ArticleBioconjugate chemistry2016
Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.
Article in Bioconjugate chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Tunable Molecular Photonic Wires via Geometric Control of Excitonically Coupled Cyanine Dimer Relays.The journal of physical chemistry. C, Nanomaterials and interfaces · 2026Article
- smDeepFLUOR: single-molecule deep learning fluorescence classification.Nature communications · 2026Article
- Cyanine-modified ssODNs enhance CRISPR-Cas9 HDR in stem cell embryo models via chromatin and chemical modulation.Nature communications · 2026Article
- Time-Resolved Fluorescence Detection of Nicked DNA via Site-Specific Stacking of Sulfo-Cy3: The Role of Charge, Polarity, Linker, and Sequence Context.The journal of physical chemistry. B · 2025Article
- Unraveling biomolecular interactions: a comprehensive review of the electromobility shift assay.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2025Review
- DNA Aptamer-Polymer Conjugates for Selective Targeting of Integrin α4β1ACS applied materials & interfaces · 2025Article
- Mimicking a Cellular Crowding Environment for Enzyme-Free Paper-Based Nucleic Acid Tests at the Point of Care.ACS sensors · 2024Article
- A rapid investigation of near-infrared (NIR) fluorescent switch-on probes for detection and in cellulo tracking of G-quadruplex and double-stranded DNA.RSC advances · 2024Review
- Interferometric excitation fluorescence lifetime imaging microscopy.Nature communications · 2024Article
- Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA.The journal of physical chemistry. B · 2024Article
- Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels.Nature nanotechnology · 2024Article
- Sculpting photoproducts with DNA origami.Chem · 2024Article
- Replication of [AT/TA]Biochemistry · 2024Article
- Fluorescent Properties of Cyanine Dyes As a Matter of the Environment.Journal of fluorescence · 2024Article
- Heterochiral modifications enhance robustness and function of DNA in living human cells.Chembiochem : a European journal of chemical biology · 2024Article
- Mimicking anbioRxiv : the preprint server for biology · 2024Article
- Replication of [AT/TA]bioRxiv : the preprint server for biology · 2023Article
- Dipodal Silanes Greatly Stabilize Glass Surface Functionalization for DNA Microarray Synthesis and High-Throughput Biological Assays.Analytical chemistry · 2023Article
- Spectroscopic Characterization of Thiacarbocyanine Dye Molecules Adsorbed on Hexagonal Boron Nitride: a Time-Resolved Study.ACS omega · 2023Article
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3 authors.
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Abstract
The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the 5' end of all 1024 possible double-stranded DNA 5mers. The fluorescence intensity was also determined for these dyes bound to the 5' end of fixed-sequence double-stranded DNA with a variable sequence 3' overhang adjacent to the dye. The labeled DNA oligonucleotides were made using light-directed, in situ microarray synthesis. The results indicate that the fluorescence intensity of both dyes is sensitive to all five bases or base pairs, that the sequence dependence is stronger for double- (vs single-) stranded DNA, and that the dyes are sensitive to both the adjacent dsDNA sequence and the 3'-ssDNA overhang. Purine-rich sequences result in higher fluorescence. The results can be used to estimate measurement error in experiments with fluorescent-labeled DNA, as well as to optimize the fluorescent signal by considering the nucleobase environment of the labeling cyanine dye.
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