Torque Spectroscopy for the Study of Rotary Motion in Biological Systems

Lipfert, Jan; Oene, Maarten M. van; Lee, Mina; Pedaci, Francesco; Dekker, Nynke H.

doi:10.1021/cr500119k

Cited by 70 publications

(92 citation statements)

References 240 publications

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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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Section: Introductionmentioning

confidence: 99%

The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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“…In addition, superparamagnetic beads are routinely employed in single-molecule magnetic tweezers (MT) as force [2] and torque [3] transducers. The ability of MT to apply both forces and torques to biological macromolecules has been used to probe their mechanical properties and to investigate enzymes and molecular motors in real time [2][3][4].…”

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confidence: 99%

“…In contrast, there is currently no well-accepted theory to predict the torque on superparamagnetic beads inside an external field. A predictive understanding of the magnetic torque would be desirable, considering the increasing use of magnetic beads to apply and measure torque and twist [3,[8][9][10][11][12][13].…”

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Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields

et al. 2015

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Superparamagnetic beads are widely used in biochemistry and single-molecule biophysics, but the nature of the anisotropy that enables the application of torques remains controversial. To quantitatively investigate the torques experienced by superparamagnetic particles, we use a biological motor to rotate beads in a magnetic field and demonstrate that the underlying potential is π periodic. In addition, we tether a bead to a single DNA molecule and show that the angular trap stiffness increases nonlinearly with magnetic field strength. Our results indicate that the superparamagnetic beads' anisotropy derives from a nonuniform intrabead distribution of superparamagnetic nanoparticles.

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“…Typical examples include the degree of coiling of the double-stranded DNA molecule (modified by specialized enzymes), ATP synthesis (accomplished by a rotary machine in mithochondria), and motility in many bacteria (based on a rotary motor). 5 Therefore, the development of techniques that allow angular manipulation will open new methods of studying biological nanoscale systems, where rotation is a relevant physical parameter.…”

Section: Introductionmentioning

confidence: 99%

Fabrication of quartz microcylinders by laser interference lithography for angular optical tweezers

Santybayeva

Meghit

Desgarceaux

et al. 2016

J. Micro/Nanolith. MEMS MOEMS

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Abstract. The use of optical tweezers (OTs) and spin angular momentum transfer to birefringent particles allows new mechanical measurements in systems where torque and rotation are relevant parameters at the singlemolecule level. There is a growing interest in developing simple, fast, and inexpensive protocols to produce a large number of submicron scale cylinders of quartz, a positive uniaxial birefringent crystal, to be employed for such angular measurements in OTs. Here, we show that laser interference lithography, a method well known for its simplicity, fulfills these requirements and produces quartz cylindrical particles that we successfully use to apply and measure optical torque in the piconewton nm range in an optical torque wrench. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.

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Torque Spectroscopy for the Study of Rotary Motion in Biological Systems

Cited by 70 publications

References 240 publications

The dynamic interplay between DNA topoisomerases and DNA topology

The dynamic interplay between DNA topoisomerases and DNA topology

Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields

Fabrication of quartz microcylinders by laser interference lithography for angular optical tweezers

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