Torque Measurement at the Single-Molecule Level

Forth, Scott; Sheinin, Maxim Y.; Inman, James T.; Wang, Michelle D.

doi:10.1146/annurev-biophys-083012-130412

Cited by 81 publications

(71 citation statements)

References 124 publications

(218 reference statements)

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“…Experimentally, there is an increasing wealth of information on DNA's biophysical properties, particularly more recently from single-molecule experiments involving active manipula- tion by optical and magnetic tweezers 3,4 or by passive fluorescent probing of single molecules as they undergo dynamic processes. 5,6 However, the detailed microscopic mechanisms underlying the observed behaviour in these experiments are not always clear.…”

Section: Introductionmentioning

confidence: 99%

Coarse-graining DNA for simulations of DNA nanotechnology

Doye¹,

Ouldridge²,

Louis³

et al. 2013

Phys. Chem. Chem. Phys.

190

220

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To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

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Section: Introductionmentioning

confidence: 99%

Coarse-graining DNA for simulations of DNA nanotechnology

Doye¹,

Ouldridge²,

Louis³

et al. 2013

Phys. Chem. Chem. Phys.

190

220

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“…Topology-dependent protein binding can be measured with several approaches, including the electrophoretic mobility shift assay (Osheroff 1986;Palecek et al 2001), atomic force microscopy (Alonso-Sarduy et al 2011;López et al 2012;Vanderlinden et al 2014), and an equilibrium topology-dependent binding assay (Litwin et al 2015). Single-molecule techniques that can control as well as measure the topology of individual DNA molecules extend our capacity to directly observe how DNA topology modulates the activities of proteins and the dynamic nature of the interplay between protein activity and topology (reviewed in Charvin et al 2004Charvin et al , 2005aForth et al 2013;Koster et al 2010;Lipfert et al 2015;Ma and Wang 2014;Neuman 2010;Strick et al 2000).…”

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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“…Both FOMT and MTT should find future applications in the study of genome processing, as the behavior of molecular motors on DNA is both influenced by and has consequences for the local twist and torque. Additional applications can be found in the emerging field of DNA nanotechnology 27 or in the wider field of rotary motors active in biological processing 7,45 . …”

Section: Significance Of the Fomt And Mtt Approaches Compared To Exismentioning

confidence: 99%

Magnetic Tweezers for the Measurement of Twist and Torque

Lipfert

Lee

Ordu

et al. 2014

JoVE

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Single-molecule techniques make it possible to investigate the behavior of individual biological molecules in solution in real time. These techniques include so-called force spectroscopy approaches such as atomic force microscopy, optical tweezers, flow stretching, and magnetic tweezers. Amongst these approaches, magnetic tweezers have distinguished themselves by their ability to apply torque while maintaining a constant stretching force. Here, it is illustrated how such a "conventional" magnetic tweezers experimental configuration can, through a straightforward modification of its field configuration to minimize the magnitude of the transverse field, be adapted to measure the degree of twist in a biological molecule. The resulting configuration is termed the freely-orbiting magnetic tweezers. Additionally, it is shown how further modification of the field configuration can yield a transverse field with a magnitude intermediate between that of the "conventional" magnetic tweezers and the freely-orbiting magnetic tweezers, which makes it possible to directly measure the torque stored in a biological molecule. This configuration is termed the magnetic torque tweezers. The accompanying video explains in detail how the conversion of conventional magnetic tweezers into freely-orbiting magnetic tweezers and magnetic torque tweezers can be accomplished, and demonstrates the use of these techniques. These adaptations maintain all the strengths of conventional magnetic tweezers while greatly expanding the versatility of this powerful instrument.

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Torque Measurement at the Single-Molecule Level

Cited by 81 publications

References 124 publications

Coarse-graining DNA for simulations of DNA nanotechnology

Coarse-graining DNA for simulations of DNA nanotechnology

The dynamic interplay between DNA topoisomerases and DNA topology

Magnetic Tweezers for the Measurement of Twist and Torque

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