of topological composites with the power of enzymatic reactions, may be leveraged for diverse material applications from wound‐healing to self‐repairing infrastructure.
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- PAR ID:
- 10469426
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Advanced Materials
- Volume:
- 35
- Issue:
- 46
- ISSN:
- 0935-9648
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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