Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching

Modeling Non-additive Effects in Neighboring Chemically Identical Fluorophores

(2022) Ayush Saurabh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures

(2021) Kristina Hübner et al.   ACS Nano

Nuclease resistance of DNA nanostructures

(2021) Arun Richard Chandrasekaran   Nature Reviews Chemistry

Rapid kinetic fingerprinting of single nucleic acid molecules by a FRET-based dynamic nanosensor

(2021) Kunal Khanna et al.   BIOSENSORS & BIOELECTRONICS

Strategies for combining triplet–triplet annihilation upconversion sensitizers and acceptors in a host matrix

(2021) Waqas Ahmad et al.   COORDINATION CHEMISTRY REVIEWS

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3

(2021) Mohammed I. Sorour et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Immobilization of Cyanines in DNA Produces Systematic Increases in Fluorescence Intensity

(2021) Natalie A. Pace et al.   Journal of Physical Chemistry Letters

Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility

(2021) Stefan Niekamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Monochromatic Fluorescent Barcodes Hierarchically Assembled from Modular DNA Origami Nanorods

(2021) Victor Pan et al.   ACS Nano

A 6-nm ultra-photostable DNA FluoroCube for fluorescence imaging

(2020) Stefan Niekamp et al.   NATURE METHODS

Multiple-Labeled Antibodies Behave Like Single Emitters in Photoswitching Buffer

(2020) Dominic A. Helmerich et al.   ACS Nano

Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay

(2020) Yosuke Hirotsu et al.   JOURNAL OF VIROLOGICAL METHODS

Live-cell super-resolved PAINT imaging of piconewton cellular traction forces

(2020) Joshua M. Brockman et al.   NATURE METHODS

Direct kinetic fingerprinting and digital counting of single protein molecules

(2020) Tanmay Chatterjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delivering DNA origami to cells

(2019) Dhanasekaran Balakrishnan et al.   Nanomedicine

Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures

(2019) Tim Schröder et al.   NANO LETTERS

DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes

(2019) Jonathan S. Huff et al.   Journal of Physical Chemistry Letters

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

(2019) Fahad Rashid et al.   Nature Communications

Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014–2019)

(2019) Zeki Semih Pehlivan et al.   MICROCHIMICA ACTA

DNA probes that store mechanical information reveal transient piconewton forces applied by T cells

(2019) Rong Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging uses of DNA mechanical devices

(2019) Aaron T. Blanchard et al.   SCIENCE

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

(2018) Loni Kringle et al.   JOURNAL OF CHEMICAL PHYSICS

Programmable Multivalent DNA-Origami Tension Probes for Reporting Cellular Traction Forces

(2018) Palash K. Dutta et al.   NANO LETTERS

Highly Photostable and Fluorescent Microporous Solids Prepared via Solid-State Entrapment of Boron Dipyrromethene Dyes in a Nascent Metal–Organic Framework

(2018) Viktorija Glembockyte et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Photophysics of J-Aggregate-Mediated Energy Transfer on DNA

(2017) James L. Banal et al.   Journal of Physical Chemistry Letters

Mapping the 3D orientation of piconewton integrin traction forces

(2017) Joshua M Brockman et al.   NATURE METHODS

Platelet integrins exhibit anisotropic mechanosensing and harness piconewton forces to mediate platelet aggregation

(2017) Yun Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electronic tuning of self-healing fluorophores for live-cell and single-molecule imaging

(2017) Qinsi Zheng et al.   Chemical Science

Sub–100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA

(2017) Johannes B. Woehrstein et al.   Science Advances

Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA

(2016) Nicole Kretschy et al.   BIOCONJUGATE CHEMISTRY

Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes

(2016) Francesca Nicoli et al.   JOURNAL OF PHYSICAL CHEMISTRY A

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

Single-molecule fluorescence resonance energy transfer in molecular biology

(2016) Dibyendu K. Sasmal et al.   Nanoscale

A stem-less probe using spontaneous pairing between Cy3 and quencher for RNA detection

(2016) Hiromu Kashida et al.   SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS

Rationally designed molecular beacons for bioanalytical and biomedical applications

(2015) Jing Zheng et al.   CHEMICAL SOCIETY REVIEWS

Cy3 Photoprotection Mediated by Ni2+ for Extended Single-Molecule Imaging: Old Tricks for New Techniques

(2015) Viktorija Glembockyte et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Kinetic fingerprinting to identify and count single nucleic acids

(2015) Alexander Johnson-Buck et al.   NATURE BIOTECHNOLOGY

Intracellular FRET-based probes: a review

(2015) Clare E Rowland et al.   Methods and Applications in Fluorescence

Design of molecular beacons: 3′ couple quenchers improve fluorogenic properties of a probe in real-time PCR assay

(2014) Dmitry Y. Ryazantsev et al.   ANALYST

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

(2014) Ralf Jungmann et al.   NATURE METHODS

Internally labeled Cy3/Cy5 DNA constructs show greatly enhanced photo-stability in single-molecule FRET experiments

(2014) Wonbae Lee et al.   NUCLEIC ACIDS RESEARCH

DNA-based digital tension probes reveal integrin forces during early cell adhesion

(2014) Yun Zhang et al.   Nature Communications

Ultra-stable organic fluorophores for single-molecule research

(2013) Qinsi Zheng et al.   CHEMICAL SOCIETY REVIEWS

A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking

(2013) Si Kyung Yang et al.   Nature Chemistry

Design and development of fluorescent nanostructures for bioimaging

(2013) Mengjun Chen et al.   PROGRESS IN POLYMER SCIENCE

Characterization of Dark Quencher Chromophores as Nonfluorescent Acceptors for Single-Molecule FRET

(2012) Ludovic Le Reste et al.   BIOPHYSICAL JOURNAL

Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery

(2012) Hyukjin Lee et al.   Nature Nanotechnology

Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair

(2011) Justin Spiriti et al.   BIOPHYSICAL JOURNAL

Cyanine fluorophore derivatives with enhanced photostability

(2011) Roger B Altman et al.   NATURE METHODS

Identification of a thermally activated process in the Cy3 photobleaching mechanism

(2011) A. L. Jouonang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Spectroscopic studies of position-specific DNA "breathing" fluctuations at replication forks and primer-template junctions

(2009) D. Jose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stabilisation of a heptamethine cyanine dye by rotaxane encapsulation

(2008) C. M. Simon Yau et al.   CHEMICAL COMMUNICATIONS

Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids

(2008) A. Iqbal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2007) Colin Echeverría Aitken et al.   BIOPHYSICAL JOURNAL