Functional Dyes Update

Chapter-1 Title: Functional Dyes in Advanced Technologies

Hiroyuki Nakazumi and Sung-Hoon Kim

1. Functional Dyes in Advanced Technologies

1.1 Introduction This introduction will give an outline of trend of new technologies and application of functional dyes used in optical data storages, new flat panel displays, various printing systems, and dye- sensitized solar cells and will cover the historical aspects which have been succeeded.

1.2 Functional Dyes for Optical Data Storages The commercially available near-infrared dyes for CD-R disk are reviewed. New technologies and characterizations of functional dyes for DVD-R and DVD-blue disks, respectively, will be outlined.

1.3 Functional Dyes for Flat Panel Displays New technologies and applications of functional dyes and pigments for the color filters in liquid crystal displays, for the high resolution filter for the CRT (cathode ray tube), for absorbing filters of NIR light emitted from plasma display panel (PDP) will be outlined.

1.4 Functional Dyes for Various Printing Systems The recent reviews of functional dyes and pigment for inkjet printers will be outlined. New advanced technologies and applications of functional dyes for reversible thermosensitive recording papers, called “digital papers”, for direct thermosensitive printing system, for full color thermosensitive printing system for digital camera, and for organic photoconductors used in laser and xerography printer will be outlined.

1.5 Functional Dyes for Dye-Sensitized Solar Cells Various functional dyes for mesoporus dye-sensitized electrochemical photovoltaic cells, called “the Gratzel cell”, will be reviewed. Chapter.2 Title: Recent Progress in Phthalocyanine Chemistry: Synthesis and Characterization Nagao Kobayashi 1. Introduction Phthalocyanine (Pc) was first synthesized in 1907 so we are now fast approaching its first centennial anniversary. Since the heteroaromatic Pc ligand has a strong blue color and is chemically stable, Pc complexes have been used extensively in pigments and dyestuffs for more than 70 years. Pcs have also been used as catalysts for the removal of sulfur from crude oil, as charge-generation materials in xerography, in optical read/write discs, as photodynamic reagents for cancer therapy, in deodrants, germicides and anti-bacterial reagents, and as growth promotion and retardation reagents of plants. Other active fields of phthalocyanine related research include chemical sensors, electrochromism, conductors, semiconductors, photovoltaic elements for electricity generation, one-dimentional metals, non-linear optics, electrocatalysis, liquid crystals, Langmuir-Blodgett films, and electrophotography. Although most of the research results have been published as patents, academic research has become very intensive over the last 20 years. The fact that over the last decade, more than one thousand papers have been published annually on phthalocyanine related research including both academic papers and industrial patents, indicates that the Pc ligand remains of interest to many researchers. A Society of Porphyrins and Phthalocyanines was established in the year 2000 by leading researchers within the field to help foster the level of future collaborative research. In this chapter, recent progress in phthalocyanine synthesis and characterization are summarized.

2. Progress in the Pc Synthesis (i) Monomeric Species

(a) Symmetrical D4h Species Many types of metalloPcs have been reported to date. Since the synthesis of some Pcs was only reported in the form of patents, however, the details are often not readily available. The syntheses of several metalloPcs are described here for the first time in the academic literature and new high-yield methods for obtaining monomeric metalloPcs are also reported. For example, ZnPc has traditionally been obtained in low yield. With the addition of DBU as a catalyst, however, the yield can be improved significantly. (b) Deformed Species The heteroaromatic Pc ligand is known to be essentially planar. However, in recent years highly deformed non-planar Pcs have been synthesized by several laboratories by introducing bulky substituents at the eight -peripheral positions closest to the Pc core. (c) Low Symmetry Species Low symmetry Pc based derivatives have traditionally been prepared by mixed condensation reactions. An example would that of phthalonitrile and naphthalonitrile. However, recently, pyrrole ring-reduced Pc and tetraazaporphyrin congeners have also been reported. The synthesis and stability of these complexes is described. (ii) Dinuclear Species (a) Cofacial Homodinuclear Species There has been progress in the synthesis of rare-earth sandwich type Pcs over the last decade. Specific examples are explored in detail. (b) Cofacial Heterodinuclear Species Several methods have been developed for the stepwise synthesis of cofacial, heterodinuclear rare-earth sandwich Pc complexes. It is now possible to use different methods to selectively obtain the various cofacial heterodimer target structures. (c) Planar Homodinuclear Species The first planar homodinuclear Pc dimer was reported almost 20 years ago. The synthesis of this type of compound has not been covered in previous books on phthalocyanine research, however. (d) Planar Heterodinuclear Species The research on planar heterodinuclear Pc derivatives has developed rapidly over the last ten years. The stepwise synthetic approach leading to these dimers is described. (iii) Trinuclear species (a) Homotrinuclear Species The synthetic routes to the most reliable trinuclear rare earth sandwich Pc derivatives are introduced. A few specific examples are explored in detail. These compounds have a very rich electrochemistry, since each redox couples of the monomer splits into three in the case of the trimer. (b) Heterotrinuclear Species There are several different combinations of mixed Pc and Nc trimers. Pc-Pc-Nc, Pc-Nc-Pc, Pc-Nc-Nc, and Nc-Pc-Nc can now be selectively synthesized by choosing appropriate experimental methods. (iv) Oligomers Various types of oligomers have been reported over the last decade. In some cases, the intermolecular linking position is specifically fixed. These compounds are important in developing an understanding of the interaction between the component monomer units.

3. Progress in the Characterization (i)Mass Spectroscopy Pcs were long notorious in the field of mass spectrometry since good mass data were not easily obtained. The development of new ionization methods over the last decade has made the detection of the parent ion peak much more facile. (ii)IR Spectroscopy With the development of the time-dependent DFT method, it has recently become possible to

fully assign the IR bands of Pc derivatives. Several examples with D4h, C2v, and D2h symmetry are explored in detail. (iii) Electronic Absorption and MCD Spectroscopy (a) Neutral species Many low symmetry Pc derivatives have been prepared in the last decade. Data on these compounds are tabulated and trends observed are interpreted on the basis of quantum mechanical calculations. (b) Oxidized and Reduced Species The optical spectra of oxidized and reduced species have been satisfactorily assigned using s band deconvolution techniques based on analysis of both electronic absorption and MCD spectra. (c) Solid State Spectra Most practical applications for Pcs are in the solid state. The analysis of solid state spectra, however, was less than satisfactory until recently. By taking into account ca. 250 Pc molecules, solid state spectra were recently successfully correlated with the solid state structure obtained by X-ray spectroscopy. This research is described in detail. (iv) Electrochemistry

(a) Mononuclear D4h Species When tetraazaporphyrins are expanded radially to form Pc, Nc, and anthracocyanines, the first oxidation potential shifts negatively while the first reduction potential remains almost constant. These trends can be readily accounted for based on the molecular orbitals derived from quantum mechanical calculations. (b) Low Symmetry Mononuclear Species In a series of low symmetry Pc derivatives, the first reduction potential shifts irregularly. In the last 12 months these trends have been rationalized based on the effect of geometry on the frontier molecular orbitals of the -system. (c) Dinuclear and Trinuclear Species In both planar and cofacial multimers of Pc, the redox couples seen in the mononuclear control complex split into several different couples depending on the number of Pc units within the complex. These data are highly relevant in research fields such as electrochromism and are described in detail. (v) Surface-adsorbed Species It is now possible in some instances to observe directly the geometry and arrangement of Pc molecules on electrode surfaces. Some examples are explored. It has been successfully demonstrated that if crowned Pcs are adsorbed and cations are added, the cations are trapped only at opposite crown ether moieties. Chapter.3

Title: Photochromic Naphthopyrans

B. M. Heron and J. D. Hepworth

1. Introduction

This introductory section will include rudimentary structure (including valence isomerisation of pyrans and

their benzologues) and nomenclature and will cover the historical aspects which have been frequently

misrepresented.

2. Synthesis and Spectroscopy

2.1 Synthesis

The most recent review of photochromic naphthopyrans briefly outlines only three of the synthetic routes that

have been employed to access commercially significant photochromic naphthopyrans. There have been some

important developments to these routes (new catalysts, additives and solid state) in the last couple of years

and there are now at least two new strategies. Furthermore some of the chemistry used to access key

precursors is also noteworthy and may, space permitting, warrant inclusion. 2.2 Spectroscopy

Detailed comparison and discussion of the infrared (Raman) and NMR (1H, 13C, 19F) spectroscopy and mass spectrometry of photochromic naphthopyrans has, to our knowledge, never been collated in a review. Recent reports on the characterisation of longer lived, though still transient intermediates, by NMR spectroscopy merit discussion. This information will prove interesting to all researchers working on naphthopyrans and more generally in photochromism and heterocyclic synthesis. Reference to structural features of interest from

X-ray crystal structure determinations will be included.

3. Photochromic Properties of the Isomeric Naphthopyran Systems

This section will cover the basic colour generation process inc. photophysical properties and the isomerisations that occur upon irradiation. The differing nature of the photochromism of the isomeric naphthopyrans will be discussed. The structure of the ring-opened forms, some have recently been trapped by, for example, carbenes will also feature.

4. Influence of substituents on photochromism

4.1 In the hetero ring

Whilst simple substitution on the geminal aryl rings has been discussed in previous review(s) some significant new work has appeared that enables (i) fine control of both colour and lifetime of the ring opened species and

(ii) access to grey and brown photogenerated colours from single molecules rather than through additive mixing of different naphthopyrans.

The fusion of the geminal aryl rings together to form a carbocycle has been discussed there has been some advances in this area through linkages involving O and S atoms. Furthermore, the role of transition metal mediated couplings has enabled the influence of bi- and ter- aryl units to be recently rationalised.

The linking of two naphthopyran units together has recently become a topic of significant interest and thus merits inclusion in the current review since there is some unusual synergism noted for some of the linked systems.

As a final point there has been some nice work reported on the incorporation of ferrocene (and related TM complexes) substituents and also of the use of crown ether units with discussion of the role of complexation of the metal cations. Discussion of these substituent and environmental effects on the photochromism are warranted and will widen the scope of the book to TM chemists and those interested in supramolecular chemistry. This section may round off with some comments on substituents that enable the photochromism to be manipulated by changes in environmental conditions e.g. pH, solvent polarity.

4.2 In the naphthalene unit

Surprisingly it has not been until quite recently that comprehensive data has appeared for the effect of substituents on the photochromic properties of each of the angular photochromic naphthopyrans. This new data will be placed in context with the earlier material and some of the more exiting substituent effects will be presented in detail.

5. Influence of ring fusion

5.1 Carbocycles

There have been numerous reports, particularly in the patent literature, concerning the fusion of additional carbocyclic rings to the basic naphthopyran skeleton. The influence of these rings and substituents on them is complex and, with the exception of a brief mention by Van Gemert, has never been reviewed.

5.2 Heterocycles

Similarly, both the replacement of one of the carbocyclic rings of the naphthalene unit by a heterocyclic ring or, more frequently, fusion of a heterocyclic unit to one of the faces of a naphthopyran has featured prominently in recent years. Many of these effects have never been collated.

6. Uses

The main use of the naphthopyrans continues to be the active constituent in photochromic ophthalmic sun lenses. Wider application in security inks and identity markers have become more common and recently their use in cosmetic formulations has appeared. Their use as ion sensors has been reported.

Dr. B. M. Heron

Department of Colour & Polymer Chemistry

University of Leeds

Leeds LS2 9JT

Email: [email protected] Chapter.4 Title: Fluorine-containing Dyes M. Matsui

1. Introduction Electronic and steric effect of fluorine for dyes molecules changes the properties. Properties of perfluoroalkyl (Rf), perfluoroalkylsulfonyl (RfSO2), fluoroacyl (RfCO), and fluorine atom(s) on aromatic rings are described.

2. Rf-containing Dyes 2.1 Azo dyes The properties of Rf-substituted dichroic azo dyes is reviewed. These compounds show improved solubility and good dichroism compared with the alkyl-substituted derivatives.

2.2 Coumarins Perfluoroalkylation reaction of coumarins with bis(perfluoroalkanoyl) peroxides to produce the 3- Rf derivatives is explained. The UV-vis absorption spectra are discussed. These products show better photostability than the Rf-free derivative.

2.3 Quinone dyes The reaction of naphtho- and anthraquinones with bis(perfluoroalkanoyl) peroxides gives the perfluoroalkylated products. The UV-vis absorption spectra are discussed.

2.4 Cyanine dyes The synthesis and properties of perfluoroalkylated cyanine dyes is reviewed.

2.5 Phthalocyanines The properties of silicone phthalocyanines substituted with RfO groups at the axial sites is explained.

2.6 Perylenedicarboxiimides Perylenedicarboxiimides containing Rf groups is explained. They show improved solubility.

3. RfSO2-containing Azo Dyes

The synthesis and properties of RfSO2-substituted azo dyes for second-order nonlinear optical chromophores are reviewed 4. RfCO-containing Dyes 4.1 Azo Dyes

It is known that a trifluoroacetyl (CF3CO) group easily forms hemiacetals and hemiaminals. Their application as humidity sensors is reviewed. Hemiacetals and hemiaminals are also produced at RfCO groups.

4.2 Styryl Dyes

CF3CO-substituted styryl dyes is reviewed.

5. Dyes Having Fluorine Atom(s) on Aromac Ring 5.1 Azo Dyes Fluorine atom(s) on aromatic rings act as a leaving group. For example, pentafluoroazobenzene reacts with amines to give the 2- and/or 4-substituted amines. The reaction is reviewed.

5.2 Anthraquinone Dyes 1,2,3,4-tetrafluoroanthraquinone reacts with bifunctional nucleophiles such as 2-aminophenol and 2-aminobenzenethiol to give the 1,2-cyclized derivatives. The reaction is reviewed.

5.3 Cyanine Dyes Synthesis and properties of cyanine dyes having fluorine atoms on heteroaromatic rings and/or olefinic bond are reviewed.

Prof. Dr. M. Matsui Department of Materials Science and Technology Faculty of Engineering Gifu University, Yanagido, Gifu 501-1193 Japan E-mail: [email protected] Chapter-5 Title: Synthesis and Application of Squarylium Dyes

Hiroyuki Nakazumi and Shigeyuki Yagi

1. Introduction Although squarylium dyes have been classified into polymethyne dyes like cyanines from the viewpoint of their electronic structures, the recent development in squarylium synthesis, yielding a variety of properties, has been establishing a new category in dye chemistry. Nowadays, squarylium dyes are receiving much attention because of their potential applicability to a wide range of industrial fields. In this introductory section, historical aspects of synthesis of squarylium dyes will be described. The electronic structures of typical squarylium dyes will be also described. In addition, classical application of squaryliums will be briefly covered.

2. Synthesis 2.1. Symmetrical Squarylium Dyes Since the first report of squarylium dyes, their derivatives have been prepared by condensation of aryl or heterocyclic compounds with squaric acid. At the beginning of the topic on squarylium dye synthesis, the traditional ways for preparation will be reviewed. This will show which kinds of squarylium dyes are possible to prepare; applicability and limitation on traditional squarylium dye synthesis.

2.2. Unsymmetrical Squarylium Dyes For the past two decades, the synthesis of unsymmetrical squarylium dyes has increased oppotunities for squaryliums to be used for industrial as well as scientific purposes. It has been established by the stepwise synthesis via intermediates, mono-substituted squaric acids (half units of the dyes). Here will be described the ways to synthesize unsymmetrical squarylium dyes as well as their intermediates.

2.3. Squarylium Dyes Drived from Bisquaric Acid It has been reported that a homologue of squaric acid, bisquaric acid, also reacts with electron-rich aromatics and heterocyclic compounds to produce a series of novel squarylium homologues. In this section, synthesis of these unique dyes will be shown. 2.4. Squarylium Dyes with Extended -Conjugation Structures As the symthesis of squarylium dyes and their related compounds has been developed, lots of new classes of squarylium dyes have been reported, which include squarylium polymers, bis- squaryliums, and so on. These dyes are expected to open the door to design of low band-gap conductive materials as well as near-infrared absorbing materials. Here will be reviewed the recent development of these new systems, especially focused on the synthetic strategy.

3. Structural Analysis The molecular structures of functional dyes often give us important information about their physicochemical properties. In this section, the X-ray structural analyses of squarylium dyes will be described.

4. Physicochemical Properties 4.1. Optical Properties Optical properties of squarylium dyes such as electronic absorption and fluorescence emission are fundamental in their application to material devices. Recent advances in the synthesis of squaryliums and their derivatives have made it possible to tune their optical properties, and thus, it has been getting easier to obtain the derivatives with suitable spectroscopic features for the application. In this section, electronic absorption and fluorescence emission spectra of squarylium dyes will be reviewed, focused on the structure-functionality relationships. In addition, the dichroic properties will be also mentioned.

4.2. Aggregation Property and Solid-State Chemistry Molecular arrangement of chromophores under highly concentrated conditions often affects the optical properties. In this term, not only the aggregation property but also solid-state chemistry of squarylium dyes has been frequently reported. In this section, such properties of squarylium dyes will be reviewed, especially focused on the effects on their optical properties.

5. Application to Advanced Materials 5.1. Application to electronic and optoelectronic devices Squarylium dyes have been often used in electronics and optoelectronics fields such as xerography, optical recording, solar batteries, electroluminescence, and so on, utilizing their photoconductive and large optical absorption properties. It is expected for the development of squarylium synthesis to promote further investigation of such devices. Here will be described recent development in these fields.

5.2. Biological and Environmental Applications The construction of sensory devices for biological and environmental analyses is one of growing topics in squarylium chemistry: the chromogenic and fluorescent properties of some squarylium dyes have been receiving much attention as candidates for such uses. Here will be described the latest advance in this field.

6. Future Perspective In this closing section, the future perspective in squarylium chemistry will be summarized. It will include the focuses on the synthesis, potential application, and what to be overcome to device construction. Chapter.6

Title: Cyanine Dyes for Photovoltaic and Information Storage

He Tian and Fanshun Meng

5. Introduction

This section will briefly summarize the general structure, the classification, the nomenclature and the

applications of cyanine dyes.

6. Synthesis

This section will briefly introduce and minireview the synthetic routes of cyanine dyes. The emphases will

focus on carbocyanine and hemicyanine, which are the most important cyanines for organic solar cells and

optical recording disks.

7. The application of cyanine dyes in organic solar cells

3.1 Cyanine dyes for dye-sensitized nanocrystalline TiO2 solar cells

Dye-sensitized solar cells (DSSCs) have attracted considerable attention since the report of highly efficient

ruthenium complex sensitized TiO2 solar cells by Grätzel and his coworkers. As an alternative to expensive

metal based polypyridyl complexes, organic dyes have also been studied as sensitizer in DSSCs due to their

large absorption coefficients, easier preparation and low cost. Among organic dye sensitizers, cyanine dyes

are very important ones. This section will review the applications of cyanine, hemicyanine and merocyanine

in DSSCs. The conversion efficiency of hemicyanine sensitized DSSCs is higher than 6%.

3.2 cyanine dyes for solid state organic solar cells

The appropriate electrochemical properties of cyanine make it possible to be used both as donor and acceptor

in thin film heterojunction solar cells. Another property of cyanine is that it can be spin coated from solution

to form good film, which is of great interest for large area photovoltaic production. The effect of counter ion on the properties of solid state solar cells will be discussed. The covalently linked cyanine-fullerene dyad is also an promising materials for photovoltaic devices due to the photo induced intramolecular electron transfer from cyanine to fullerene.

8. The application of cyanine dyes in optical recording disks

This section will cover various cyanine dyes used as optical recording medium in CD-R and DVD-R discs.

The basic structure and the recording mechanism of CD-R and DVD-R are similar, while the laser wavelength to write information as well as information recording density are quite different. The key requirements for

CD-R and DVD-R will be summarized.

4.1 cyanine dyes for CD-R

Since the reading and writing laser wavelength for CD-R is 780nm, the cyanine used for this purpose is mainly pentamenthine cyanine dyes. The properties of cyanine dyes play an important role in the quality of

CD-R disks. The structure, such as heterocycles, substitutent of the heterocycles and the counter ion, have a great effect on the absorption spectra, refractive index, reflectivity and writing speed, which are very important parameters for cyanine dyes used as recording medium. The variation of these parameters with the structure of cyanine dyes will be discussed.

4.2 cyanine dyes for DVD-R

DVD-R is the next generation optical recording medium and will replace CD-R in the market. The recording density of DVD-R is 7-8 times higher than CD-R due to its shorter writing and reading laser wavelength at

630~650nm. According with the laser wavelength, cyanines used for DVD-R is mainly trimethine cyanine dyes and hemicyanine dyes. The latest development of cyanine dyes for DVD-R disks will be reviewed.

Prof. He Tian

Institute of Fine Chemicals

East China University of Science and Technology Shanghai 200237

P. R. China

Email: [email protected] Chapter 7

Title: Applications of Recognition-Functional Dyes Toward Developing Surface Plasmon

Resonance-Based Sensing System

Sung Hoon Kim, Kwangnak Koh

1. Introduction

This introductory section will include fundamental theory of surface plasmon resonance (SPR) spectroscopy and it’s potential application toward developing SPR based sensing system with recognition-functional dyes.

2. Formations and Characterization of Sensing Layer Containing Functional Dyes

2.1. Recognition-Functional Dyes

Sensors are devices that “announce” the presence of analytes via molecular interaction. Molecular recognition deals with the way of noncovalent molecular interaction or molecular association.

Therefore selective molecular interaction can function as, or as a part of, a sensor. The

Characteristics of recognition-functional dyes such as squarylium and spiroxazine derivatives as sensing molecules will be discussed in this section.

2.2. Formation and Characterization of Sensing Layers Containing Functional Dyes

Formation of recognition-functional layers on the metal surfaces are one of the most important areas to tailor the properties of chemical sensing based on SPR. This section will provide formation technologies and spectroscopic characterization methodologies of sensing layers having recognition-functional dyes.

3. Surface Plasmon Resonance Study The measurement of refractive index can be used to determine the concentration of an analyte in solution. Which can be explained that the refractive index of a solution depends on analyte concentration. This kind of study can be performed effectively by SPR technique with selective sensing layers containing recognition-functional dyes. A sensing layer consists of a thin-film (e.g. polymeric membrane or self-assembled monolayer) having optical properties that vary with concentration of the analyte to be sensed. This section will cover the changes of sensing layers having squarylium and spiroxazine derivatives in the optical properties according to the variation of analyte concentration.

4. Conclusions

The use of sensing layers containing recognition-functional dyes can offer a new strategy to the highly sensitive analyte detection, i.e., functional dye derivative system used as a sensing layer guarantees the high sensitivity in the SPR spectroscopy due to the change of optical properties which resulted in enhanced refractive index change. Chapter.8 Title: Non-activated Indolinobenzospiropyrans Sam-Rok Keum

9. Introduction The principal aim of this chapter is to be complementary to the earlier books covering the photochromic phenomena of indolinobenzospiropyran derivatives. This introduction will cover the comparative historical aspects of activated and non-activated indolinobenzospiropyran derivatives.

10. Synthesis and Spectroscopic Characterization 10.1 Synthesis The synthetic routes that have been employed to access commercially significant photochromic indolinobenzospiropyran derivatives will be briefly outlined. In addition, some of the chemistry used to access DC (dicondensed spiropyran) molecules is also noteworthy.

10.2 Spectroscopic Characterization Detailed discussion of 1H, 13C NMR & UV-Vis. spectroscopy of spiropyrans, merocyanines and dicondensed spiropyrans will be included. This information will prove the mechanistic processes on formation and deformation of those species mentioned. Those mechanistic processes are interesting to all researchers working on indolinobenzospiropyrans and more generally in photochromism. Our recent report on the detailed X-ray crystal structure determination of DC formed during the preparation of SP’s will also be included. This structural analysis has, to our knowledge, never been reported.

3. Non-activated Indolinobenzospiropyrans This section will cover the basic concept of the non-activated indolinobenzospiropyrans. The differing nature of the photochromism of the activated versus non-activated indolinobenzospiropyrans will be comparatively discussed.

3.1 Kinetic Measurement General kinetic measurement for the ring-closure of MC forms will be discussed. This method consists of an acid-induced ring-opening of the spiropyran followed by neutralization and stopped-flow measurement of ring-closure of the resulting merocyanine.

3.2 Reverse Photochromism This section will covered the reverse photochromism in neat solvents and aqueous binary solvent systems. This reverse photochromism in aqueous binary solvent systems, to our knowledge, never been reported. Preferential solvation and solvent polarity parameter, ET(BM), for the spiropyranyl systems are also discussed.

4. Application: Photoactive spiropyran-contained liquid dye molecules will be discussed in this section. This will cover a) liquid crystals containing a SP unit and b) liquid crystals optical switch. Their use as a chiral dopant in a nematic LC molecules has also been reported. Chapter 9

Title: Cyanine Dyes as Fluorescent Labels for Nucleic Acid Research

Todor Deligeorgiev

1. Introduction

Modification of proteins, DNA and other biopolymers by labeling them with reporter molecules has become a very powerful research tool in molecular biology. In addition, there are a growing number of commercial applications of these modified biomolecules including clinical immunoassay, DNA hybridization tests, gene fusion detection tests, etc. In these techniques, a small molecule with spectral properties such as fluorescent or binding specificity, is covalently or non-covalently bound to biomolecules. The interaction of small molecules with nucleic acids giving detectable signal is a very useful method for the investigation of biological processes on the molecular level. The fluorescent dyes that either associate selectively with macromolecules, or partition into specific sites within cells, are site-selective probes. Most of the site-selective probes are used to label cellular organelles, cytoskeletal components, DNA, RNA, nucleotides, neurotransmitters and many other biological macromolecules. The development in the last several years of cyanine dyes as fluorescent labels is reviewed. The dyes are covering the spectrum from the blue to the near infrared region. The non-covalently binding labels have no fluorescence of their own, but a strong fluorescence enhancement is observed in the presence of nucleic acids.

2. Cyanine Dyes for Nucleic Acid Detection

Lee et al. have shown that the monomethine cyanine dye Thiazole orange(TO) has excellent properties as biological non-covalent DNA or RNA label. This finding stimulates the research in the field of cyanine dyes as nucleic acid stains and many representatives of this new class of dyes, covering the spectrum from blue to NIR region, are developed. 2.1 Monomethine Cyanine Dyes as Nucleic Acid Stains

It has been shown that the fluorescence enhancement of TO on binding to DNA is over 1000-fold.

This dye has proven to have suitable physical properties for flow cytometric analysis of blood reticulocytes. The dye does not fluoresce until intercalated in to DNA or RNA and after binding with DNA it has a fluorescence quantum yiels of 0.2. It is cell-membrane permeable and absorbs at

509 nm, which allows its excitation with one of the lines of the argon laser. These valuable properties have attracted the attention of the researchers and new representatives based on TO and

Oxazole yellow(YO) were designed, synthesized and commercialized and the authors claim fluorescence quantum yield up to 0.9 for some of them.

2.2 Polymethine Dyes as Nucleic Acid Stains

Benson et al. also designed new heterodimeric dyes in which two different chromophores are connected with a spacer longer than 10 A, allowing bis-interaction of the two dye fragments. Both dye fragments- of Thiazole orange and Thiazole blue- are chosen to serve as a donor-acceptor pair to generate a heterodimeric dye molecule which could be efficiently excited at a single wavelength, but with well separated emission maximum. We designed and synthesized a trimethine cyanine NIR dye with acridinium, and benz[c,d]indole end groups. We mentioned some of the application of these non-covalent binding nucleic acis stains.

2.3 Polymethine Dyes for Covalent Labelling of Nucleic Acids

Recently cyanines with tri-, penta-, and heptamethine chains, having amine-reactive groups, are used for covalent labeling of nucleic acids. Nucleotides or oligonucleotides having synthetically incorporated amino groups are labeled with fluorescent reactive dyes, and then enzymatically converted into fluorescent nucleic acid polymers or directly used as primers or hybridization probes.

3. Conclusion Within the last 5 years there is a substantial progress in the development of cyanine dyes for nucleic acid fluorescence detection. These dyes are covering the visible and NIR region. Most of the dyes can be excited with argon laser ast 488 and 514 nm while those for excitation with He-Ne laser at

633 nm are less numerous. The development of cost effective and rapid methods for sequencing, interpreting and strong DNA sequences for diagnostic applications, ranging from healthcare to agriculture and environmental monitoring, makes a very bright future of the cyanine dyes as fluorescent probes for nucleic acid detection. For the further design and synthesis of new and better nucleic acid dyes, joint efforts of synthetic dye chemists, molecular biologists, physicists and medical scientists are needed.