Cyanine dyes intercalation

Araki K, Yoshikawa I (2005) Nucleobase-Containing Gelators. 256 133-165 Armitage BA (2005) Cyanine Dye-DNA Interactions Intercalation, Groove Binding and Aggregation. 253 55-76... 

Rye, H. S, Yue, S, Wemmer, D. E, Quesada, M. A, Haugland, R. P, Mathies, R. A. and Glazer, A. N. (1992). Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes -Properties and applications. Nucleic Acids Res. 20, 2803-2812. 

Biver, T., De Biasi, A., Secco, E, Venturing M., and Yarmoluk, S. (2005) Cyanine dyes as intercalating agents Kinetic and thermodynamic studies on the DNA/Cyan40 and DNA/CCyan2 systems. Biophys. J. 89, 374-383. 

Armitage BA (2005) Cyanine Dye-DNA Interactions Intercalation, Groove Binding and... 

An efficient combinatorial solid-phase synthesis of asymmetric cyanine dyes was developed by Isacsson and Westman [17] using a Rink amide polystyrene resin. The picolinium and lepidinium salts 6 were linked to the solid-phase resin by amide coupling, then the benzothiazole derivatives 7 were subsequently condensed with the coupled picoline and lepidine moieties to give the yellow to blue (Amax ahs = 420-590 nm) asymmetric, fluorescent (Amax em = 480-650 nm) cyanine dyes 8 (Scheme 5.2, Fig. 5.3). As a consequence of restricted rotation upon intercalation, the fluorescence quantum yields increase significantly when these dyes are bound to DNA. 

Noncovalent interaction of dyes and related compormds with various biomacromolecules attracts considerable attention due to the possibility of proceeding of a variety of photochemical processes in vivo [1]. It makes possible to use dyes both in biomedical studies as DNA labels and in clinical practice [2], Complex formation of cyanine dyes with doublehelical DNA is of great interest due to rmique photophysical and photochemical properties of these dyes, which change dramatically in the presence of DNA [1, 3, 4], There are two main types of dye-DNA bonding complexes of dyes intercalated between DNA base pairs and complexes in which dye molecules are located in the minor groove of the double helix of the biopolymer (superficial bonding) [5],... 

In summary, the triplet decay kinetics of KI-K4 in the presence of DNA are biexponential the two observed components are attributed to two different complexes between the dye and DNA. Using nitroxyl radical and iodide ion as quenchers, we have shown that cyanine dyes form with DNA two types of complexes formed by binding of the dye in the groove of a DNA molecule and by intercalation of the dye between base pairs. 

DNA accessibility can be determined by how well the DNA binds fluorescent intercalating dyes. TO-PRO-1 is a cyanine dye that fluoresces only when bound to nucleic acid (82). It is more sensitive for fluorescence detection than ethidium bromide and binds stably to the DNA. The relative degree of protection of the DNA can be quantified. 

Fluorescently labeled plasmid can be quite useful for cellular uptake and distribution studies (112). The main concern with fluorescently tagged DNA is that the presence of the dye molecules may interfere with the interactions between the DNA and the carrier, or the DNA and cellular components. Of equal importance, the binding of the dye to the DNA must be irreversible, so that the dye molecules do not dissociate from the DNA once internalized by the cell. A number of fluorescent DNA-intercalating dyes are available for DNA labeling, such as ethidium bromide, ethidium monoazide, the TO-PRO series, various other cyanine dyes, and many others (82). For example, the membrane-impermeable compound YO-YO... 

Bis-intercalating cyanine dyes (e.g. 291) have been shown to form stable highly fluorescent... 

As we go from microfluidics to nanofluidics, the distinction between the scalar-based and particle-based methods becomes obsolete, and in turn, the small dimensions of the microfluidic and nanofluidic channels also allow for increased sensitivity in the fluorescence detections. This, along with the invention of intercalating cyanine dyes, spurs other major applications of fluorescence measurements in microfluidics and nanofluidics the investigation on individual DNA molecules. 

The PNA FIT probes contain a single cyanine dye that belongs to the thiazole orange (TO) family of intercalator dyes. The dye replaces a canonical nucleobase and, thereby, serves as a fluorescent base surrogate. PNA FIT probes respond to changes of the viscosity around the environmentally sensitive TO dye. 

---