ArticlePloS one2014
Comparison of the sequence-dependent fluorescence of the cyanine dyes Cy3, Cy5, DyLight DY547 and DyLight DY647 on single-stranded DNA.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- Fluorescent modifications in aptamer switches-positional, structural, and neighboring pair effects on sensor performance.Nucleic acids research · 2025Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
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- An 8-bit monochrome palette of fluorescent nucleic acid sequences for DNA-based painting.Nanoscale · 2022Article
- Sequence-dependence of Cy3 and Cy5 dyes in 3' terminally-labeled single-stranded DNA.Scientific reports · 2022Article
- Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA.RSC advances · 2022Article
- Multi-level patterning nucleic acid photolithography.Nature communications · 2019Article
- Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation.Nature communications · 2019Article
- High-Efficiency Reverse (5'→3') Synthesis of Complex DNA Microarrays.Scientific reports · 2018Article
- Introduction of various substitutions to the methine bridge of heptamethine cyanine dyes Via substituted dianil linkers.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2018Article
- Highly chromophoric Cy5-methionine for N-terminal fluorescent tagging of proteins in eukaryotic translation systems.Scientific reports · 2017Article
- Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays.Biology · 2016Article
- Single-molecule imaging of electroporated dye-labelled CheY in live Escherichia coli.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Article
- Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers.Scientific reports · 2016Article
- Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.Bioconjugate chemistry · 2016Article
- The Impact of Photobleaching on Microarray Analysis.Biology · 2015Article
- A New Spectral Shift-Based Method to Characterize Molecular Interactions.Assay and drug development technologiesArticle
Corrections and comments
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2 authors.
Funding
Abstract
Cyanine dyes are commonly used for fluorescent labeling of DNA and RNA oligonucleotides in applications including qPCR, sequencing, fluorescence in situ hybridization, Förster resonance energy transfer, and labeling for microarray hybridization. Previous research has shown that the fluorescence efficiency of Cy3 and Cy5, covalently attached to the 5' end of single-stranded DNA, is strongly sequence dependent. Here, we show that DY547 and DY647, two alternative cyanine dyes that are becoming widely used for nucleic acid labeling, have a similar pattern of sequence-dependence, with adjacent purines resulting in higher intensity and adjacent cytosines resulting in lower intensity. Investigated over the range of all 1024 possible DNA 5mers, the intensities of Cy3 and Cy5 drop by ∼ 50% and ∼ 65% with respect to their maxima, respectively, whereas the intensities of DY547 and DY647 fall by ∼ 45% and ∼ 40%, respectively. The reduced magnitude of change of the fluorescence intensity of the DyLight dyes, particularly of DY647 in comparison with Cy5, suggests that these dyes are less likely to introduce sequence-dependent bias into experiments based on fluorescent labeling of nucleic acids.
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