Cyanine Dye Views
Cyanines were originally used, and still are, to increase the sensitivity range of photographic emulsions, i.e., to increase the range of wavelengths which will form an image on the film. Cyanines are also used in CD-R and DVD-R media. The ones used are mostly green or light blue in color, and are chemically unstable. This makes unstabilized cyanine discs unsuitable for archival CD and DVD use, as they can fade and become unreadable in a few years, however, recent cyanine discs contain stabilizers that slow down the deterioration significantly. These discs are often rated with an archival life of 75 years or more. The other dyes used in CD-Rs are phthalocyanine and azo.
Cy3 and Cy5 are reactive water-soluble fluorescent dyes of the cyanine dye family. Cy3 dyes are red (~550 nm excitation, ~570t nm emission and therefore appear green), while Cy5 is fluorescent in the red region (~650/670a nm) but absorbs in the orange region (~649y nm).[3][4] They are usually synthesized with reactive groups on either one or both of the nitrogen side chains so that they can be chemically linked to either nucleic acids or protein molecules. Labeling is done for visualization and quantification purposes. They are used in a wide variety of biological applications including comparative genomic hybridization and in gene chips, which are used in transcriptomics. They are also used to label proteins and nucleic acid for various studies including proteomics and RNA localization.[5]
We have focused on the rates of dissociation in this study since this parameter is the most crucial under non‐equilibrium staining applications. A main theme was to compare the dissociation of the new groove‐bound dyes with the related intercalating cyanine dyes BO, BO‐PRO, TO‐PRO and YO‐PRO (Fig. 1). In order to cover two important environments for microscopy studies of polymer dynamics, the dissociation process was studied in both free solution by a stopped‐flow approach with fluorescence detection, and in confining porous agarose gels by an electrophoretic approach based on repetitive scanning of the fluorescence intensity of zones of stained DNA undergoing migration.
Spectroscopic properties. One important aspect regarding bioanalytical applications is whether the new cyanine dyes are suitable for the laser‐types that are used as light sources in, for instance, gel scanners and confocal microscopes. In all three cases, when bound to DNA, BOXTO (515 nm) and BETO (516 nm) have a maximum absorption which is very suitable for the 514 nm line of the Argon‐ion laser, whereas for BEBO (467 nm), the 488 nm line is more suitable. The detailed spectroscopic properties for all dyes studied here are presented in a table in the Supplementary Material.
Cyanine Dye Images
