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Dye–biomolecule conjugation is frequently accompanied by considerable spectral changes of the dyes absorption spectrum that limit the use of the common photometrical method for the determination of labeling densities. Here, we describe an improvement of this method using the integral absorbance of the dye instead of its absorbance at the long wavelength maximum to determine the concentration of the biomolecule-coupled dye. This approach is illustrated for three different cyanine dyes conjugated to the antibody IgG.
Organic fluorescent dyes are a fundamental component in biomedical research and diagnostic imaging. The major classes encompass polymethine dyes, xanthene dyes, 4,4'-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) dyes, phenoxazines, and rare earth metal complexes. These compounds have been synthesized in manifold variations to optimize their photophysical properties and physicochemical behavior in physiological media and to enable conjugation to targeting molecules and nanocarriers. Furthermore, stimuli-responsive structural motifs were designed to apply these fluorophores as sensors for disease-related physiological and molecular conditions. This chapter is devoted to the chemical base of optical imaging agents, covering the relevant properties of fluorophores and the synthetic concepts toward intelligent optical imaging probes.
Efficient signal generation in DNA-based assays requires understanding of the influence of fluorophores interactions on the spectroscopic properties. The resulting changes in fluorescence intensity, quantum yield, emission anisotropy, and fluorescence lifetime provide straightforward tools for the study of molecular dynamics and interaction between labels and nucleic acids. Searching for bright fluorescent reporters for rolling circle amplification (RCA) as efficient signal enhancement strategy for biological formats, we investigated the spectroscopic properties of seven dyes: cyanines, rhodamines, and BODIPYs. They spectrally resemble Cy3, the most frequently used fluorophore in biodetection formats, and are measured in six samples (free dye, dye-dUTP, internally labeled ssDNA and dsDNA—single- and triple-labeled) using steady-state and time-resolved fluorometry. Special emphasis was dedicated to characterizing the nature of the interaction of these fluorophores differing in dye class, charge, and rigidity. Our results suggest dye charge and structure as main factors governing the dyes interactions, with DY-555 and Cy3B presenting the best candidates for our envisaged signal amplification strategy. This label comparison underlines the importance of a proper understanding of structure-property relations and dyebiomolecule interactions for reporter choice and presents a road map towards the design and interpretation of experiments using these labels on DNA of known sequence.