ArticlePloS one2011
Sequence-dependent fluorescence of cyanine dyes on microarrays.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
23 citing papers in PubMed, 46 citations in OpenAlex.
- 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
- Interferometric excitation fluorescence lifetime imaging microscopy.Nature communications · 2024Article
- A Canvas of Spatially Arranged DNA Strands that Can Produce 24-bit Color Depth.Journal of the American Chemical Society · 2023Article
- Dipodal Silanes Greatly Stabilize Glass Surface Functionalization for DNA Microarray Synthesis and High-Throughput Biological Assays.Analytical chemistry · 2023Article
- An 8-bit monochrome palette of fluorescent nucleic acid sequences for DNA-based painting.Nanoscale · 2022Article
- Article
- 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
- Near Infrared-Activated Dye-Linked ZnO Nanoparticles Release Reactive Oxygen Species for Potential Use in Photodynamic Therapy.Materials (Basel, Switzerland) · 2019Article
- Article
- Uptake and Fate of Fluorescently Labeled DNA Nanostructures in Cellular Environments: A Cautionary Tale.ACS central science · 2019Article
- Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation.Nature communications · 2019Article
- Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite.PloS one · 2017Article
- Synthesis and Assessment of DNA/Silver Nanoclusters Probes for Optimal and Selective Detection of Tristeza Virus Mild Strains.Journal of fluorescence · 2016Article
- Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA.Bioconjugate chemistry · 2016Article
- Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties.Scientific reports · 2015Article
- Assembling programmable FRET-based photonic networks using designer DNA scaffolds.Nature communications · 2014Article
- Base-cleavable microarrays for the characterization of DNA and RNA oligonucleotides synthesized in situ by photolithography.Chemical communications (Cambridge, England) · 2014Article
- Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics.The journal of physical chemistry. B · 2014Article
- Comparison of the sequence-dependent fluorescence of the cyanine dyes Cy3, Cy5, DyLight DY547 and DyLight DY647 on single-stranded DNA.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5'-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5' guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5'-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.