Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update

Activatable Organic Near-Infrared Fluorescent Probes Based on a Bacteriochlorin Platform: Synthesis and Multicolor in Vivo Imaging with a Single Excitation

(2014) Toshiko Harada et al.   BIOCONJUGATE CHEMISTRY

Single Molecule Fluorescence Approaches Shed Light on Intracellular RNAs

(2014) Sethuramasundaram Pitchiaya et al.   CHEMICAL REVIEWS

The bright future of single-molecule fluorescence imaging

(2014) Manuel F Juette et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair

(2014) Mathew Stracy et al.   FEBS LETTERS

Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle

(2014) Elvin A. Alemán et al.   Journal of Physical Chemistry Letters

Dynamic Assembly/Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface

(2014) Yuki Suzuki et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Discovering anomalous hybridization kinetics on DNA nanostructures using single-molecule fluorescence microscopy

(2014) Alexander Johnson-Buck et al.   METHODS

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

(2014) Ralf Jungmann et al.   NATURE METHODS

Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm

(2014) Jinglin Fu et al.   Nature Nanotechnology

X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

(2014) Jochen Küpper et al.   PHYSICAL REVIEW LETTERS

Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging

(2014) S. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

(2014) N. F. Dupuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization of Dynamics of Single Endogenous mRNA Labeled in Live Mouse

(2014) H. Y. Park et al.   SCIENCE

On the right track

(2014) Amir Mor et al.   Nucleus

Single-Molecule Fluorescence Imaging in Living Cells

(2013) Tie Xia et al.   Annual Review of Physical Chemistry

A Single-Molecule View of the Assembly Pathway, Subunit Stoichiometry, and Unwinding Activity of the Bacteriophage T4 Primosome (helicase–primase) Complex

(2013) Wonbae Lee et al.   BIOCHEMISTRY

Long-Lived Intracellular Single-Molecule Fluorescence Using Electroporated Molecules

(2013) Robert Crawford et al.   BIOPHYSICAL JOURNAL

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

(2013) J. R. Alvarez-Dominguez et al.   BLOOD

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

Fluorescent proteins for live-cell imaging with super-resolution

(2013) Karin Nienhaus et al.   CHEMICAL SOCIETY REVIEWS

Shedding light on protein folding landscapes by single-molecule fluorescence

(2013) Priya R. Banerjee et al.   CHEMICAL SOCIETY REVIEWS

RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messengers Cyclic di-GMP and Cyclic AMP-GMP

(2013) Colleen A. Kellenberger 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

Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards

(2013) Alexander Johnson-Buck et al.   NANO LETTERS

DNA unwinding heterogeneity by RecBCD results from static molecules able to equilibrate

(2013) Bian Liu et al.   NATURE

Modulation of allostery by protein intrinsic disorder

(2013) Allan Chris M. Ferreon et al.   NATURE

Imaging bacterial protein expression using genetically encoded RNA sensors

(2013) Wenjiao Song et al.   NATURE METHODS

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

(2013) Rita L Strack et al.   NATURE METHODS

A synthetic DNA motor that transports nanoparticles along carbon nanotubes

(2013) Tae-Gon Cha et al.   Nature Nanotechnology

Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies

(2013) Andrew Robinson et al.   NATURE REVIEWS MICROBIOLOGY

Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging

(2013) Andreas Gahlmann et al.   NATURE REVIEWS MICROBIOLOGY

Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing

(2013) Ramya Krishnan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure

(2013) Krishna C. Suddala et al.   NUCLEIC ACIDS RESEARCH

Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions

(2013) C. Phelps et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Helicase-mediated changes in RNA structure at the single-molecule level

(2013) Sebastian L.B. König et al.   RNA Biology

Scalable Parallel Screening of Catalyst Activity at the Single-Particle Level and Subdiffraction Resolution

(2013) Xiaochun Zhou et al.   ACS Catalysis

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Photophysics of Fluorescent Probes for Single-Molecule Biophysics and Super-Resolution Imaging

(2012) Taekjip Ha et al.   Annual Review of Physical Chemistry

Far-red to near infrared analyte-responsive fluorescent probes based on organic fluorophore platforms for fluorescence imaging

(2012) Lin Yuan et al.   CHEMICAL SOCIETY REVIEWS

Unraveling the dynamics of ribosome translocation

(2012) Jin Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Visualizing Cell Structure and Function with Point-Localization Superresolution Imaging

(2012) Prabuddha Sengupta et al.   DEVELOPMENTAL CELL

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

(2012) Sethuramasundaram Pitchiaya et al.   EMBO REPORTS

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Hidden complexity in the isomerization dynamics of Holliday junctions

(2012) Changbong Hyeon et al.   Nature Chemistry

RNA catalysis through compartmentalization

(2012) Christopher A. Strulson et al.   Nature Chemistry

Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA

(2012) Chenxiang Lin et al.   Nature Chemistry

Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy

(2012) J. P. Siebrasse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorescence Imaging of Cellular Metabolites with RNA

(2012) Jeremy S. Paige et al.   SCIENCE

Actin, Spectrin, and Associated Proteins Form a Periodic Cytoskeletal Structure in Axons

(2012) K. Xu et al.   SCIENCE

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

Single-Molecule Fluorescence Measurements of Ribosomal Translocation Dynamics

(2011) Chunlai Chen et al.   MOLECULAR CELL

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

Cell-to-cell variability of alternative RNA splicing

(2011) Z. Waks et al.   Molecular Systems Biology

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

Nuclear export dynamics of RNA–protein complexes

(2011) David Grünwald et al.   NATURE

Femtosecond X-ray protein nanocrystallography

(2011) Henry N. Chapman et al.   NATURE

Dynamic DNA nanotechnology using strand-displacement reactions

(2011) David Yu Zhang et al.   Nature Chemistry

Direct observation of stepwise movement of a synthetic molecular transporter

(2011) Shelley F. J. Wickham et al.   Nature Nanotechnology

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes

(2011) Raul Perez-Jimenez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The shape-shifting quasispecies of RNA: one sequence, many functional folds

(2011) Matthew S. Marek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ordered and Dynamic Assembly of Single Spliceosomes

(2011) A. A. Hoskins et al.   SCIENCE

Nanoscale imaging in DNA nanotechnology

(2011) Ralf Jungmann et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology

(2011) Nicole Michelotti et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Alteration of the α-Synuclein Folding Landscape by a Mutation Related to Parkinson’s Disease

(2010) Allan Chris M. Ferreon et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single Ribosome Dynamics and the Mechanism of Translation

(2010) Colin Echeverría Aitken et al.   Annual Review of Biophysics

Superresolution Imaging using Single-Molecule Localization

(2010) George Patterson et al.   Annual Review of Physical Chemistry

Laser-Assisted Single-Molecule Refolding (LASR)

(2010) Rui Zhao et al.   BIOPHYSICAL JOURNAL

Ground-State Depletion Microscopy: Detection Sensitivity of Single-Molecule Optical Absorption at Room Temperature

(2010) Shasha Chong et al.   Journal of Physical Chemistry Letters

Single-Molecule Sensitivity in Optical Absorption at Room Temperature

(2010) Philipp Kukura et al.   Journal of Physical Chemistry Letters

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

(2010) David Grünwald et al.   NATURE

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

(2010) Sotaro Uemura et al.   NATURE

Molecular robots guided by prescriptive landscapes

(2010) Kyle Lund et al.   NATURE

Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker

(2010) Yu He et al.   Nature Nanotechnology

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

(2010) John Abelson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Three-dimensional distribution of transient interactions in the nuclear pore complex obtained from single-molecule snapshots

(2010) J. Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

(2010) S. E. McDowell et al.   RNA

Room-Temperature Detection of a Single Molecule's Absorption by Photothermal Contrast

(2010) A. Gaiduk et al.   SCIENCE

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Bipedal DNA Brownian Motor with Coordinated Legs

(2009) Tosan Omabegho et al.   SCIENCE

Advances in Single-Molecule Fluorescence Methods for Molecular Biology

(2008) Chirlmin Joo et al.   Annual Review of Biochemistry

Tethering of proteins to RNAs by bacteriophage proteins

(2008) Cecile Keryer-Bibens et al.   BIOLOGY OF THE CELL

Single VS Ribozyme Molecules Reveal Dynamic and Hierarchical Folding Toward Catalysis

(2008) Miguel J.B. Pereira et al.   JOURNAL OF MOLECULAR BIOLOGY

Do-it-yourself guide: how to use the modern single-molecule toolkit

(2008) Nils G Walter et al.   NATURE METHODS

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS

A rugged free energy landscape separates multiple functional RNA folds throughout denaturation

(2008) Mark A. Ditzler et al.   NUCLEIC ACIDS RESEARCH

Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme

(2008) C. de Silva et al.   RNA

Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy

(2008) B. Huang et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE