S1. In this work, we report the fluorescence and photophysical properties of Cy3 attached covalently to single-stranded and duplex DNA. The unusually high activation energy measured for Cy3-5' ssDNA is an indication of dye-ssDNA interactions. 2004 Apr;21(2):45-50. doi: 10.1016/j.bioeng.2003.09.001. Fluorescence Quantum Yield Standards. Cy3 Conjugated Anti-Mouse IgG SABC Kit is a four-component system for indirect sensitive immunofluorescent detection of proteins on tissue sections via ICC, IHC-P or IHC-F probed with mouse primary antibody by utilizing a biotinylated secondary antibody that links target-bound primary antibodies to streptavidin-Cy3 conjugate forming a stable StreptAvidin-Biotin Complex (SABC) . The emission peaks of Cy 3 and Cy 5 are 570 and 670. Once six dyes are attached, however, the intensity decreases. Anyone know where the 0.15 number came from? The R groups do not have to be identical. Q Rev Biophys. Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by, NCI CPTC Antibody Characterization Program. I think the quantum yield of Cy3 is closer to 0.04. Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6. interactions of Cy3 with proteins andnucleic acids can influence its quantum yield by hindering or promoting the photo-induced isomerisation around thecentral C= double- bond. 2020 Oct 16;11(1):5244. doi: 10.1038/s41467-020-19018-y. Please enable it to take advantage of the complete set of features! Cy3 fluoresces greenish yellow (~550 nm excitation, ~570 nm emission), while Cy5 is fluorescent in the red region (~650 excitation, 670 nm emission). Multicolor Detection and Analysis. Substantial differences were also observed between the 5'-modified strands and strands modified through an internal amino-modified deoxy uridine. The rate of this change can be measured to determine enzyme kinetic parameters. Cy5 became a popular replacement for far red fluorescent dyes because of its high extinction coefficient (as small as 1 nanomol can be detected in gel electrophoresis by naked eye) and its fluorophore emission maximum in the red region, where many CCD detectors have maximum sensitivity and biological objects give low background interference. Measurement Excitation [nm] Ref. In the original paper the number designated the count of the methines (as shown), and the side chains were unspecified. Photochem Photobiol Sci. , Ex (nm): Excitation wavelength in nanometers The fluorescence quantum yield of Cy3 is highest when attached to the 5' terminus of single-stranded DNA (Cy3-5' ssDNA), and decreases by a â¦ KristinLee 20:08, 2 June 2008 (UTC) Far Red and Red. Clipboard, Search History, and several other advanced features are temporarily unavailable. A good ratio is a label every 60 bases such that the labels are not too close to each other, which would result in quenching effects. Epub 2009 Jun 8. Labeling is done for visualization and quantification purposes. Biomol Eng. Many analogs of standard Cy 2 / 3 / 3.5 / 5 / 5.5 / 7 / 7.5 dyes were developed, using diverse modification: Because they yield brighter and more stable fluorescence, cyanines can advantageously replace conventional dyes such as fluorescein and rhodamines. The dyes can be used for similar purposes in FRET experiments. NIH The â¦ Cy3 is commonly combined with green-fluorescent dyes for double labeling. The quantum yield drops to 0.1 while gaining signiï¬cant structure in the emission spectrum (Figure 4), making it an ideal probe of DNA structure. Alexa Fluor dyes, Dylight, FluoProbes dyes, Sulfo Cy dyes, Seta dyes, IRIS dyes from Cyanine Technologies  and others can be used interchangeably with Cy dyes in most biochemical applications, with claimed improvements in solubility, fluorescence, or photostability..
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