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Article
Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I
Type I restriction enzymes bind sequence-specifically to unmodified DNA and subsequently pull the adjacent DNA toward themselves. Cleavage then occurs remotely from the recognition site. The mechanism by which...
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Article
Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB
The manoeuvres involved in replication and transcription lead to a build-up of twisting or torsional strain in DNA, and the job of relieving the strain falls to the topoisomerases. Type IB topoisomerases (TopI...
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Article
Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA
Atherosclerotic plaques form when blood flow is disturbed and unusual patterns of mechanical stress are applied to the blood vessel wall. The endothelial cells lining these vessels play an important role in th...
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Article
Direct force measurements on DNA in a solid-state nanopore
Among the variety of roles for nanopores in biology, an important one is enabling polymer transport, for example in gene transfer between bacteria1 and transport of RNA through the nuclear membrane2. Recently, th...
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Article
Antitumour drugs impede DNA uncoiling by topoisomerase I
Topoisomerases are enzymes that act to relax supercoiling, a form of built-up strain in DNA. Topoisomerase inhibitors are important antitumour drugs, thought to act by stabilizing a covalent complex between th...
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Protocol
Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases
The past few years have seen the application of single-molecule force spectroscopy techniques to the study of topoisomerases. Magnetic tweezers are particularly suited to the study of topoisomerases due to the...
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Article
Origin of the electrophoretic force on DNA in solid-state nanopores
When a single strand of DNA is threaded through a nanopore, a direct test of the effect of pore size indicates that a hydrodynamic model for the process should include the coupled Poisson–Boltzmann and Stokes ...
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Article
Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments
Magnetic torque tweezers are used to directly measure the torsional stiffness of single molecules of bare DNA and RecA filaments.
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Article
Excitable particles in an optical torque wrench
The optical torque wrench is a laser trap** technique capable of applying and directly measuring torque on microscopic birefringent particles using spin momentum transfer, and has found application in the me...
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Article
Open AccessFreely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids
The double-stranded nature of DNA links its replication, transcription and repair to rotational motion and torsional strain. Magnetic tweezers (MT) are a powerful single-molecule technique to apply both forces...
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Article
Studying genomic processes at the single-molecule level: introducing the tools and applications
We present key examples of the use of single-molecule approaches to study transcription, translation, splicing and replication.
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Article
Open AccessElectron beam fabrication of a microfluidic device for studying submicron-scale bacteria
Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth ...
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Article
Open AccessSlow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells
The ubiquitous sliding clamp facilitates processivity of the replicative polymerase and acts as a platform to recruit proteins involved in replication, recombination and repair. While the dynamics of the E. coli ...
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Article
Correction: Corrigendum: Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids
Nature Communications 2: Article number: 439 (2011); Published: 23 August 2011; Updated: 27 May 2015 The published version of this article contains two errors. In equation (18), there is a typographical error ...
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Article
Open AccessEssential validation methods for E. coli strains created by chromosome engineering
Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used ...
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Article
Strand separation establishes a sustained lock at the Tus–Ter replication fork barrier
Tus protein bound to Ter sites on circular bacterial chromosomes provides a way to avoid random crashes of opposing replication forks. DNA-unzip** experiments show that the Tus–Ter–induced lock during unzip**...
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Article
Open AccessRecent insights from in vitro single-molecule studies into nucleosome structure and dynamics
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a shor...
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Protocol
Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics
Studying the dynamics of intracellular processes and investigating the interaction of individual macromolecules in live cells is one of the main objectives of cell biology. These macromolecules move, assemble,...
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Article
Open AccessApplying torque to the Escherichia coli flagellar motor using magnetic tweezers
The bacterial flagellar motor of Escherichia coli is a nanoscale rotary engine essential for bacterial propulsion. Studies on the power output of single motors rely on the measurement of motor torque and rotation...
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Protocol
Probing Chromatin Structure with Magnetic Tweezers
Magnetic tweezers form a unique tool to study the topology and mechanical properties of chromatin fibers. Chromatin is a complex of DNA and proteins that folds the DNA in such a way that meter-long stretches o...