Biochemical applications, fluorescent dyes

Noise can be also introduced by biochemical heterogeneity of the specimen. This can be a major cause of uncertainty in biological imaging. The high (three-dimensional) spatial resolution of fluorescence microscopy results in low numbers of fluorophores in the detection volume. In a typical biological sample, the number of fluorophores in the detection volume can be as low as 2-3 fluorophores for a confocal microscope equipped with a high NA objective at a fluorescent dye concentration of 100 nM. This introduces another source of noise for imaging applications, chemical or molecular noise, related to the inherent randomness of diffusion and the interaction of molecules. 

Biochemical Applications of Fluorescence Spectroscopy Biomacromolecular Applications of Circular Dichroism and ORD Biomacromolecular Applications of UV-Visible Absorption Spectroscopy Chemical Reactions Studied By Electronic Spectroscopy Circularly Polarized Luminescence and Fluorescence Detected Circular Dichroism Dyes and Indicators, Use of UV-Visible Absorption Spectroscopy... 

Most biochemical assays used to determine the potency of inhibitors against (1) aminopeptidases and (2) endopeptidases with minor contributions to the substrate binding efficiency by the S site, are based on the measurement of FI as readout. AMC and RhllO are the most common fluorophores in these cases. For studies of enzyme kinetics, the application of AMC is sufficient. If an assay is intended to determine the inhibitory potencies of small chemical compounds, it is recommended to use red-shifted dyes like RhllO to minimize interference of compound fluorescence with the fluorescence originating from the assay dye. 

Design and synthesis of fluorescence energy transfer dye-labeled primers and their application for DNA sequencing and analysis Anal. Biochem. 231 131 0... 

Ju, J., Kheterpal, L, Scherer, J.R., Ruan, C., Fuller, C.W., Glazer, A.N., and Mathies, R.A., Design and synthesis of fluorescence energy transfer dye-labeled primers and their application for DNA sequencing and analysis, AnaZ. Biochem., 231,131,1995. 

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