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Article
Open AccessA chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint
Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to t...
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Article
Open AccessNucleotide binding halts diffusion of the eukaryotic replicative helicase during activation
The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understandin...
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Article
Open AccessDNA replication origins retain mobile licensing proteins
DNA replication in eukaryotes initiates at many origins distributed across each chromosome. Origins are bound by the origin recognition complex (ORC), which, with Cdc6 and Cdt1, recruits and loads the Mcm2-7 (...
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Article
Open AccessChromatin fibers stabilize nucleosomes under torsional stress
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrap** and thereby the progression of polymerases. However, the propagation of twist in conde...
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Article
Open AccessCorrection: Corrigendum: Applying torque to the Escherichia coli flagellar motor using magnetic tweezers
Scientific Reports 7: Article number: 43285; published online: 07 March 2017; updated: 18 May 2018 The Acknowledgements section in this Article is incomplete. “We thank Seungkyu Ha, Yera Ye. Ussembayev, Richar...
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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...
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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
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 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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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 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
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 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
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
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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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
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
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
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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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...
