Comparison of the Sequence-Dependent Fluorescence of the Cyanine Dyes Cy3, Cy5, DyLight DY547 and DyLight DY647 on Single-Stranded DNA
作者： Nicole Kretschy , Mark M. Somoza
DOI: 10.1371/JOURNAL.PONE.0085605
关键词: Cyanine 、 Fluorescence in situ hybridization 、 DNA microarray 、 Nucleic acid 、 Oligonucleotide 、 Biophysics 、 Fluorescence 、 Förster resonance energy transfer 、 DNA 、 Chemistry 、 Biochemistry
摘要: Cyanine dyes are commonly used for fluorescent labeling of DNA and RNA oligonucleotides in applications including qPCR, sequencing, fluorescence situ hybridization, Forster resonance energy transfer, microarray hybridization. Previous research has shown that the efficiency Cy3 Cy5, covalently attached to 5′ end single-stranded DNA, is strongly sequence dependent. Here, we show DY547 DY647, two alternative cyanine becoming widely nucleic acid labeling, have a similar pattern sequence-dependence, with adjacent purines resulting higher intensity cytosines lower intensity. Investigated over range all 1024 possible 5mers, intensities Cy5 drop by ∼50% ∼65% respect their maxima, respectively, whereas DY647 fall ∼45% ∼40%, respectively. The reduced magnitude change DyLight dyes, particularly comparison suggests these less likely introduce sequence-dependent bias into experiments based on acids.
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