Following the messenger: Recent innovations in live cell single molecule fluorescence imaging

SMALL-LABS: Measuring Single-Molecule Intensity and Position in Obscuring Backgrounds

(2019) Benjamin P. Isaacoff et al.   BIOPHYSICAL JOURNAL

Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality

(2019) Sethuramasundaram Pitchiaya et al.   MOLECULAR CELL

Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay

(2019) Tim A. Hoek et al.   MOLECULAR CELL

Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope

(2019) Ameya P. Jalihal et al.   Cold Spring Harbor Perspectives in Biology

Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

(2019) Sanne Boersma et al.   CELL

The dynamic lifecycle of mRNA in the nucleus

(2019) Rakefet Ben-Yishay et al.   CURRENT OPINION IN CELL BIOLOGY

Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting

(2019) Kenneth Lyon et al.   MOLECULAR CELL

A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo

(2019) Ning Zhao et al.   Nature Communications

Optimizing the fluorescent protein toolbox and its use

(2019) Sam Duwé et al.   CURRENT OPINION IN BIOTECHNOLOGY

Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs

(2019) Xianjun Chen et al.   NATURE BIOTECHNOLOGY

Live imaging of mRNA using RNA-stabilized fluorogenic proteins

(2019) Jiahui Wu et al.   NATURE METHODS

Mechanisms of nuclear mRNA export: A structural perspective

(2019) Yihu Xie et al.   TRAFFIC

Imaging mRNA In Vivo, from Birth to Death

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

Toward a Kinetic Understanding of Eukaryotic Translation

(2018) Masaaki Sokabe et al.   Cold Spring Harbor Perspectives in Biology

Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells

(2018) Alexis Autour et al.   Nature Communications

A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells

(2018) Esther Braselmann et al.   Nature Chemical Biology

Choosing the right label for single-molecule tracking in live bacteria: side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes

(2018) Nehir Banaz et al.   JOURNAL OF PHYSICS D-APPLIED PHYSICS

Imaging the Life and Death of mRNAs in Single Cells

(2018) Jeffrey A. Chao et al.   Cold Spring Harbor Perspectives in Biology

An in Vivo Binding Assay for RNA-Binding Proteins Based on Repression of a Reporter Gene

(2018) Noa Katz et al.   ACS Synthetic Biology

Intracellular RNA-tracking methods

(2018) Logan George et al.   Open Biology

Non-AUG translation: a new start for protein synthesis in eukaryotes

(2017) Michael G. Kearse et al.   GENES & DEVELOPMENT

Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications

(2017) Farah Bouhedda et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Trick or TREAT: A Scary-Good New Approach for Single-Molecule mRNA Decay Analysis

(2017) Joseph Russo et al.   MOLECULAR CELL

The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells

(2017) Ivana Horvathova et al.   MOLECULAR CELL

Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks

(2017) Flavia Michelini et al.   NATURE CELL BIOLOGY

A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

(2017) Katherine Deigan Warner et al.   Nature Chemical Biology

Imaging RNA polymerase III transcription using a photostable RNA–fluorophore complex

(2017) Wenjiao Song et al.   Nature Chemical Biology

An improved MS2 system for accurate reporting of the mRNA life cycle

(2017) Evelina Tutucci et al.   NATURE METHODS

In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines

(2017) Thomas C. Custer et al.   PROTEIN SCIENCE

Ribonucleoprotein purification and characterization using RNA Mango

(2017) Shanker Shyam S. Panchapakesan et al.   RNA

Imaging Translational and Post-Translational Gene Regulatory Dynamics in Living Cells with Antibody-Based Probes

(2017) Kenneth Lyon et al.   TRENDS IN GENETICS

Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution

(2017) Sethuramasundaram Pitchiaya et al.   Cell Reports

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

(2016) Chong Wang et al.   CELL

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

More than just scanning: the importance of cap-independent mRNA translation initiation for cellular stress response and cancer

(2016) Rafaela Lacerda et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

(2016) Xavier Pichon et al.   JOURNAL OF CELL BIOLOGY

Super-resolution Imaging of Live Bacteria Cells Using a Genetically Directed, Highly Photostable Fluoromodule

(2016) Saumya Saurabh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Light-up and FRET aptamer reporters; evaluating their applications for imaging transcription in eukaryotic cells

(2016) Muslum Ilgu et al.   METHODS

In vitro and ex vivo strategies for intracellular delivery

(2016) Martin P. Stewart et al.   NATURE

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

(2016) Dmitry E. Andreev et al.   NUCLEIC ACIDS RESEARCH

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

(2016) J. U. Guo et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

Versatile protein tagging in cells with split fluorescent protein

(2016) Daichi Kamiyama et al.   Nature Communications

KRAS Engages AGO2 to Enhance Cellular Transformation

(2016) Sunita Shankar et al.   Cell Reports

Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences

(2015) Bin Wu et al.   GENES & DEVELOPMENT

Inferring transient particle transport dynamics in live cells

(2015) Nilah Monnier et al.   NATURE METHODS

New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation

(2015) Jeffrey S Kieft et al.   RNA Biology

An RNA biosensor for imaging the first round of translation from single cells to living animals

(2015) J. M. Halstead et al.   SCIENCE

Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast

(2015) David Guet et al.   Nature Communications

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

(2015) Jichuan Zhang et al.   Scientific Reports

Self-labelling enzymes as universal tags for fluorescence microscopy, super-resolution microscopy and electron microscopy

(2015) Viktoria Liss et al.   Scientific Reports

RNA Mango Aptamer-Fluorophore: A Bright, High-Affinity Complex for RNA Labeling and Tracking

(2014) Elena V. Dolgosheina et al.   ACS Chemical Biology

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Single Molecule Fluorescence Approaches Shed Light on Intracellular RNAs

(2014) Sethuramasundaram Pitchiaya et al.   CHEMICAL REVIEWS

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

(2014) Katherine Deigan Warner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Contact-Mediated Quenching for RNA Imaging in Bacteria with a Fluorophore-Binding Aptamer

(2013) Murat Sunbul et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Understanding the Photophysics of the Spinach–DFHBI RNA Aptamer–Fluorogen Complex To Improve Live-Cell RNA Imaging

(2013) Kyu Young Han et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dissecting non-coding RNA mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting

(2013) Sethuramasundaram Pitchiaya et al.   METHODS

A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA

(2013) Rita L Strack et al.   NATURE METHODS

Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly

(2012) Sethuramasundaram Pitchiaya et al.   EMBO REPORTS

The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges

(2012) A. G. Hinnebusch et al.   Cold Spring Harbor Perspectives in Biology

Chemically Modulating the Photophysics of the GFP Chromophore

(2011) Jamie Conyard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling

(2010) X. Zhang et al.   RNA

Fluorinated Analogs of Malachite Green: Synthesis and Toxicity

(2008) George Kraus et al.   MOLECULES

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS