Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules

Abstract

Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.

Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy

“…Nevertheless, these dyes do not have selectivity and can stain DNA and RNA; furthermore, they act as nuclear stains in live cells and can also stain other compartments, such as mitochondria . For fluorescent probes, the low fluorescence quantum yield in the free state and the high quantum yield in the bound state, that is, a sharp increase in fluorescence intensity upon binding to a biomolecule, are essential . These fluorescent dyes differ from fluorescent labels such as cyanines of the Cy3-Cy5 family dyes, which work as fluorescent labels attached chemically to the target molecule .…”

“…Dyes from the Cy family have high intrinsic fluorescence, quantum yield, and extinction coefficient and cannot be used as fluorescently sensitive probes for noncovalent binding and visualization of cell components. Thus, fluorescent probes should have a wide range of opposite properties, which is difficult to achieve in one molecule …”

“…Thus, fluorescent probes should have a wide range of opposite properties, which is difficult to achieve in one molecule. 15 Another example is SYBR family dyes, e.g., SYBR Green I, which intensely stained DNA in live cells but has the disadvantage that the fluorescence fades rapidly, and observation must be done as quickly as possible. 17 Moreover, it has been reported that monomethine cyanine dye Cyan 40 can be used for the two-photon fluorescent visualization of KB cells (oral epidermoid carcinoma).…”

“…14 For fluorescent probes, the low fluorescence quantum yield in the free state and the high quantum yield in the bound state, that is, a sharp increase in fluorescence intensity upon binding to a biomolecule, are essential. 15 These fluorescent dyes differ from fluorescent labels such as cyanines of the Cy3-Cy5 family dyes, which work as fluorescent labels attached chemically to the target molecule. 16 Dyes from the Cy family have high intrinsic fluorescence, quantum yield, and extinction coefficient and cannot be used as fluorescently sensitive probes for noncovalent binding and visualization of cell components.…”

“…Thus, fluorescent probes should have a wide range of opposite properties, which is difficult to achieve in one molecule. 15 …”