Maxwell Relations for Single-DNA Experiments: Monitoring Protein Binding and Double-Helix Torque with Force-Extension Measurements

Zhang, Houyin; Marko, John F.

doi:10.1016/j.bpj.2010.12.3515

Cited by 12 publications

(22 citation statements)

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“…Although topoisomerases are the primary focus of the review, we also discuss RNA transcription as a canonical example to illustrate the interplay between DNA topology and enzyme activity. Many of these results have been made possible by the advent of single-molecule methods to control and measure DNA topology, primarily magnetic tweezers (Charvin et al 2005a;Ma and Wang 2014;Revyakin et al 2004), complimented by the development of extensive theoretical and computational approaches (Marko 2007;Neukirch and Marko 2011;Ouldridge et al 2011;Vologodskii and FrankKamenetskii 1992;Vologodskii and Marko 1997;Zhang and Marko 2008). Single-molecule approaches complement ensemble approaches, but the former uniquely provide a means of distinguishing the effects of twist and writhe that are typically convolved in ensemble measurements.…”

Section: Introductionmentioning

confidence: 99%

The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

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Section: Introductionmentioning

confidence: 99%

The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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“…Recently, Zhang and Marko [23] proposed a thermodynamic approach, which may be used to estimate the number of non-specifically bound proteins from extension versus force measurements. In this paper, we determine the change in the number of λ repressor proteins bound to a 16 kbp-long fragment of λ DNA by applying the Zhang–Marko approach [23] to our experimental data.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper, we determine the change in the number of λ repressor proteins bound to a 16 kbp-long fragment of λ DNA by applying the Zhang–Marko approach [23] to our experimental data. The λ repressor, also known as CI protein, binds both specifically and non-specifically to DNA.…”

Section: Introductionmentioning

confidence: 99%

Determination of the number of proteins bound non-specifically to DNA

Liebesny

Goyal

Dunlap

et al. 2010

J. Phys.: Condens. Matter

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We have determined the change in the number of proteins bound non-specifically to DNA as a function of applied force using force–extension measurements on tethered DNA. Using magnetic tweezers, single molecules of λ DNA were repeatedly stretched and relaxed in the absence and presence of 170 nM λ repressor protein (CI). CI binds to six specific sites of λ DNA with nanomolar affinity and also binds non-specifically with micromolar affinity. The force versus extension data were analyzed using a recently developed theoretical framework for quantitative determination of protein binding to the DNA. The results indicate that the non-specific binding of CI changes the force–extension relation significantly in comparison to that of naked DNA. The DNA tether used in our experiment would have about 640 bound repressors, if it was completely saturated with bound proteins. We find that as the pulling force on DNA is reduced from 4.81 to 0.13 pN, approximately 138 proteins bind to DNA, which is about 22% of the length of the tethered DNA. Our results show that 0.13 pN is not low enough to cause saturation of DNA by repressor and 4.81 pN is also not high enough to eliminate all the repressors bound to DNA. This demonstrates that the force–extension relation provides an effective approach for estimating the number of proteins bound non-specifically to a DNA molecule.

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“…This linear decrease corresponds to the formation of plectonemes: any additional turn beyond the buckling transition is absorbed into the growing plectoneme without changes in the torque [10]. As standard magnetic tweezers cannot measure torques, the buckling torque can be only indirectly deduced by integrating the change of the molecule extension with respect to the applied force [32], [38]. However, new set ups have recently been proposed that enforce a torque and allow its measurement: one of them uses an angular optical trap [39]–[41], another one a magnetic nanorod coupled to a magnetic bead [42] and a third one a soft magnetic tweezer [43].…”

Section: Resultsmentioning

confidence: 99%

In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

2014

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We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally.

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Maxwell Relations for Single-DNA Experiments: Monitoring Protein Binding and Double-Helix Torque with Force-Extension Measurements

Cited by 12 publications

References 0 publications

The dynamic interplay between DNA topoisomerases and DNA topology

The dynamic interplay between DNA topoisomerases and DNA topology

Determination of the number of proteins bound non-specifically to DNA

In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

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