Studying genomic processes at the single-molecule level: introducing the tools and applications (Q38059632)

28 August 2017

Studying genomic processes at the single-molecule level: introducing the tools and applications (English)

1 reference

28 August 2017

David Dulin

1

0 references

Jan Lipfert

object named as

Jan Lipfert

series ordinal

2

0 references

Nynke Dekker

object named as

Nynke H Dekker

series ordinal

4

0 references

M Charl Moolman

series ordinal

3

object named as

M Charl Moolman

1 reference

PubMed ID

23150038

28 August 2017

language of work or name

1 reference

30 October 2012

1 reference

28 August 2017

Nature Reviews Genetics

1 reference

28 August 2017

14

1 reference

28 August 2017

1

1 reference

28 August 2017

9-22

1 reference

https://scigraph.springernature.com/pub.10.1038/nrg3316

28 August 2017

0 references

cites work

Sequencing technologies and genome sequencing

1 reference

Single-molecule imaging brings Rad51 nucleoprotein filaments into focus

21 January 2018

1 reference

Single molecule studies of homologous recombination

21 January 2018

1 reference

The twisted circular form of polyoma viral DNA

21 January 2018

1 reference

Patch Clamp Techniques for Studying Ionic Channels in Excitable Membranes

21 January 2018

1 reference

Single pentacene molecules detected by fluorescence excitation in a p-terphenyl crystal

21 January 2018

1 reference

Green fluorescent protein as a marker for gene expression

21 January 2018

1 reference

Force and velocity measured for single molecules of RNA polymerase.

21 January 2018

1 reference

Linking RNA polymerase backtracking to genome instability in E. coli

21 January 2018

1 reference

Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB.

21 January 2018

1 reference

Protein friction limits diffusive and directed movements of kinesin motors on microtubules

21 January 2018

1 reference

Transcription by single molecules of RNA polymerase observed by light microscopy

21 January 2018

1 reference

Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation

21 January 2018

1 reference

Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism

21 January 2018

1 reference

Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching

21 January 2018

1 reference

Dynamic Architecture of a Minimal RNA Polymerase II Open Promoter Complex

21 January 2018

1 reference

Direct observation of base-pair stepping by RNA polymerase

21 January 2018

1 reference

Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking.

21 January 2018

1 reference

Sequence-resolved detection of pausing by single RNA polymerase molecules.

21 January 2018

1 reference

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution

21 January 2018

1 reference

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

21 January 2018

1 reference

The origin of short transcriptional pauses

21 January 2018

1 reference

Thermal probing of E. coli RNA polymerase off-pathway mechanisms

21 January 2018

1 reference

Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA.

21 January 2018

1 reference

E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase

21 January 2018

1 reference

Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing

21 January 2018

1 reference

A unified model of transcription elongation: what have we learned from single-molecule experiments?

21 January 2018

1 reference

Fluctuations, pauses, and backtracking in DNA transcription

21 January 2018

1 reference

Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

21 January 2018

1 reference

In vivo dynamics of RNA polymerase II transcription.

21 January 2018

1 reference

Applied force reveals mechanistic and energetic details of transcription termination

21 January 2018

1 reference

The mechanism of intrinsic transcription termination.

21 January 2018

1 reference

Dynamics of the translational machinery

21 January 2018

1 reference

GTP hydrolysis by IF2 guides progression of the ribosome into elongation

21 January 2018

1 reference

Spontaneous intersubunit rotation in single ribosomes.

21 January 2018

1 reference

Following the intersubunit conformation of the ribosome during translation in real time

21 January 2018

1 reference

Identification of two distinct hybrid state intermediates on the ribosome

21 January 2018

1 reference

Following translation by single ribosomes one codon at a time.

21 January 2018

1 reference

A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting.

21 January 2018

1 reference

Real-time DNA sequencing from single polymerase molecules

21 January 2018

1 reference

Real-time tRNA transit on single translating ribosomes at codon resolution

21 January 2018

1 reference

The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State

21 January 2018

1 reference

Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling

21 January 2018

1 reference

The ribosome modulates nascent protein folding

21 January 2018

1 reference

Imaging of single-molecule translocation through nuclear pore complexes

21 January 2018

1 reference

Nuclear transport of single molecules: dwell times at the nuclear pore complex.

21 January 2018

1 reference

Selectivity mechanism of the nuclear pore complex characterized by single cargo tracking

21 January 2018

1 reference

Single molecule study of the intrinsically disordered FG-repeat nucleoporin 153.

21 January 2018

1 reference

In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport

21 January 2018

1 reference

Conformational dynamics of single pre-mRNA molecules during in vitro splicing

21 January 2018

1 reference

Single-molecule analysis of Mss116-mediated group II intron folding.

21 January 2018

1 reference

Ordered and dynamic assembly of single spliceosomes

21 January 2018

1 reference

Cell-to-cell variability of alternative RNA splicing

21 January 2018

1 reference

Single-molecule imaging of transcriptionally coupled and uncoupled splicing

21 January 2018

1 reference

Replisome architecture and dynamics in Escherichia coli

21 January 2018

1 reference

The bacterial replisome: back on track?

21 January 2018

1 reference

21 January 2018

SnapShot: The replisome

1 reference

Replisome-mediated DNA replication.

21 January 2018

1 reference

CELLULAR DNA REPLICASES: Components and Dynamics at the Replication Fork

21 January 2018

1 reference

Replication by a single DNA polymerase of a stretched single-stranded DNA

21 January 2018

1 reference

Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome

21 January 2018

1 reference

DnaB helicase activity is modulated by DNA geometry and force

21 January 2018

1 reference

Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase

21 January 2018

1 reference

SSB functions as a sliding platform that migrates on DNA via reptation.

21 January 2018

1 reference

Collaborative coupling between polymerase and helicase for leading-strand synthesis

21 January 2018

1 reference

DNA primase acts as a molecular brake in DNA replication

21 January 2018

1 reference

Single-molecule studies of fork dynamics in Escherichia coli DNA replication

21 January 2018

1 reference

Uncoupling of sister replisomes during eukaryotic DNA replication

21 January 2018

1 reference

Coordinating DNA replication by means of priming loop and differential synthesis rate

21 January 2018

1 reference

Characterization of a triple DNA polymerase replisome.

21 January 2018

1 reference

Polymerase switching in DNA replication.

21 January 2018

1 reference

Single-molecule approach to molecular biology in living bacterial cells

21 January 2018

1 reference

Stoichiometry and architecture of active DNA replication machinery in Escherichia coli

21 January 2018

1 reference

Polymerase exchange during Okazaki fragment synthesis observed in living cells.

21 January 2018

1 reference

Single-molecule studies reveal the function of a third polymerase in the replisome

21 January 2018

1 reference

DNA replicases from a bacterial perspective

21 January 2018

1 reference

Cellular strategies for regulating DNA supercoiling: a single-molecule perspective

21 January 2018

1 reference

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments.

21 January 2018

1 reference

Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids

21 January 2018

1 reference

Mechanochemical analysis of DNA gyrase using rotor bead tracking

21 January 2018

1 reference

Structural transitions and elasticity from torque measurements on DNA.

21 January 2018

1 reference

Optical torque wrench: angular trapping, rotation, and torque detection of quartz microparticles.

21 January 2018

1 reference

Ultrahigh-resolution optical trap with single-fluorophore sensitivity

21 January 2018

1 reference

Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction

21 January 2018

1 reference

Mechanical characterization of protein L in the low-force regime by electromagnetic tweezers/evanescent nanometry.

21 January 2018

1 reference

Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics

21 January 2018

1 reference

Single-molecule approach to immunoprecipitated protein complexes: insights into miRNA uridylation

21 January 2018

1 reference

Probing cellular protein complexes using single-molecule pull-down

21 January 2018

1 reference

Multiplexed single-molecule measurements with magnetic tweezers

21 January 2018

1 reference

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation

21 January 2018

1 reference

Binding-activated localization microscopy of DNA structures.

21 January 2018

1 reference

Imaging individual mRNA molecules using multiple singly labeled probes

21 January 2018

1 reference

Single-mRNA counting using fluorescent in situ hybridization in budding yeast

21 January 2018

1 reference

RNA mimics of green fluorescent protein

21 January 2018

1 reference

Super-resolution imaging of the nucleoid-associated protein HU in Caulobacter crescentus

21 January 2018

1 reference

Chromosome organization by a nucleoid-associated protein in live bacteria

21 January 2018

1 reference

Fluorescent probes for super-resolution imaging in living cells

21 January 2018

1 reference

A hitchhiker's guide to mechanobiology

21 January 2018

1 reference

Force nanoscopy of living cells.

21 January 2018

1 reference

Microfabricated tissue gauges to measure and manipulate forces from 3D microtissues

21 January 2018

1 reference

Vertical nanopillars for highly localized fluorescence imaging

21 January 2018

1 reference

Probing dynein and kinesin stepping with mechanical manipulation in a living cell

21 January 2018

1 reference

Magnetic manipulation of nanorods in the nucleus of living cells

21 January 2018

1 reference

Intracellular stress tomography reveals stress focusing and structural anisotropy in cytoskeleton of living cells

21 January 2018

1 reference

Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics

21 January 2018

1 reference

Visualizing dynamic cytoplasmic forces with a compliance-matched FRET sensor

21 January 2018

1 reference

Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus

21 January 2018

1 reference

Ten years of tension: single-molecule DNA mechanics

21 January 2018

1 reference

High-resolution, single-molecule measurements of biomolecular motion

21 January 2018

1 reference

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

21 January 2018

1 reference

Quantitative modeling and optimization of magnetic tweezers

21 January 2018

1 reference

The elasticity of a single supercoiled DNA molecule

21 January 2018

1 reference

Single-molecule studies of the replisome

21 January 2018

1 reference

Force measurements with the atomic force microscope: Technique, interpretation and applications

21 January 2018

1 reference

Biological applications of optical forces

21 January 2018

1 reference

Recent advances in optical tweezers

21 January 2018

1 reference

Passive all-optical force clamp for high-resolution laser trapping.

21 January 2018

1 reference

Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat

21 January 2018

1 reference

Fluorescent proteins: a cell biologist's user guide

21 January 2018

1 reference

Type III restriction enzymes communicate in 1D without looping between their target sites

21 January 2018

1 reference

Total internal reflection fluorescence microscopy in cell biology

21 January 2018

1 reference

Precise nanometer localization analysis for individual fluorescent probes

21 January 2018

1 reference

Beyond Rayleigh's criterion: a resolution measure with application to single-molecule microscopy.

21 January 2018

1 reference

Fast, single-molecule localization that achieves theoretically minimum uncertainty

21 January 2018

1 reference

Optimized localization analysis for single-molecule tracking and super-resolution microscopy.

21 January 2018

1 reference

Microscopy and its focal switch.

21 January 2018

1 reference

Superresolution imaging using single-molecule localization

21 January 2018

1 reference

Single molecule studies of nucleocytoplasmic transport

21 January 2018

1 reference

Single-molecule transport across an individual biomimetic nuclear pore complex

21 January 2018

1 reference

Microsystems for cellular force measurement: a review

21 January 2018

1 reference

Template supercoiling by a chimera of yeast GAL4 protein and phage T7 RNA polymerase

21 January 2018

1 reference

Single molecules observed by near-field scanning optical microscopy

31 March 2020

1 reference

Five challenges to bringing single-molecule force spectroscopy into living cells

31 March 2020

1 reference

Structure of replicating simian virus 40 deoxyribonucleic acid molecules

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23150038

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Genetically encoded force sensors for measuring mechanical forces in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23150038

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3316

1 reference

PubMed ID

23150038

Dimensions Publication ID

28 August 2017

0 references

1 reference

PubMed ID

23150038