Fluorescence Imaging Using Deep-Red Indocyanine Blue, a Complementary Partner for Near-Infrared Indocyanine Green

Indocyanine Blue (ICB) is the deep-red pentamethine analogue of the widely used clinical near-infrared heptamethine cyanine dye Indocyanine Green (ICG). The two fluorophores have the same number of functional groups and molecular charge and vary only by a single vinylene unit in the polymethine chain, which produces a predictable difference in spectral and physicochemical properties. We find that the two dyes can be employed as a complementary pair in diverse types of fundamental and applied fluorescence imaging experiments. A fundamental fluorescence spectroscopy study used ICB and ICG to test a recently proposed Förster Resonance Energy Transfer (FRET) mechanism for enhanced fluorescence brightness in heavy water (D2O). The results support two important corollaries of the proposal: (a) the strategy of using heavy water to increase the brightness of fluorescent dyes for microscopy or imaging is most effective when the dye emission band is above 650 nm, and (b) the magnitude of the heavy water florescence enhancement effect for near-infrared ICG is substantially diminished when the ICG surface is dehydrated due to binding by albumin protein. Two applied fluorescence imaging studies demonstrated how deep-red ICB can be combined with a near-infrared fluorophore for paired agent imaging in the same living subject. One study used dual-channel mouse imaging to visualize increased blood flow in a model of inflamed tissue, and a second mouse tumor imaging study simultaneously visualized the vasculature and cancerous tissue in separate fluorescence channels. The results suggest that ICB and ICG can be incorporated within multicolor fluorescence imaging methods for perfusion imaging and hemodynamic characterization of a wide range of diseases.

A Modular Approach for the Synthesis of Diverse Heterobifunctional Cyanine Dyes

Herein, we present a straightforward synthetic route for the design and synthesis of diverse heterobifunctional cyanine 5 dyes. We optimized the workup by harnessing the pH- and functional group-dependent solubility of the asymmetric cyanine 5 dyes. Therefore, purification through chromatography is deferred until the last synthesis step. Demonstrating successful large-scale synthesis, our modular approach prevents functional group degradation by introducing them in the last synthesis step. These modifiable heterobifunctional dyes offer significant utility in advancing biological studies.

Classification and naming of polymethine dyes used as staining agents for microscopy. A short guide for biomedical investigators

The scientific literature contains many accounts of application of polymethine dyes, including cyanine dyes, as imaging agents, i.e., "biological stains," for microscopic investigation of biological materials. Currently, many such dyes are used as probes for living cells, i.e., "fluorescent probes." Polymethine dyes are defined here by two criteria. First, they possess a conjugated chain of (2n + 1) sp2-hybridized carbon atoms that connect a terminal π-electron-accepting (π-electron withdrawing) group with a terminal π-electron-donating group. Second, they have an odd number (2n + 3) of π-centers and an even number (2n + 4) of π-electrons in this chain, where n equals the number of -CR2=CR3- groups, usually vinylene groups -CH=CH-. Commercialization of diverse chemical types of many polymethine dyes has been attempted. The dyes that have achieved wide application, however, are limited in number and it is these dyes that are emphasized here. Because these polymethine dyes sometimes have been described by confusing, and sometimes confused, names, we clarify here the chemical categories and names of such dyes for the nonchemist, biomedical end user of such imaging agents. Nevertheless, the nomenclature presented here is not intended to replace the traditional "chromophore" categories of dyestuff chemistry, because the latter are held in place both by wide usage and by venerable authorities, such as the Colour Index.

Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules

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.

Light-Harvesting Crystals Formed from BODIPY-Proline Biohybrid Conjugates: Antenna Effects and Excitonic Coupling

A boron dipyrromethene (BODIPY) derivative bearing a cis-proline residue at the meso-position crystallizes in the form of platelets with strong (i.e., Φ_F = 0.34) red fluorescence, but the absorption and emission spectra differ markedly from those for dilute solutions. A key building block for the crystal is a pseudo-dimer where hydrogen bonding aligns the proline groups and separates the terminal chromophores by ca. 25 Å. Comparison with a covalently linked bichromophore suggests that one-dimensional (1D) excitonic coupling between the terminals is too small to perturb the optical properties. However, accretion of the pseudo-dimer forms narrow channels possessing a high density of chromophores. The resultant absorption spectrum exhibits strong excitonic splitting, which can be explained quantitatively using the extended dipole approach and allowing for coupling between ca. 30 BODIPY units. Fluorescence, which decays with a lifetime of 2.2 ns, is assigned to a delocalized and (slightly) super-radiant BODIPY dimer situated at the interface and populated via electronic energy transfer from the interior.

Hemicyanine dyes

Hemicyanine dyes are a subclass of polymethine colorants. At one end of their polymethine chain is an unsaturated heterocyclic ring possessing a nitrogen atom as would be found in a cyanine dye. However, the other end is terminated by a nitrogen atom that does not form part of an unsaturated heterocycle. The name alludes to their half-cyanine substitution pattern. Later the scope of the term “hemicyanine” was extended to the phenylogous dyes where there is a phenyl group between the two terminal nitrogen atoms. The first main technical application of hemicyanine dyes was in textile coloration. Nowadays hemicyanine dyes are used extensively as optical probes of cell membrane potential.

Spiropyran dyes

This article furnishes an introduction to one of the most well-known classes of photochromic colorant. While the properties of spiropyran dyes inspired pioneering efforts to exploit photochromism for industrial applications, their lack of robustness held them back from commercialization. Nevertheless, this type of dye remains at the heart of much of the work to develop light-responsive materials upon which many potential applications in different fields of scientific and technological endeavor depend. The article describes the photochromism, synthesis, and applications of spiropyran colorants with an emphasis on the structural subtype that has attracted the greatest scrutiny. It also acts as a springboard to sources of more detail on these aspects.

Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy

Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. The results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.

DNA Minor Groove-Induced cis-trans Isomerization of a Near-Infrared Fluorescent Probe

The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.

Streptocyanine dyes

The simplest possible type of polymethine dye consists of an odd-numbered polymethine chain sandwiched between two terminal nitrogen atoms, which do not form part of an unsaturated heterocyclic ring. Originally, this type of colorant was termed streptopolymethine dyes. For systematic reasons they are usually called streptocyanine dyes today. Their color is mainly determined by the lengths of their polymethine chains. Owing to their simple structure they are the favorite compounds for investigation of fundamental structure–property relationships. In the form of dianil hydrochlorides mainly streptocyanines are used to prepare cyanine, hemicyanine, merocyanine, oxonol, pyrylium and thiopyrylium dyes.

Oxonol dyes

Oxonol dyes are classified as anionic polymethine dyes, which cover a wide variety of structural types. The name of the class originates from the oxygen atoms which terminate each end of the polymethine chains that form the backbone of their structure. In technically useful dyes, these oxygen atoms tend to be substituents of heterocycles. The main technical application of water soluble oxonol dyes was in silver halide photography as filter dyes and antihalation dyes. Lipophilic oxonol dyes are used in bio-analysis and medical diagnostics to stain cells, bacteria or liposomes for example. Their main bioanalytical usage is in the determination of membrane potentials in eukaryotic cells and prokaryotic bacteria.

Hemioxonol dyes

Following the classification of hemicyanine dyes Leslie G. S. Brooker suggested the term hemioxonol dye be applied to the case of an oxonol colorant in which one of its terminal unsaturated heterocycles has been replaced by an open chain N(R1)R2 group or saturated heterocyclic ring. For historical reasons, dyes formed from the reaction of 4-N,N-dialkylaminobenzaldehydes or 4-N,N-dialkylaminocinnamaldehydes with a heterocycle containing an active methylene group adjacent to a carbonyl group are often called benzylidene dyes and cinnamylidene dyes, respectively. In terms of systematic nomenclature, their proper classification is as hemioxonol dyes. They are used as filter dyes and antihalation dyes in silver halide photography. Their current main usage is in dye diffusion thermal transfer printing (D2T2).

Merocyanine dyes

Merocyanine dyes belong to the class of neutral polymethine dyes, where one terminal component is typically found in cyanine dyes and the second obtained from an active methylene compound. The different electron acceptor/donator abilities of the two terminal components have a marked impact on the electronic structure of a merocyanine dye and its equilibrium structure and electronic spectra. Their first technical application was spectral sensitization in silver halide photography. Today they have numerous of applications in textile dyeing and as membrane potential sensitive fluorescent dyes.

Cyanine dyes

Cyanine dyes are characterized by an odd number 2n + 3 of π-centers and 2n + 4 π-electrons (where n is the number of vinyl groups –CH = CH–). This special feature has a marked impact on their electronic structure and thus their equilibrium structure in the electronic ground state as well their color and electronic spectrum, respectively. Their first technical application was the use as spectral sensitizers in silver halide photography. Today they have numerous of applications in digital optical data storage, Computer-to-Plate lithographic printing plates, bio-analysis and medical diagnostics.