ArticleNucleic acids research2012
A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 38 citations in OpenAlex.
- Tunable Molecular Photonic Wires via Geometric Control of Excitonically Coupled Cyanine Dimer Relays.The journal of physical chemistry. C, Nanomaterials and interfaces · 2026Article
- Synthesis, Photophysical Properties, and Practical Hg(II)-Sensing Applications of a Rigidified Phenolo-Merocyanine Dye.Chemistry, an Asian journal · 2025Article
- Fluorescent modifications in aptamer switches-positional, structural, and neighboring pair effects on sensor performance.Nucleic acids research · 2025Article
- Indocarbocyanine-Indodicarbocyanine (sCy3-sCy5) Absorptive Interactions in Conjugates and DNA Duplexes.Molecules (Basel, Switzerland) · 2024Article
- Fluorescent Properties of Cyanine Dyes As a Matter of the Environment.Journal of fluorescence · 2024Article
- A general strategy to develop fluorogenic polymethine dyes for bioimaging.Nature chemistry · 2024Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
- Article
- Fluorescently Labeled PLGA Nanoparticles for Visualization In Vitro and In Vivo: The Importance of Dye Properties.Pharmaceutics · 2021Article
- Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair.Molecules (Basel, Switzerland) · 2020Article
- Conformationally restrained pentamethine cyanines and use in reductive single molecule localization microscopy.Methods in enzymology · 2020Article
- A Porphyrin-DNA Chiroptical Molecular Ruler With Base Pair Resolution.Frontiers in chemistry · 2020Article
- Investigation of 8-Aza-7-Deaza Purine Nucleoside Derivatives.Molecules (Basel, Switzerland) · 2019Article
- Identification and characterization of nucleobase-modified aptamers by click-SELEX.Nature protocols · 2018Article
- Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.Bioconjugate chemistry · 2016Article
- FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. This severely limits its use in the fields of genomics, biology and nanotechnology. We have optimized the synthesis of Cy3B, and for the first time produced a diverse range of Cy3B monomers for use in solid-phase oligonucleotide synthesis. This molecular toolkit includes phosphoramidite monomers with Cy3B linked to deoxyribose, to the 5-position of thymine, and to a hexynyl linker, in addition to an oligonucleotide synthesis resin in which Cy3B is linked to deoxyribose. These monomers have been used to incorporate single and multiple Cy3B units into oligonucleotides internally and at both termini. Cy3B Taqman probes, Scorpions and HyBeacons have been synthesized and used successfully in mutation detection, and a dual Cy3B Molecular Beacon was synthesized and found to be superior to the corresponding Cy3B/DABCYL Beacon. Attachment of Cy3, Cy3B and Cy5 to the 5-position of thymidine by an ethynyl linker enabled the synthesis of an oligonucleotide FRET system. The rigid linker between the dye and nucleobase minimizes dye-dye and dye-DNA interactions and reduces fluorescence quenching. These reagents open up new future applications of Cy3B, including more sensitive single-molecule and cell-imaging studies.
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