Probing steps in DNA transcription using single-molecule methods

A novel high-throughput single-molecule technique: DNA curtain

(2021) Jongjin Cha et al.   JOURNAL OF THE KOREAN PHYSICAL SOCIETY

Closing and opening of the RNA polymerase trigger loop

(2020) Abhishek Mazumder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

R-loop induced G-quadruplex in non-template promotes transcription by successive R-loop formation

(2020) Chun-Ying Lee et al.   Nature Communications

Single-molecule fluorescence studies on cotranscriptional G-quadruplex formation coupled with R-loop formation

(2020) Gunhyoung Lim et al.   NUCLEIC ACIDS RESEARCH

The elemental mechanism of transcriptional pausing

(2019) Jason Saba et al.   eLife

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Transcription activation in bacteria: ancient and modern

(2019) Stephen J. W. Busby   MICROBIOLOGY-SGM

Single-molecule approach for studying Pol II transcription initiation using magnetic tweezers

(2019) Eric J. Tomko et al.   METHODS

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Mechanisms of Bacterial Transcription Termination

(2019) Jeffrey W. Roberts   JOURNAL OF MOLECULAR BIOLOGY

Mechanisms of Transcriptional Pausing in Bacteria

(2019) Jin Young Kang et al.   JOURNAL OF MOLECULAR BIOLOGY

A Single-Molecule View of Archaeal Transcription

(2019) Kevin Kramm et al.   JOURNAL OF MOLECULAR BIOLOGY

Single-molecule characterization of extrinsic transcription termination by Sen1 helicase

(2019) S. Wang et al.   Nature Communications

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Loss of Dynamic RNA Interaction and Aberrant Phase Separation Induced by Two Distinct Types of ALS/FTD-Linked FUS Mutations

(2019) Amirhossein Ghanbari Niaki et al.   MOLECULAR CELL

Imaging mRNA In Vivo, from Birth to Death

(2018) Evelina Tutucci et al.   Annual Review of Biophysics

The cryo-EM resolution revolution and transcription complexes

(2018) Jonas Hanske et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Visualizing transcription factor dynamics in living cells

(2018) Zhe Liu et al.   JOURNAL OF CELL BIOLOGY

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution

(2018) Hye Ran Koh et al.   MOLECULAR CELL

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer

(2018) Eitan Lerner et al.   SCIENCE

Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins

(2018) Pinki Dey et al.   Scientific Reports

Single-molecule analysis reveals the mechanism of transcription activation in M. tuberculosis

(2018) Rishi Kishore Vishwakarma et al.   Science Advances

Mimicking Co-Transcriptional RNA Folding Using a Superhelicase

(2018) Boyang Hua et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Bacteriophage T7 transcription system: an enabling tool in synthetic biology

(2018) Wenya Wang et al.   BIOTECHNOLOGY ADVANCES

TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning

(2017) Eric J Tomko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence

(2017) Yazan Alhadid et al.   PROTEIN SCIENCE

TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning

(2017) Eric J Tomko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanisms of Bacterial Transcription Termination: All Good Things Must End

(2016) Ananya Ray-Soni et al.   Annual Review of Biochemistry

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation

(2016) Maria Vera et al.   Annual Review of Genetics

Dephosphorylating eukaryotic RNA polymerase II

(2016) Joshua E. Mayfield et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

(2016) Zhengjian Zhang et al.   GENES & DEVELOPMENT

What have single-molecule studies taught us about gene expression?

(2016) Huimin Chen et al.   GENES & DEVELOPMENT

NusG Is a Sequence-specific RNA Polymerase Pause Factor That Binds to the Non-template DNA within the Paused Transcription Bubble

(2016) Alexander V. Yakhnin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement–Förster-Type Resonance Energy Transfer (PIFE-FRET)

(2016) Eitan Lerner et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA Scanning of a Molecular Machine with a Built-in Ruler

(2016) Hye Ran Koh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA Polymerase Pausing during Initial Transcription

(2016) Diego Duchi et al.   MOLECULAR CELL

Local and global regulation of transcription initiation in bacteria

(2016) Douglas F. Browning et al.   NATURE REVIEWS MICROBIOLOGY

Nucleosomal arrangement affects single-molecule transcription dynamics

(2016) Veronika Fitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Termination: Variations on Common Themes

(2016) Odil Porrua et al.   TRENDS IN GENETICS

Demystifying PIFE: The Photophysics Behind the Protein-Induced Fluorescence Enhancement Phenomenon in Cy3

(2015) Elana M. S. Stennett et al.   Journal of Physical Chemistry Letters

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble

(2015) Christopher O. Barnes et al.   MOLECULAR CELL

Simultaneous Single-Molecule Force and Fluorescence Sampling of DNA Nanostructure Conformations Using Magnetic Tweezers

(2015) Felix E. Kemmerich et al.   NANO LETTERS

Real-time observation of the initiation of RNA polymerase II transcription

(2015) Furqan M. Fazal et al.   NATURE

Subangstrom single-molecule measurements of motor proteins using a nanopore

(2015) Ian M Derrington et al.   NATURE BIOTECHNOLOGY

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence

(2015) Alex Kreig et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Molecular Mechanism of Resolving Trinucleotide Repeat Hairpin by Helicases

(2015) Yupeng Qiu et al.   STRUCTURE

Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS

(2015) Julia Nagy et al.   Nature Communications

Strength in numbers: quantitative single-molecule RNA detection assays

(2015) Imre Gaspar et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Optical Tweezers Analysis of DNA–Protein Complexes

(2014) Iddo Heller et al.   CHEMICAL REVIEWS

Molecular Mechanisms of Transcription through Single-Molecule Experiments

(2014) Manchuta Dangkulwanich et al.   CHEMICAL REVIEWS

RNA polymerase II pausing during development

(2014) B. Gaertner et al.   DEVELOPMENT

Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing

(2014) Hye Ran Koh et al.   NUCLEIC ACIDS RESEARCH

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Single-molecule tracking of the transcription cycle by sub-second RNA detection

(2014) Zhengjian Zhang et al.   eLife

Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

(2014) Ignacio Izeddin et al.   eLife

Kinetic competition during the transcription cycle results in stochastic RNA processing

(2014) Antoine Coulon et al.   eLife

Protein induced fluorescence enhancement (PIFE) for probing protein–nucleic acid interactions

(2013) Helen Hwang et al.   CHEMICAL SOCIETY REVIEWS

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

RNA polymerase approaches its promoter without long-range sliding along DNA

(2013) L. J. Friedman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

Systematic Identification of Signal-Activated Stochastic Gene Regulation

(2013) G. Neuert et al.   SCIENCE

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

(2013) Manchuta Dangkulwanich et al.   eLife

The transcription cycle in eukaryotes: From productive initiation to RNA polymerase II recycling

(2012) Jayasha Shandilya et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA polymerase II transcription: Structure and mechanism

(2012) Xin Liu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

CoSMoS Unravels Mysteries of Transcription Initiation

(2012) Richard L. Gourse et al.   CELL

Mechanism of Transcription Initiation at an Activator-Dependent Promoter Defined by Single-Molecule Observation

(2012) Larry J. Friedman et al.   CELL

Fast microscopical dissection of action scenes played byEscherichia coliRNA polymerase

(2012) Yuki Suzuki et al.   FEBS LETTERS

Transcription initiation by human RNA polymerase II visualized at single-molecule resolution

(2012) A. Revyakin et al.   GENES & DEVELOPMENT

Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level

(2012) Daniel J. Koslover et al.   JOURNAL OF MOLECULAR BIOLOGY

Nanopore Detection of Single Molecule RNAP–DNA Transcription Complex

(2012) C. Raillon et al.   NANO LETTERS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion

(2012) Feng Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-molecule studies of DNA transcription using atomic force microscopy

(2012) Daniel J Billingsley et al.   PHYSICAL BIOLOGY

Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II

(2012) M. H. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Observation of Cotranscriptional Folding in an Adenine Riboswitch

(2012) K. L. Frieda et al.   SCIENCE

Opening and Closing of the Bacterial RNA Polymerase Clamp

(2012) A. Chakraborty et al.   SCIENCE

Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A

(2012) Géraldine Farge et al.   Nature Communications

Single-Molecule Studies of Transcription: From One RNA Polymerase at a Time to the Gene Expression Profile of a Cell

(2011) Feng Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

(2011) Ruth M. Saecker et al.   JOURNAL OF MOLECULAR BIOLOGY

Applied Force Provides Insight into Transcriptional Pausing and Its Modulation by Transcription Factor NusA

(2011) Jing Zhou et al.   MOLECULAR CELL

Single-Molecule Studies of RNA Polymerase: One Singular Sensation, Every Little Step It Takes

(2011) Matthew H. Larson et al.   MOLECULAR CELL

RNIE: genome-wide prediction of bacterial intrinsic terminators

(2011) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity

(2011) H. Hwang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sensing DNA Opening in Transcription Using Quenchable Förster Resonance Energy Transfer

(2010) Thorben Cordes et al.   BIOCHEMISTRY

Single-molecule Measurements of DNA Topology and Topoisomerases

(2010) Keir C. Neuman   JOURNAL OF BIOLOGICAL CHEMISTRY

Fluorescent Lifetime Trajectories of a Single Fluorophore Reveal Reaction Intermediates During Transcription Initiation

(2009) Maria Sorokina et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase

(2009) Guo-Qing Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Studies of RNA Polymerase: Motoring Along

(2008) Kristina M. Herbert et al.   Annual Review of Biochemistry

Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination

(2008) Matthew H. Larson et al.   CELL

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS

The Structure of a Transcribing T7 RNA Polymerase in Transition from Initiation to Elongation

(2008) K. J. Durniak et al.   SCIENCE