Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair

Single-Molecule Chemistry. Part I: Monitoring Oxidation of G in Oligonucleotides Using CY3 Fluorescence

(2020) Jens Sobek et al.   Methods and Applications in Fluorescence

Identification of Nonradiative Decay Pathways in Cy3

(2020) Stephanie M. Hart 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

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip

(2018) Addie Kingsland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments

(2018) Kara K. Grotz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Formation and processing of DNA damage substrates for the hNEIL enzymes

(2017) Aaron M. Fleming et al.   FREE RADICAL BIOLOGY AND MEDICINE

Formation and repair of oxidatively generated damage in cellular DNA

(2017) Jean Cadet et al.   FREE RADICAL BIOLOGY AND MEDICINE

8-Oxo-7,8-dihydro-2′-deoxyguanosine and abasic site tandem lesions are oxidation prone yielding hydantoin products that strongly destabilize duplex DNA

(2017) Aaron M. Fleming et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

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

Single-molecule DNA hybridisation studied by using a modified DNA sequencer: a comparison with surface plasmon resonance data

(2016) Jens Sobek et al.   Methods and Applications in Fluorescence

Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: Predictive thermodynamic model

(2015) Bernardo G. Moreira et al.   BIOPHYSICAL CHEMISTRY

Triple helix conformation-specific blinking of Cy3 in DNA

(2015) Kiyohiko Kawai et al.   CHEMICAL COMMUNICATIONS

Delocalized Hole Domains in Guanine-Rich DNA Oligonucleotides

(2015) Amedeo Capobianco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

The current state of eukaryotic DNA base damage and repair

(2015) Nicholas C. Bauer et al.   NUCLEIC ACIDS RESEARCH

Hole delocalization over adenine tracts in single stranded DNA oligonucleotides

(2015) Amedeo Capobianco et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Guanine to Inosine Substitution Leads to Large Increases in the Population of a Transient G·C Hoogsteen Base Pair

(2014) Evgenia N. Nikolova et al.   BIOCHEMISTRY

Cy3 and Cy5 Dyes Terminally Attached to 5′C End of DNA: Structure, Dynamics, and Energetics

(2014) Ondřej Kroutil et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanistic Aspects of Hydration of Guanine Radical Cations in DNA

(2014) Yekaterina Rokhlenko et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Photophysical and Dynamical Properties of Doubly Linked Cy3–DNA Constructs

(2013) Elana M. S. Stennett et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Indocyanine Dyes Approach Free Rotation at the 3′ Terminus of A-RNA: A Comparison with the 5′ Terminus and Consequences for Fluorescence Resonance Energy Transfer

(2013) Peker Milas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Stacking Interactions between Adenines in Oxidized Oligonucleotides

(2013) Amedeo Capobianco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence

(2013) J. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

(2013) J. Cadet et al.   Cold Spring Harbor Perspectives in Biology

Direct labeling rolling circle amplification as a straightforward signal amplification technique for biodetection formats

(2012) Lena Linck et al.   Analytical Methods

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

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

Lifetimes and Reaction Pathways of Guanine Radical Cations and Neutral Guanine Radicals in an Oligonucleotide in Aqueous Solutions

(2012) Yekaterina Rokhlenko et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Advanced Fluorescence Microscopy Techniques—FRAP, FLIP, FLAP, FRET and FLIM

(2012) Hellen C. Ishikawa-Ankerhold et al.   MOLECULES

A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers

(2012) Lucy M. Hall et al.   NUCLEIC ACIDS RESEARCH

Spectroscopic and Photophysical Properties of dUTP and Internally DNA Bound Fluorophores for Optimized Signal Detection in Biological Formats

(2012) Lena Linck et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

(2012) Natalie B. Muren et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2011) Justin Spiriti et al.   BIOPHYSICAL JOURNAL

Orientation of Cyanine Fluorophores Terminally Attached to DNA via Long, Flexible Tethers

(2011) Jonathan Ouellet et al.   BIOPHYSICAL JOURNAL

Temperature dependence of interaction between double stranded DNA and Cy3 or Cy5

(2011) Xun Li et al.   CHEMICAL PHYSICS LETTERS

Linking Single-Molecule Blinking to Chromophore Structure and Redox Potentials

(2011) Ingo H. Stein et al.   CHEMPHYSCHEM

Theoretical Determination of One-Electron Redox Potentials for DNA Bases, Base Pairs, and Stacks

(2011) Y. Paukku et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Characterization of 2′-deoxyguanosine oxidation products observed in the Fenton-like system Cu(ii)/H2O2/reductant in nucleoside and oligodeoxynucleotide contexts

(2011) Aaron M. Fleming et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Voltammetric Characterization of DNA Intercalators across the Full pH Range: Anthraquinone-2,6-disulfonate and Anthraquinone-2-sulfonate

(2010) Christopher Batchelor-McAuley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

One-electron oxidation of DNA: thymine versus guanine reactivity

(2010) Sriram Kanvah et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments

(2010) Marcia Levitus et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Oxidation of DNA: Damage to Nucleobases

(2009) Sriram Kanvah et al.   ACCOUNTS OF CHEMICAL RESEARCH

Mechanisms for DNA Charge Transport

(2009) Joseph C. Genereux et al.   CHEMICAL REVIEWS

Fluorescence Quenching by Photoinduced Electron Transfer: A Reporter for Conformational Dynamics of Macromolecules

(2009) Sören Doose et al.   CHEMPHYSCHEM

Direct Observation of the Hole Protonation State and Hole Localization Site in DNA-Oligomers

(2009) Amitava Adhikary et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA sequence-dependent enhancement of Cy3 fluorescence

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

Single molecule fluorescence fluctuations of the cyanine dyes linked covalently to DNA

(2009) Wei Lv et al.   Science in China. Series B, Chemistry

Oxidatively Generated Damage to the Guanine Moiety of DNA: Mechanistic Aspects and Formation in Cells

(2008) Jean Cadet et al.   ACCOUNTS OF CHEMICAL RESEARCH

DNA Sequence Context as a Determinant of the Quantity and Chemistry of Guanine Oxidation Produced by Hydroxyl Radicals and One-electron Oxidants

(2008) Yelena Margolin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nucleobase-Specific Enhancement of Cy3 Fluorescence

(2008) Billie J. Harvey et al.   JOURNAL OF FLUORESCENCE

Charge Separation in Acridine- and Phenothiazine-Modified DNA

(2008) Kiyohiko Kawai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum dots versus organic dyes as fluorescent labels

(2008) Ute Resch-Genger et al.   NATURE METHODS

Selective one-electron oxidation of duplex DNA oligomers: reaction at thymines

(2008) Avik Ghosh et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

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

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE