Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation

Cynthia Shaheen; Cameron Hastie; Kimberly Metera; Shane Scott; Zhi Zhang; Sitong Chen; Gracia Gu; Lisa Weber; Brian Munsky; Fedor Kouzine; David Levens; Craig Benham; Sabrina Leslie

doi:10.1093/nar/gkac101

Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation

Cynthia Shaheen, Cameron Hastie, Kimberly Metera, Shane Scott, Zhi Zhang, Sitong Chen, Gracia Gu, Lisa Weber, Brian Munsky, Fedor Kouzine, David Levens, Craig Benham, Sabrina Leslie

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

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.

Original language	English
Pages (from-to)	2754-2764
Number of pages	11
Journal	Nucleic Acids Research
Volume	50
Issue number	5
DOIs	https://doi.org/10.1093/nar/gkac101
State	Published - 21 Mar 2022
Externally published	Yes

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title = "Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation",

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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T1 - Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation

AU - Shaheen, Cynthia

AU - Hastie, Cameron

AU - Metera, Kimberly

AU - Scott, Shane

AU - Zhang, Zhi

AU - Chen, Sitong

AU - Gu, Gracia

AU - Weber, Lisa

AU - Munsky, Brian

AU - Kouzine, Fedor

AU - Levens, David

AU - Benham, Craig

AU - Leslie, Sabrina

PY - 2022/3/21

Y1 - 2022/3/21

N2 - 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.

AB - 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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EP - 2764

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 5

ER -

Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation

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