Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series**

Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation

(2019) Fahad Rashid et al.   Nature Communications

Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers

(2019) Marijn de Boer et al.   eLife

ABCE1 Controls Ribosome Recycling by an Asymmetric Dynamic Conformational Equilibrium

(2019) Giorgos Gouridis et al.   Cell Reports

Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics

(2018) Lena Voith von Voithenberg et al.   BIOESSAYS

Simulation of FRET dyes allows quantitative comparison against experimental data

(2018) Ines Reinartz et al.   JOURNAL OF CHEMICAL PHYSICS

Effective photo-enhancement of cellular activity of fluorophore-octaarginine antisense PNA conjugates correlates with singlet oxygen formation, endosomal escape and chromophore lipophilicity

(2018) Reza Yarani et al.   Scientific Reports

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase

(2018) Wen Ma et al.   eLife

The Protein Microenvironment Governs the Suitability of Labeling Sites for Single-Molecule Spectroscopy of RNP Complexes

(2018) Andreas Schmidt et al.   ACS Chemical Biology

Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

(2018) Florence Husada et al.   EMBO JOURNAL

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

(2018) Björn Hellenkamp et al.   NATURE METHODS

Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately

(2017) Thomas-Otavio Peulen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Changes Spanning Angstroms to Nanometers via a Combined Protein-Induced Fluorescence Enhancement–Förster Resonance Energy Transfer Method

(2017) Yasser Gidi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

(2016) Yitao Feng et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Regulation of a Coupled MARCKS–PI3K Lipid Kinase Circuit by Calmodulin: Single-Molecule Analysis of a Membrane-Bound Signaling Module

(2016) Brian P. Ziemba et al.   BIOCHEMISTRY

Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems

(2016) Mykola Dimura et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

(2016) Jasper H. M. van der Velde 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

Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6

(2016) Yawei Dai et al.   Scientific Reports

Watching conformational dynamics of ABC transporters with single-molecule tools

(2015) F. Husada et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Quantitative Interpretation of FRET Experiments via Molecular Simulation: Force Field and Validation

(2015) Robert B. Best et al.   BIOPHYSICAL JOURNAL

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

The 2015 super-resolution microscopy roadmap

(2015) Stefan W Hell et al.   JOURNAL OF PHYSICS D-APPLIED PHYSICS

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

A review of the analysis of complex time-resolved fluorescence anisotropy data

(2015) Trevor A Smith et al.   Methods and Applications in Fluorescence

Triphosphate Induced Dimerization of Human Guanylate Binding Protein 1 Involves Association of the C-Terminal Helices: A Joint Double Electron–Electron Resonance and FRET Study

(2014) Tobias Vöpel et al.   BIOCHEMISTRY

AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations

(2014) Timo Graen et al.   Journal of Chemical Theory and Computation

A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research

(2014) Alexander Gust et al.   MOLECULES

Inter-Dye Distance Distributions Studied by a Combination of Single-Molecule FRET-Filtered Lifetime Measurements and a Weighted Accessible Volume (wAV) Algorithm

(2014) Henning Höfig et al.   MOLECULES

A spontaneously blinking fluorophore based on intramolecular spirocyclization for live-cell super-resolution imaging

(2014) Shin-nosuke Uno et al.   Nature Chemistry

Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ

(2014) Giorgos Gouridis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Choose Your Label Wisely: Water-Soluble Fluorophores Often Interact with Lipid Bilayers

(2014) Laura D. Hughes et al.   PLoS One

Single-molecule FRET supports the two-state model of Argonaute action

(2014) Adrian Zander et al.   RNA Biology

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

(2013) Helen Hwang et al.   CHEMICAL SOCIETY REVIEWS

Mechanism of Intramolecular Photostabilization in Self-Healing Cyanine Fluorophores

(2013) Jasper H. M. van der Velde et al.   CHEMPHYSCHEM

Ensemble and Single-Molecule Studies on Fluorescence Quenching in Transition Metal Bipyridine-Complexes

(2013) Dominik Brox et al.   PLoS One

Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding

(2013) Laura C. Zanetti-Domingues et al.   PLoS One

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

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

'Self-healing' dyes: intramolecular stabilization of organic fluorophores

(2012) Philip Tinnefeld et al.   NATURE METHODS

Enhanced photostability of cyanine fluorophores across the visible spectrum

(2012) Roger B Altman et al.   NATURE METHODS

A toolkit and benchmark study for FRET-restrained high-precision structural modeling

(2012) Stanislav Kalinin et al.   NATURE METHODS

The Molecular Probes handbook. A guide to fluorescent probes and labeling technologies

(2011) G. Ya. Wiederschain   BIOCHEMISTRY-MOSCOW

Natural history of ABC systems: not only transporters

(2011) Elie Dassa   Essays in Biochemistry

Cyanine fluorophore derivatives with enhanced photostability

(2011) Roger B Altman et al.   NATURE METHODS

Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy

(2011) Thorben Cordes et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Fungal recognition is mediated by the association of dectin-1 and galectin-3 in macrophages

(2011) A. Esteban et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Domain Orientation in the N-Terminal PDZ Tandem from PSD-95 Is Maintained in the Full-Length Protein

(2011) James J. McCann et al.   STRUCTURE

Four-color single-molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexes

(2010) Vanessa C. DeRocco et al.   BIOTECHNIQUES

Fast and accurate algorithm for the simulation of NMR spectra of large spin systems

(2010) Andrés M. Castillo et al.   JOURNAL OF MAGNETIC RESONANCE

Identification of the Product of Photoswitching of an Oxazine Fluorophore Using Fourier Transform Infrared Difference Spectroscopy

(2010) Tilman Kottke et al.   Journal of Physical Chemistry Letters

Molecular mechanism of the synaptotagmin–SNARE interaction in Ca2+-triggered vesicle fusion

(2010) Marija Vrljic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mitigating Unwanted Photophysical Processes for Improved Single-Molecule Fluorescence Imaging

(2009) Richa Dave et al.   BIOPHYSICAL JOURNAL

On the Mechanism of Trolox as Antiblinking and Antibleaching Reagent

(2009) Thorben Cordes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Microfluidic Device for Single-Molecule Experiments with Enhanced Photostability

(2009) Edward A. Lemke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Photoswitching Mechanism of Cyanine Dyes

(2009) Graham T. Dempsey et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA sequence-dependent enhancement of Cy3 fluorescence

(2009) Billie Jo Harvey et al.   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

Engineered cystine knot peptides that bind αvβ3, αvβ5, and α5β1 integrins with low-nanomolar affinity

(2009) Richard H. Kimura et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Reducing and Oxidizing System Minimizes Photobleaching and Blinking of Fluorescent Dyes

(2008) Jan Vogelsang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes

(2008) Mike Heilemann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Simulation of Structure, Orientation, and Energy Transfer between AlexaFluor Molecules Attached to MscL

(2008) Ben Corry et al.   BIOPHYSICAL JOURNAL

Antibody microarray analysis of directly labelled complex proteomes

(2008) Christer Wingren et al.   CURRENT OPINION IN BIOTECHNOLOGY

Neuronal viability is controlled by a functional relation between synaptic and extrasynaptic NMDA receptors

(2008) F. Léveillé et al.   FASEB JOURNAL

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

(2008) A. L. Davidson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Direct observation of the nanoscale dynamics of membrane lipids in a living cell

(2008) Christian Eggeling et al.   NATURE

A nano-positioning system for macromolecular structural analysis

(2008) Adam Muschielok et al.   NATURE METHODS

Microscopy and its focal switch

(2008) Stefan W Hell   NATURE METHODS

Colocalization of fluorescent markers in confocal microscope images of plant cells

(2008) Andrew P French et al.   Nature Protocols

Investigating the Movement of Intravitreal Human Serum Albumin Nanoparticles in the Vitreous and Retina

(2008) Hyuncheol Kim et al.   PHARMACEUTICAL RESEARCH

An Oxygen Scavenging System for Improvement of Dye Stability in Single-Molecule Fluorescence Experiments

(2007) Colin Echeverría Aitken et al.   BIOPHYSICAL JOURNAL