Near-IR dye

The easiest method for creating many vibrational excitations is to use convenient pulsed visible or near-UV lasers to pump electronic transitions of molecules which undergo fast nonradiative processes such as internal conversion (e.g. porjDhyrin [64, 65] or near-IR dyes [66, 62, 68 and 62]), photoisomerization (e.g. stilbene [12] or photodissociation (e.g. Hgl2 [8]). Creating a specific vibrational excitation D in a controlled way requires more finesse. The easiest method is to use visible or near-UV pulses to resonantly pump a vibronic transition (e.g. 

In the case of the naphthoquinone methine-type near-IR dye 55, reduction with tin(II) chloride under acidic conditions gives the leuco dye 56, which has weak absorption maxima at 350-359nm in methanol. The leuco dye 56 can be isolated as a stable pale yellow compound. The oxidation behavior of 56 has been studied by adding benzoquinone as oxidant in methanol solution. Compound 56 immediately produced new absorption at 760 nm which is consistent with the absorption maximum of 55 (Scheme 19).30 The absorption spectra of the leuco, quinone, and metal complex forms are summarized in Table 3. 

Ajayaghosh A (2005) Chemistry of squaraine-derived materials near-IR dyes, low band gap systems, and cation sensors. Acc Chem Res 38 449 159... 

Arunkumar E, Forbes CC, Noll BC, Smith BD (2005) Squaraine-derived rotaxanes steri-cally protected fluorescent near-IR dyes. J Am Chem Soc 127 3288-3289... 

Arunkumar E, Fu N, Smith BD (2006) Squaraine-derived rotaxanes highly stable, fluorescent near-IR dyes. Chem Eur J 12 4684-4690... 

Hsueh S Y, Lai CC, Liu YH, Wang Y, Peng SM, Chiu SH (2007) Protecting a squaraine near-IR dye through its incorporation in a slippage-derived [2]rotaxane. Org Lett 9 4523 1526... 

Poly(2-hydroxyethyl methylmethacrylate) (PHEMA) has been used as a matrix for the detection of metal ions. 79 A near-IR dye (2,3-naphthalocyanine-tetrasulphonic acid) was immobilized in a polymer matrix which was attached to the reaction phase of two optical fibers. A mixture of the matrix and the dye was prepared by mixing PHEMA and dye in a 60/40 ratio. The optimum ratio of polymer and dye were not fully investigated. The dye/polymer mixture was applied to the tip of the probe in 10-to 15-/iL aliquots forming a thin coating on the probe after solvent evaporation as shown in Figure 7.9. 

CGE separation of dsDNA fragments was performed on a PMMA chip using a near-IR dye (TOPRO-3). This allows the LIF detection of fragments (603-1353 bp) as low as 0.1 [tg/mL. DNA sizing of hepatitis C virus (HCV) amplicon was demonstrated [149]. 

Optical fibers (excitation and emission) have also been integrated on a PMM A chip for fluorescent detection. An intercalating near-IR dye (TOPRO-5) with an excitation wavelength of 755 nm was used to label DNA fragments. Sub-attomol detection limit of the labeled DNA fragments was achieved [674]. 

Laser excitation has also been provided by laser diodes. For instance, a red diode laser (635 nm) has been used as the light source for LIF detection [619,678]. Detection of the Cy 5 dye in a 13-pm-deep channel in a Pyrex glass chip has produced a LOD of 20 iM, as optimized using different filter sets. However, with a 20-pm-deep channel, the LOD of Cy 5 can be further improved to 9 pM [678]. A laser diode (GaAlAs, 780 nm) was also used for near-IR excitation [679]. A near-IR dye, IRD800, was used to label DNA primers for their LIF detection after separation on a PMMA chip [380]. 

A (triphenylene)Cr(CO)3 complex and its crystal structure212 has been described in which the Cr—C distance of this -complex is around 2.2 A, common for transition-metal-carbon bond distances. A redox-tunable near-IR dye based on a trinuclear ruthenium-(II) complex of hexahydroxytriphenylene 87 has been prepared.220 Here, the absorption maximum of the... 

Ni(bddt)2 compound (366). This compound shows a remarkable absorption at 1035 nm with = 63,000 dm3 mol-1 cm-1 and is therefore an excellent candidate as a near-IR dye for Q-switching neodymium lasers. 

Organic dye materials represent the largest and best characterized class of probes used in all manner of fluorescent analysis. As an overall class, these dyes are used in almost all areas of biotechnology, including biosensing, cellular imaging, clinical immunofluorescence, and in DNA/protein microarrays (42-45). Several major structural classes of organic fluorophore span the UV-to-near-IR spectrum see Fig. 4. UV dyes are typically pyrene-based, naphthalene-based, and coumarin-based structures, whereas the Vis/near-IR dyes include a variety of... 

Avalanche photodiode Band-pass filters 20 X 80 Electrokinetic PMMA Near-IR dye NN382 fluorescence intercalating dye TOPRO-5 1.4 X 10- moles Capillary electrophoresis... 

---