The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Using nucleotide architectures to very closely and precisely place chromophores on a nucleic acid template to form dye aggregates that produce quantum coherent excitons, biexcitons, and triexcitons upon excitement to create excitonic quantum wires, switching, and gates that would then form the basis of quantum computation. Creating the various excitons and controlling the timing of the excitons would be performed using light of the corresponding wavelength and polarization to stimulate the corresponding chromophores.

Using nucleotide architectures to very closely and precisely place chromophores on a nucleic acid template to form dye aggregates that produce quantum coherent excitons, biexcitons, and triexcitons upon excitement to create excitonic quantum wires, switching, and gates that would then form the basis of quantum computation. Creating the various excitons and controlling the timing of the excitons would be performed using light of the corresponding wavelength and polarization to stimulate the corresponding chromophores.

The invention describes the preparation and use of fluorescent stains for nucleic acids derived from unsymmetrical cyanine dyes. The dyes of the invention possess superior fluorescent properties when complexed with nucleic acids, and have utility in any application which requires detection of nucleic acids, such as detection of nucleic acids in solution, in gels, in blots, in microarrays, and in bacteria and cells, and for use in analysis of cell structure, membrane integrity, and function. The dyes of the invention have the formula ##STR00001##
where X is O, S, or C(CH.sub.3).sub.2; Each of R.sup.1 and R.sup.6 is independently hydrogen, carboxy, sulfo, sulfonamide, halogen, CN, or alkoxy; Each of t and s is an integer from 0 to 4; R.sup.2 is an alkyl, or alkyl group substituted by a carboxy, or a sulfo; R.sup.3 is H, C.sub.6H.sub.4CO.sub.2R.sup.7, or C.sub.6H.sub.4CH.sub.2N(R.sup.7).sub.2, where R.sup.7 is an alkyl; R.sup.4 is H, alkyl, aryl, halogen, alkoxy, alkylamino, or alkylthio; R.sup.5 is an alkyl, aryl, alkyl group substituted by a carboxy, or a sulfo, or —(CH.sub.2).sub.a—[O—(CH.sub.2).sub.b].sub.m—O—Z, where Z is H, alkyl, or carboxy; each of a and b is an integer from 1 to 4; m is an integer selected from 0 to 4.

Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.

Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.

Near infrared and shortwave infrared dyes can have polymethine structures.

The invention relates to cleavable chemistry in general, and in particular, to tunable fluorescence using cleavable linkers present in fluorochrome-quencher conjugates.

The invention relates to cleavable chemistry in general, and in particular, to tunable fluorescence using cleavable linkers present in fluorochrome-quencher conjugates.

An object of the present invention is to provide a cancer cell inhibitory drug, particularly a cancer stem-cell inhibitory drug, or a cancer stem-cell detection probe. The present invention provides a cancer cell inhibitory drug comprising at least one compound represented by general formula (1) as an active ingredient

##STR00001##