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

Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry

(2016) Guanshi Wang et al.   CELL

RNA Polymerase Pausing during Initial Transcription

(2016) Diego Duchi et al.   MOLECULAR CELL

Bacterial RNA polymerase can retain σ70throughout transcription

(2016) Timothy T. Harden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ppGpp negatively impacts ribosome assembly affecting growth and antimicrobial tolerance in Gram-positive bacteria

(2016) Rebecca M. Corrigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Backtracked and paused transcription initiation intermediate ofEscherichia coliRNA polymerase

(2016) Eitan Lerner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Open complex scrunching before nucleotide addition accounts for the unusual transcription start site ofE. coliribosomal RNA promoters

(2016) Jared T. Winkelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection

(2016) J. T. Winkelman et al.   SCIENCE

Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA

(2016) Keisuke Fujita et al.   Nature Communications

Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers

(2016) Evelyn Ploetz et al.   Scientific Reports

Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription

(2015) Jørgen Skancke et al.   BIOCHEMISTRY

Promoter Escape with Bacterial Two-component σ Factor Suggests Retention of σ Region Two in the Elongation Complex

(2015) Shreya Sengupta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Studying RNAP–promoter interactions using atomic force microscopy

(2015) Yuki Suzuki et al.   METHODS

Multi-wavelength single-molecule fluorescence analysis of transcription mechanisms

(2015) Larry J. Friedman et al.   METHODS

Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes

(2015) Jared T. Winkelman et al.   MOLECULAR CELL

Massively Systematic Transcript End Readout, “MASTER”: Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields

(2015) Irina O. Vvedenskaya et al.   MOLECULAR CELL

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble

(2015) Yuhong Zuo et al.   MOLECULAR CELL

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

(2015) Furqan M. Fazal et al.   NATURE

The revolution will not be crystallized: a new method sweeps through structural biology

(2015) Ewen Callaway   NATURE

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

(2015) Brian Bae et al.   eLife

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

(2014) Andrey Feklístov et al.   Annual Review of Microbiology

Molecular Mechanisms of Transcription through Single-Molecule Experiments

(2014) Manchuta Dangkulwanich et al.   CHEMICAL REVIEWS

Structural Basis of Transcription Initiation by Bacterial RNA Polymerase Holoenzyme

(2014) Ritwika S. Basu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape

(2014) Danil Pupov et al.   NUCLEIC ACIDS RESEARCH

Interactions between RNA polymerase and the "core recognition element" counteract pausing

(2014) I. O. Vvedenskaya et al.   SCIENCE

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

RNA polymerase: in search of promoters

(2013) Andrey Feklistov   Annals of the New York Academy of Sciences

Single-Molecule Studies of RNA Polymerases

(2013) Jens Michaelis et al.   CHEMICAL REVIEWS

Alternating-laser excitation: single-molecule FRET and beyond

(2013) Johannes Hohlbein et al.   CHEMICAL SOCIETY REVIEWS

Insights into the Mechanism of Initial Transcription inEscherichia coliRNA Polymerase

(2013) Satamita Samanta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Looking for a promoter in 3D

(2013) Vladimir Svetlov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Disentangling Subpopulations in Single-Molecule FRET and ALEX Experiments with Photon Distribution Analysis

(2012) Toma E. Tomov et al.   BIOPHYSICAL JOURNAL

The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection

(2012) Nicole C. Robb et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Opening and Closing of the Bacterial RNA Polymerase Clamp

(2012) A. Chakraborty et al.   SCIENCE

Structural Basis of Transcription Initiation

(2012) Y. Zhang et al.   SCIENCE

Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis

(2011) Joseph P. Torella et al.   BIOPHYSICAL JOURNAL

σ70-dependent Transcription Pausing in Escherichia coli

(2011) Sarah A. Perdue et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolution of multisubunit RNA polymerases in the three domains of life

(2011) Finn Werner et al.   NATURE REVIEWS MICROBIOLOGY

Sensing DNA Opening in Transcription Using Quenchable Förster Resonance Energy Transfer

(2010) Thorben Cordes et al.   BIOCHEMISTRY

Promoter melting triggered by bacterial RNA polymerase occurs in three steps

(2010) Jie Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

(2010) Natacha Opalka et al.   PLOS BIOLOGY

RNA Polymerase Active Center: The Molecular Engine of Transcription

(2009) Evgeny Nudler   Annual Review of Biochemistry

Early Transcriptional Arrest atEscherichia coli rplNandompXPromoters

(2009) Ekaterina Stepanova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Direct Detection of Abortive RNA Transcripts in Vivo

(2009) S. R. Goldman et al.   SCIENCE

Single-Molecule Studies of RNA Polymerase: Motoring Along

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

(p)ppGpp: Still Magical?

(2008) Katarzyna Potrykus et al.   Annual Review of Microbiology

Red light, green light: probing single molecules using alternating-laser excitation

(2008) Yusdi Santoso et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

DNA Bubble Formation in Transcription Initiation†

(2008) Vladimir Tchernaenko et al.   BIOCHEMISTRY

Formation of the Open Complex by Bacterial RNA Polymerase—A Quantitative Model

(2008) Marko Djordjevic et al.   BIOPHYSICAL JOURNAL

Optical investigations of the RNA polymerase molecular motor

(2008) Terence R. Strick   Journal of Biophotonics

Monitoring abortive initiation

(2008) Lilian M. Hsu   METHODS

Transcription Initiation in a Single-Subunit RNA Polymerase Proceeds through DNA Scrunching and Rotation of the N-Terminal Subdomains

(2008) Guo-Qing Tang et al.   MOLECULAR CELL

Advances in bacterial promoter recognition and its control by factors that do not bind DNA

(2008) Shanil P. Haugen et al.   NATURE REVIEWS MICROBIOLOGY