Classifications

• • C—CHEMISTRY; METALLURGY
  • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
  • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
  • C09B57/00—Other synthetic dyes of known constitution
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
  • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
  • C07F9/02—Phosphorus compounds
  • C07F9/06—Phosphorus compounds without P—C bonds
  • C07F9/08—Esters of oxyacids of phosphorus
  • C07F9/09—Esters of phosphoric acids
  • C07F9/091—Esters of phosphoric acids with hydroxyalkyl compounds with further substituents on alkyl
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07C—ACYCLIC OR CARBOCYCLIC COMPOUNDS
  • C07C215/00—Compounds containing amino and hydroxy groups bound to the same carbon skeleton
  • C07C215/68—Compounds containing amino and hydroxy groups bound to the same carbon skeleton having amino groups bound to carbon atoms of six-membered aromatic rings and hydroxy groups bound to acyclic carbon atoms or to carbon atoms of rings other than six-membered aromatic rings of the same carbon skeleton
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
  • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
  • C07F9/02—Phosphorus compounds
  • C07F9/06—Phosphorus compounds without P—C bonds
  • C07F9/08—Esters of oxyacids of phosphorus
  • C07F9/09—Esters of phosphoric acids
  • C07F9/094—Esters of phosphoric acids with arylalkanols
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
  • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
  • C07F9/02—Phosphorus compounds
  • C07F9/06—Phosphorus compounds without P—C bonds
  • C07F9/22—Amides of acids of phosphorus
  • C07F9/24—Esteramides
  • C07F9/2404—Esteramides the ester moiety containing a substituent or a structure which is considered as characteristic
  • C07F9/2429—Esteramides the ester moiety containing a substituent or a structure which is considered as characteristic of arylalkanols
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07F—ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM
  • C07F9/00—Compounds containing elements of Groups 5 or 15 of the Periodic Table
  • C07F9/02—Phosphorus compounds
  • C07F9/547—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom
  • C07F9/553—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having one nitrogen atom as the only ring hetero atom
  • C07F9/572—Five-membered rings
• • C—CHEMISTRY; METALLURGY
  • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
  • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
  • C09B23/00—Methine or polymethine dyes, e.g. cyanine dyes
  • C09B23/14—Styryl dyes
  • C09B23/141—Bis styryl dyes containing two radicals C6H5-CH=CH-
• • C—CHEMISTRY; METALLURGY
  • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
  • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
  • C09B69/00—Dyes not provided for by a single group of this subclass
• • C—CHEMISTRY; METALLURGY
  • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
  • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
  • C09B69/00—Dyes not provided for by a single group of this subclass
  • C09B69/10—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds
  • C09B69/101—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing an anthracene dye
• • C—CHEMISTRY; METALLURGY
  • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
  • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
  • C09B69/00—Dyes not provided for by a single group of this subclass
  • C09B69/10—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds
  • C09B69/109—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing other specific dyes
• • C—CHEMISTRY; METALLURGY
  • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
  • C09K—MATERIALS FOR MISCELLANEOUS APPLICATIONS, NOT PROVIDED FOR ELSEWHERE
  • C09K11/00—Luminescent, e.g. electroluminescent, chemiluminescent materials
  • C09K11/06—Luminescent, e.g. electroluminescent, chemiluminescent materials containing organic luminescent materials
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/52—Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper and including single- and multilayer analytical elements
• • G—PHYSICS
  • G03—PHOTOGRAPHY; CINEMATOGRAPHY; ANALOGOUS TECHNIQUES USING WAVES OTHER THAN OPTICAL WAVES; ELECTROGRAPHY; HOLOGRAPHY
  • G03C—PHOTOSENSITIVE MATERIALS FOR PHOTOGRAPHIC PURPOSES; PHOTOGRAPHIC PROCESSES, e.g. CINE, X-RAY, COLOUR, STEREO-PHOTOGRAPHIC PROCESSES; AUXILIARY PROCESSES IN PHOTOGRAPHY
  • G03C1/00—Photosensitive materials

Definitions

• the present invention is directed to novel fluorescent or colored dyes comprising a phenylethynylnapthalene moiety and methods for their preparation and use in various analytical methods.
• the presence of a particular analyte can often be determined by binding methods that exploit the high degree of specificity that characterizes many biochemical and biological systems. Frequently used methods are based on, for example, antigen- antibody systems, nucleic acid hybridization techniques, and protein-ligand systems. In these methods, the existence of a complex of diagnostic value is typically indicated by the presence or absence of an observable "label" which is attached to one or more of the interacting materials.
• the specific labeling method chosen often dictates the usefulness and versatility of a particular system for detecting an analyte of interest. Preferred labels are inexpensive, safe, and capable of being attached efficiently to a wide variety of chemical, biochemical, and biological materials without significantly altering the important binding affinities of those materials.
• the label should give a highly characteristic signal, and should be rarely, and preferably never, found in nature.
• the label should be stable and detectable in aqueous systems over periods of time ranging up to months. Detection of the label is preferably rapid, sensitive, and reproducible without the need for expensive, specialized facilities or the need for special precautions to protect personnel. Quantification of the label is preferably relatively independent of variables such as temperature and the composition of the mixture to be assayed.
• a wide variety of labels have been developed, each with particular advantages and disadvantages. For example, radioactive labels are quite versatile, and can be detected at very low concentrations. However, such labels are expensive, hazardous, and their use requires sophisticated equipment and trained personnel. Thus, there is wide interest in non-radioactive labels, particularly in labels that are observable by spectrophotometric, spin resonance, and luminescence techniques, and reactive materials, such as enzymes that produce such molecules.
• Labels that are detectable using fluorescence spectroscopy are of particular interest because of the large number of such labels that are known in the art. Moreover, the literature is replete with syntheses of fluorescent labels that are derivatized to allow their attachment to other molecules, and many such fluorescent labels are commercially available.
• Cyanine dyes have been widely used for labeling biomolecules including antibodies, DNA probes, avidin, streptavidin, lipids, biochemical analogs, peptides, and drugs, as well as for a variety of applications including DNA sequencing, DNA microarray, western blotting, flow cytometry analysis, and protein microarrays, to name a few.
• cyanine dyes 1) are biocompatible; 2) have high molar absorptivity (c.a. 10 5 M "1 cm " ); 3) are readily modified to match a wide range of desired excitation and detection wavelengths (e.g., about 500 to about 900 nm); 4) are capable of
• the present invention is generally directed to compounds useful as water soluble, fluorescent or colored dyes and probes that enable visual detection of biomolecules and other analytes, as well as reagents for their preparation. Methods for visually detecting a biomolecule and for determining the size of a biomolecule are also described.
• the water soluble, fluorescent or colored dyes of the invention are intensely colored and/or fluorescent and can be readily observed by visual inspection or other means. In some embodiments the compounds may be observed without prior illumination or chemical or enzymatic activation.
• embodiments of the dyes have a maximum excitation wavelength ranging from about 400 nm to about 420 nm and a maximum emission wavelength ranging from about 520 nm to about 540 nm.
• the dyes have a maximum excitation wavelength at about 410 nm and a maximum emission wavelength at about 533 nm.
• the dyes are thus ideal for use in various analytical methods.
• visually detectable biomolecules of a variety of colors may be obtained.
• a method for staining a sample comprises adding to said sample a representative compound as described herein in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
• the present disclosure provides a method for visually detecting a biomolecule, comprising:
• Other disclosed methods include a method for visually detecting a biomolecule, the method comprising:
• compositions comprising any one of the disclosed compounds and one or more biomolecules.
• Use of such composition in analytical methods for detection of the one or more biomolecules is also provided.
• FIG. 1 depicts a UV spectrum of an exemplary compound.
• the exemplary compound shows a maximum excitation wavelength at about 410 nm and a maximum emission wavelength at about 533 nm.
• Amino refers to the -NH 2 group.
• Carboxy refers to the -C0 2 H group.
• Cyano refers to the -CN group.
• Niro refers to the -N0 2 group.
• alkyl refers to a straight or branched hydrocarbon chain group consisting solely of carbon and hydrogen atoms, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds).
• alkyl groups have from one to twelve carbon atoms (C 1 -C 12 alkyl), preferably one to eight carbon atoms (C 1 -C 8 alkyl) or one to six carbon atoms (C 1 -C 6 alkyl), and which is attached to the rest of the molecule by a single bond, e.g., methyl, ethyl, ⁇ -propyl, 1-methylethyl (z ' so-propyl), «-butyl, «-pentyl, 1, 1-dimethylethyl (t-butyl), 3-methylhexyl,
• Alkylene or “alkylene chain” refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a substituent group, consisting solely of carbon and hydrogen, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds), and having from one to twelve carbon atoms, e.g., methylene, ethylene, propylene, «-butylene, ethenylene, propenylene, «-butenylene, propynylene, «-butynylene, and the like.
• the alkylene chain is attached to the rest of the molecule through a single or double bond and to the substituent group through a single or double bond.
• Heteroalkylene refers to an alkylene in which at least one carbon- carbon bond has been replaced with a carbon heteroatom (e.g., N, S, or O) bond.
• the heteroatom may be at any position in the heteroalkylene, including a terminal position such that the heteroatom links the heteroalkylene to the reminder of the molecule.
• an alkylene chain is optionally substituted.
• aminoalkylene refers to an alkylene, as defined, comprising one or more amino substituents. Unless stated otherwise specifically in the specification, aminoalkylene groups are optionally substituted.
• Alkoxy refers to a group of the formula -OR a where R a is an alkyl group as defined above containing one to twelve carbon atoms.
• a "hydroxylalkoxy” is an alkoxy moiety comprising at least one hydroxyl substituent.
• An “aminoalkoxy” is an alkoxy moiety comprising at least one amino substituent. Unless stated otherwise specifically in the specification, alkoxy, hydroxylalkoxy and/or aminoalkoxy groups are optionally substituted.
• Alkylamino refers to a group of the formula -NHR a or -NR a R a where each R a is, independently, an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkylamino group is optionally substituted.
• Alkylether refers to any alkyl group as defined above, wherein at least one carbon-carbon bond is replaced with a carbon-oxygen bond.
• the carbon-oxygen bond may be on the terminal end (as in an alkoxy group) or the carbon oxygen bond may be internal (i.e., C-O-C).
• Alkylethers include at least one carbon oxygen bond, but may include more than one (i.e., a "polyalkylether”).
• polyethylene glycol (PEG) which is a polyalkylether, is included within the meaning of alkylether.
• Hydrodroxylpolyalkylether refers to a polyalkylether comprising one or more hydroxyl substituents.
• Aminopolyalkylether refers to a polyalkylether comprising one or more amino substituents. Unless stated otherwise specifically in the specification, an alkylether, polyalkylether, hydroxylpolyalkylether and/or aminopolyalkylether group is optionally substituted.
• Alkylenether refers to an alkylene group as defined above, wherein at least one carbon-carbon bond is replaced with a carbon-oxygen bond.
• the carbon- oxygen bond may be on the terminal end (as in an alkoxy group) or the carbon oxygen bond may be internal (i.e., C-O-C).
• Alkylenethers include at least one carbon oxygen bond, but may include more than one (i.e., a "polyalkylenether”).
• PEG linking groups are examples of polyalkylenethers.
• Hydrodroxylpolyalkylenether refers to a
• polyalkylenether comprising at least on hydroxyl substituent.
• Aminopolyalkylenether refers to a polyalkylenether comprising at least one amino (including alkylamino, arylamino and aralkylamino) substituent. Unless stated otherwise specifically in the specification, alkylenether, polyalkylenether,
• hydroxylpolyalkylenether and aminopolyalkylenether groups are optionally
• Aryl refers to a carbocyclic ring system group comprising 6 to 18 carbon atoms and at least one carbocyclic aromatic ring.
• the aryl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems.
• Aryl groups include, but are not limited to, aryl groups derived from aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, chrysene, fluoranthene, fluorene, as-indacene, s-indacene, indane, indene, naphthalene, phenalene, phenanthrene, pleiadene, pyrene, and triphenylene.
• aryl or the prefix "ar-" (such as in "aralkyl”) is meant to include aryl groups that are optionally substituted.
• Arylamino refers to a group of the formula -NR a R- b where R a is aryl, as defined above, and 3 ⁇ 4 is H, alkyl, as defined above containing one to twelve carbon atoms, or aryl as defined above. Unless stated otherwise specifically in the
• an arylamino group is optionally substituted.
• Aryloxy refers to a group of the formula -OR a , where R a is an aryl moiety as defined above, for example phenoxy and the like. Unless stated otherwise specifically in the specification, an aryloxy group is optionally substituted.
• Aralkyl refers to a group of the formula -R b -Rc where R b is an alkylene chain as defined above and Rc is one or more aryl groups as defined above, for example, benzyl, diphenylmethyl and the like. Unless stated otherwise specifically in the specification, an aralkyl group is optionally substituted.
• Aralkylamino refers to a group of the formula -NR a R b where R a is aralkyl, as defined above, and R b is H, alkyl, as defined above containing one to twelve carbon atoms, aryl as defined above, or aralkyl, as defined above. Unless stated otherwise specifically in the specification, an arylamino group is optionally substituted.
• a "carbocyclic ring” is a ring wherein each ring atom is carbon.
• Carbocyclic rings may staturated or unsaturated, including aromatic rings. Unless stated otherwise specifically in the specification, a carbocylic group is optionally substituted.
• Cycloalkyl refers to a stable non-aromatic monocyclic or polycyclic carbocyclic ring, which may include fused or bridged ring systems, having from three to fifteen carbon atoms, preferably having from three to ten carbon atoms, and which is saturated or unsaturated and attached to the rest of the molecule by a single bond.
• Monocyclic cycloalkyl groups include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
• Polycyclic cycloalkyl groups include, for example, adamantyl, norbornyl, decalinyl, 7,7-dimethyl- bicyclo[2.2.1]heptanyl, and the like. Unless otherwise stated specifically in the specification, a cycloalkyl group is optionally substituted.
• Multicyclic refers to any molecule having more than one ring.
• the rings may be either, fused, spirocyclic or separated by one or more atoms (e.g., linked via an acyclic linker).
• “Spirocyclic” refers to a multicyclic molecule wherein two rings share a single carbon atom. "Fused” refers to any ring structure described herein which is fused to an existing ring structure in the compounds of the invention. When the fused ring is a heterocyclyl ring or a heteroaryl ring, any carbon atom on the existing ring structure which becomes part of the fused heterocyclyl ring or the fused heteroaryl ring may be replaced with a nitrogen atom.
• Halo or halogen refers to bromo, chloro, fluoro or iodo.
• Heterocyclyl or “heterocyclic ring” refers to a stable 3- to 18-membered aromatic (heteroaryl) or non-aromatic ring group, wherein at least one ring atom is a heteroatom selected from the group consisting of nitrogen, oxygen and sulfur, and the remaining ring atoms are selected from the group consisting of carbon nitrogen, oxygen and sulfur.
• the heterocyclyl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems; and the nitrogen, carbon or sulfur atoms in the heterocyclyl group may be optionally oxidized; the nitrogen atom may be optionally quaternized; and the heterocyclyl group may be partially or fully saturated.
• heterocyclyl groups include, but are not limited to, dioxolanyl, thienyl[l,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1-oxo-thio
• Heteroaryl refers to a 5- to 14-membered ring system group comprising one to thirteen carbon atoms, one to six heteroatoms selected from the group consisting of nitrogen, oxygen and sulfur, and at least one aromatic ring.
• the heteroaryl group may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems; and the nitrogen, carbon or sulfur atoms in the heteroaryl group may be optionally oxidized; the nitrogen atom may be optionally quaternized.
• Examples include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzothiazolyl, benzindolyl, benzodioxolyl, benzofuranyl, benzooxazolyl, benzothiazolyl, benzothiadiazolyl,
• Hydroxylalkyl refers to an alkyl group comprising at least one hydroxyl substituent.
• the one or more -OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkyl group is optionally substituted.
• Hydroxylalkylene refers to an alkylene group comprising at least one hydroxyl substituent.
• the one or more -OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkylene group is optionally substituted.
• Hydrolalkylether refers to an alkylether group comprising at least one hydroxyl substituent.
• the one or more -OH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, hydroxyalkylether group is optionally substituted.
• Rc is a counter ion (e.g., H+, Na+ and the like).
• a phosphoalkyl group is optionally substituted.
• the alkyl moiety in a phosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl or a phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl,
• the alkylene moiety in a phosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl or a phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, which substituent is optionally substituted.
• the alkylether moiety in a phosphoalkylether group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, phospho, thiophospho, thiophosphate, phosphoalkyl,
• Phosphoramidite refers to the -OP(OR a )(NR b 2 ) group, wherein R a is alkyl and each R b is independently H or alkyl. Unless stated otherwise specifically in the specification, a phosphoramidite group is optionally substituted.
• Activated phosphorous refers to any moiety comprising phosphorous which is cable of reaction with a nucleophile, for example reacting with a nucleophile at the phosphorous atom.
• phosphoramidites and moieties comprising P- halogen bonds are included within the definition of activated phosphorous moieties. Unless stated otherwise specifically in the specification, an activated phosphorous group is optionally substituted.
• R a counter ion e.g., H + , Na+ and the like
• thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl,
• a thiophosphoalkylene group is optionally substituted.
• the alkylene moiety in a thiophosphoalkylene group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, which substituents are optionally substituted.
• R a is S; or R b is S " or SR d ; or R c is -Salkylether; or R d is S, or combinations thereof.
• a thiophosphoalkylether group is optionally substituted.
• the alkylether moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, phospho, thiophospho, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether, which substituents are optionally substituted.
• substituted means any of the above groups (e.g., alkyl, alkylene, aminoalkylene, alkoxy, alkylamino, alkylcarbonyl, alkylcarbonyloxy, alkylether, polyalkylether, hydroxylpolyalkylether, aminopolyalkylether, alkylenether, polyalkylenether, hydroxylpolyalkylenether, aminopolyalkylenether, aryl, arylamino, aryloxy, arylcarbonyl, arylcarbonyloxy, aralkyl, aralkylamino, carbocyclic ring, cycloalkyl, heterocyclyl, heteroaryl, heteroarylalkyl, hydroxylalkyl, hydroxylalkylene, hydroxylalkylether, phosphoalkyl, phosphoalkylene, phosphoalkylether,
• a non-hydrogen atom such as, but not limited to: a halogen atom such as F, CI, Br, and I; an oxygen atom in groups such as hydroxyl groups, alkoxy groups, and ester groups; a sulfur atom in groups such as thiol groups, thioalkyl groups, sulfone groups, sulfonyl groups, and sulfoxide groups; a nitrogen atom in groups such as amines, amides, alkylamines, dialkylamines, arylamines, alkylarylamines, diarylamines, N-oxides, imides, and enamines; a silicon atom in groups such as trialkylsilyl groups,
• “Substituted” also means any of the above groups in which one or more hydrogen atoms are replaced by a higher-order bond (e.g., a double- or triple-bond) to a heteroatom such as oxygen in oxo, carbonyl, carboxyl, and ester groups; and nitrogen in groups such as imines, oximes, hydrazones, and nitriles.
• -OS0 2 R g , -S0 2 OR g NS0 2 R g , and -S0 2 NR g R h .
• R g and R h are the same or different and independently hydrogen, alkyl, alkoxy, alkylamino, thioalkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N- heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl and/or heteroarylalkyl.
• Substituted further means any of the above groups in which one or more hydrogen atoms are replaced by a bond to an amino, cyano, hydroxyl, imino, nitro, oxo, thioxo, halo, alkyl, alkoxy, alkylamino, thioalkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl and/or heteroarylalkyl group.
• each of the foregoing substituents may also be optionally substituted with one or more of the above substituents.
• Fluorescent refers to a molecule which is capable of absorbing light of a particular frequency and emitting light of a different frequency. Fluorescence is well- known to those of ordinary skill in the art. "Colored” refers to a molecule which absorbs light within the colored spectrum (i.e., red, yellow, blue and the like).
• a “linker” refers to a contiguous chain of at least one atom, such as carbon, oxygen, nitrogen, sulfur, phosphorous and combinations thereof, which connects a portion of a molecule to another portion of the same molecule or to a different molecule, moiety or solid support (e.g., microparticle).
• Linkers may connect the molecule via a covalent bond or other means, such as ionic or hydrogen bond interactions.
• Linkers include linear linkers, cyclic linkers and combinations thereof.
• a linker is alkylene or heteroalkylene.
• biomolecule refers to any of a variety of biological materials, including nucleic acids, carbohydrates, amino acids, polypeptides, glycoproteins, hormones, aptamers and mixtures thereof. More specifically, the term is intended to include, without limitation, RNA, DNA, oligonucleotides, modified or derivatized nucleotides, enzymes, receptors, prions, receptor ligands (including hormones), antibodies, antigens, and toxins, as well as bacteria, viruses, blood cells, and tissue cells.
• the visually detectable biomolecules of the invention i.e., compounds of structure (I) having a biomolecule linked thereto
• a biomolecule having a "M” group that enables attachment of the biomolecule to the compound via any available atom or functional group, such as an amino, hydroxy, carboxyl, or sulfhydryl group on the biomolecule.
• visible and “visually detectable” are used herein to refer to substances that are observable by visual inspection, without prior illumination, or chemical or enzymatic activation. Such visually detectable substances absorb and emit light in a region of the spectrum ranging from about 300 to about 900 nm. Preferably, such substances are intensely colored, preferably having a molar extinction coefficient of at least about 40,000, more preferably at least about 50,000, still more preferably at least about 60,000, yet still more preferably at least about 70,000, and most preferably at least about 80,000 M ⁇ cm "1 .
• the biomolecules of the invention may be detected by observation with the naked eye, or with the aid of an optically based detection device, including, without limitation, absorption spectrophotometers, transmission light microscopes, digital cameras and scanners.
• Visually detectable substances are not limited to those which emit and/or absorb light in the visible spectrum. Substances which emit and/or absorb light in the ultraviolet (UV) region (about 10 nm to about 400 nm), infrared (IR) region (about 700 nm to about 1 mm), and substances emitting and/or absorbing in other regions of the electromagnetic spectrum are also included with the scope of "visually detectable" substances.
• UV ultraviolet
• IR infrared
• the term "photostable visible dye” refers to a chemical moiety that is visually detectable, as defined hereinabove, and is not significantly altered or decomposed upon exposure to light.
• the photostable visible dye does not exhibit significant bleaching or decomposition after being exposed to light for at least one hour. More preferably, the visible dye is stable after exposure to light for at least 12 hours, still more preferably at least 24 hours, still yet more preferably at least one week, and most preferably at least one month.
• Nonlimiting examples of photostable visible dyes suitable for use in the compounds and methods of the invention include azo dyes, thioindigo dyes, quinacridone pigments, dioxazine, phthalocyanine, perinone, diketopyrrolopyrrole, quinophthalone, and truarycarbonium.
• the visually detectable biomolecules of embodiments of the invention are useful for a wide variety of biochemical and biomedical applications in which there is a need to determine the presence, location, or quantity of a particular biomolecule.
• the invention provides a method for visually detecting a biomolecule, comprising: (a) providing a biological system with a visually detectable biomolecule comprising the compound of structure (I) linked to a biomolecule; and (b) detecting the biomolecule by its visible properties.
• the phrase "detecting the biomolecule by its visible properties” means that the biomolecule, without illumination or chemical or enzymatic activation, is observed with the naked eye, or with the aid of a optically based detection device, including, without limitation, absorption spectrophotometers, transmission light microscopes, digital cameras and scanners.
• a densitometer may be used to quantify the amount of visually detectable biomolecule present.
• the relative quantity of the biomolecule in two samples can be determined by measuring relative optical density. If the stoichiometry of dye molecules per biomolecule is known, and the extinction coefficient of the dye molecule is known, then the absolute concentration of the biomolecule can also be determined from a measurement of optical density.
• biological system is used to refer to any solution or mixture comprising one or more biomolecules in addition to the visually detectable
• Microparticle refers to any of a number of small particles useful for attachment to compounds of the invention, including, but not limited to, glass beads, magnetic beads, polymeric beads, nonpolymeric beads, and the like.
• a microparticle comprises polystyrene, such as polystyrene beads.
• Embodiments of the invention disclosed herein are also meant to encompass all compounds of structure (I) being isotopically-labelled by having one or more atoms replaced by an atom having a different atomic mass or mass number.
• isotopes that can be incorporated into the disclosed compounds include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine, and iodine, such as 2 H, 3 H, U C, 13 C, 14 C, 13 N, 15 N, 15 0, 17 0, 18 0, 31 P, 32 P, 35 S, 18 F, 36 C1, 123 I, and 125 I, respectively.
• Isotopically-labeled compounds of structure (I) can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described below and in the following Examples using an appropriate isotopically-labeled reagent in place of the non-labeled reagent previously employed.
• Solid compound and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
• Salt includes both acid and base addition salts.
• Acid addition salt refers to those salts which are formed with inorganic acids such as, but not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as, but not limited to, acetic acid, 2,2-dichloroacetic acid, adipic acid, alginic acid, ascorbic acid, aspartic acid, benzenesulfonic acid, benzoic acid, 4-acetamidobenzoic acid, camphoric acid, camphor- 10-sulfonic acid, capric acid, caproic acid, caprylic acid, carbonic acid, cinnamic acid, citric acid, cyclamic acid, dodecylsulfuric acid, ethane- 1,2-disulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, formic acid, fumaric acid, galactaric acid, gentisic acid, glucoheptonic
• naphthalene-l,5-disulfonic acid naphthalene-2-sulfonic acid, l-hydroxy-2-naphthoic acid, nicotinic acid, oleic acid, orotic acid, oxalic acid, palmitic acid, pamoic acid, propionic acid, pyroglutamic acid, pyruvic acid, salicylic acid, 4-aminosalicylic acid, sebacic acid, stearic acid, succinic acid, tartaric acid, thiocyanic acid, ⁇ -toluenesulfonic acid, trifluoroacetic acid, undecylenic acid, and the like.
• Base addition salt refers to those salts which are prepared from addition of an inorganic base or an organic base to the free acid. Salts derived from inorganic bases include, but are not limited to, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like.
• Salts derived from organic bases include, but are not limited to, salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as ammonia, isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, diethanolamine, ethanolamine, deanol, 2-dimethylaminoethanol, 2-diethylaminoethanol,
• dicyclohexylamine lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, benethamine, benzathine, ethylenediamine, glucosamine, methylglucamine, theobromine, triethanolamine, tromethamine, purines, piperazine, piperidine,
• N-ethylpiperidine polyamine resins and the like.
• Particularly preferred organic bases are isopropylamine, diethylamine, ethanolamine, trimethylamine, dicyclohexylamine, choline and caffeine.
• solvate refers to an aggregate that comprises one or more molecules of a compound of the invention with one or more molecules of solvent.
• the solvent may be water, in which case the solvate may be a hydrate.
• the solvent may be an organic solvent.
• the compounds of the present invention may exist as a hydrate, including a monohydrate, dihydrate, hemihydrate, sesquihydrate, trihydrate, tetrahydrate and the like, as well as the corresponding solvated forms.
• the compounds of the invention may be true solvates, while in other cases the compounds of the invention may merely retain adventitious water or another solvent or be a mixture of water plus some adventitious solvent.
• the compounds of the invention may contain one or more asymmetric centers and may thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that may be defined, in terms of absolute stereochemistry, as (R)- or (S)- or, as (D)- or (L)- for amino acids.
• the present invention is meant to include all such possible isomers, as well as their racemic and optically pure forms.
• Optically active (+) and (-), (R)- and (5)-, or (D)- and (L)- isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques, for example, chromatography and fractional crystallization.
• Conventional techniques for the preparation/isolation of individual enantiomers include chiral synthesis from a suitable optically pure precursor or resolution of the racemate (or the racemate of a salt or derivative) using, for example, chiral high pressure liquid chromatography (HPLC).
• HPLC high pressure liquid chromatography
• stereoisomer refers to a compound made up of the same atoms bonded by the same bonds but having different three-dimensional structures, which are not interchangeable.
• the present invention contemplates various stereoisomers and mixtures thereof and includes “enantiomers”, which refers to two stereoisomers whose molecules are nonsuperimposeable mirror images of one another.
• a “tautomer” refers to a proton shift from one atom of a molecule to another atom of the same molecule.
• the present invention includes tautomers of any said compounds.
• Various tautomeric forms of the compounds are easily derivable by those of ordinary skill in the art.
• Bonding refers to the process by which one molecule or atom associates with another atom or molecule. Bonding includes, ionic bonding, covalent bonding, chelation, association complexes, hydrogen bonding and the like.
• a moiety capable of bonding with an analyte molecule or solid support is moiety capable of associating with the analyte molecule or solid support by any of the above means. In one embodiments, the moiety binds with the analyte molecule or solid support by covalent bonding (i.e., the moiety is capable of forming a covalent bond with the analyte molecule or solid support).
• compounds useful as fluorescent and/or colored dyes in various analytical methods are provided.
• the compounds have the following structure (I):
• R LA , R LB , R LC , R LD , R LE and R LF are each independently absent, H, halo, nitro, C 1 -C 6 alkyl, -SO 3 " , -SChalkyl, C 1 -C 6 alkoxy, aryl, aryloxy, C 1 -C 6 alkylcarbonyl, C 1 -C 6 alkylcarbonyloxy, arylcarbonyl, arylcarbonyloxy, amino, alkylamino, arylamino, aralklyamino, where I represents, independently, a further compound of structure (I); or one of R LA , R LB , R LC , R LD , R LE or R LF joins with another one of R LA , R LB , R LC , R LD , R LE or R LF to form a carbocyclic or heterocyclic ring and the remaining R LA , R LB , R LC , R
• R 2A , R 2B , R 2C , R 2D , R 2E , R 2F , R 2G , R 2H , R 21 and R 2J are each independently H, halo, C 1 -C 6 alkoxy, aryloxy, amino, alkylamino, arylamino, aralklyamino, heterocyclyl, -L -(R 3 ) Z -L 2 -M or where I represents, independently, a further compound of structure (I); or one or more of R 2A , R 2B , R 2C , R 2D , R 2E , R 2F , R 2G , R 2H , R 2I or R 2J join with another one or more (e.g., one or two) of R 2A , R 2B , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 2i or R 2j on the same ring to
• R 3 is, at each occurrence, independently a mono or bivalent functional group selected from the group consisting of polyalkyether, polyalkylenether, hydroxylalkoxy, hydroxylalkyl, hydroxylalkylene, aminoalkylene, aminoalkoxy, hydroxylpolyalky ether, hydroxylpolyalkylenether, aminopolyalky ether,
• aminopolyalkylenether phosphate, thiophosphate, phospho, thiophospho
• M is absent, H or a moiety capable of bonding with an analyte molecule or a solid support; or M is an analyte molecule or solid support;
• L 1 and L 2 are, at each occurrence, independently an optional linker; x and y are each independently an integer from 0 to 4, and the sum of x and y is 2 or greater;
• z is an integer from 1 to 10;
• R la , R lb , R lc , R ld , R le , R lf , R 2a , R 2b , R 2c , R 2d , R 2e , R 2f R 2g R 2h R 2i or R 3 ⁇ 4 is _ L i _( R 3) z _ L 2_ M Qr where I represents, independently, a further compound of structure (I).
• At least one of R la , R lb , R lc , R ld , R le , R lf , R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 2i or R 2j is In other embodiments, at least one of R la , R lb , R lc , R ld , R le or R lf is -L -(R 3 ) Z -L 2 -M.
• At least one of R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 or R 2j is -L 1 -(R 3 ) Z -L 2 -M.
• the compound of structure (I) comprises two ethynylphenyl moieties, and the sum of x and y is 2. In some of these embodiments x is 0 and y is 2
• the compound has the following structure (la):
• the compound has the following structure (lb):
• R la is -L l -(B?) Z -L 2 -M.
• one of R ld , R le or R lf is - ⁇ -(R ⁇ -T ⁇ -M.
• one of R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 2i or R 2j is -L -(R 3 ) Z -L 2 -M.
• R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 or R 2j are two of R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 or R 2j.
• R la and R lb are both -L 1 -(R 3 ) Z -L 2 -M.
• one of R la or R lb is -L -(R 3 ) Z -L 2 -M and one of R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 2i or R 2j is - ⁇ 3 ) ⁇ - ⁇ . 2 - ⁇ .
• one of R 1 or R lb is -L -(R 3 ) Z -L 2 -M and one of R ld , R le or R lf is -L -(RVL 2 -M.
• At least one of R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 or R 2 -" is amino, alkylamino, arylamino, aralklyamino or heterocyclyl.
• R 2c or R 2h or both, is amino, alkylamino, arylamino, aralklyamino or heterocyclyl.
• alkylamino is dimethylamino, diethylamino, diisopropylamino or ethylisopropylamino.
• arylamino is diphenylamino.
• heterocyclyl is N-pyrrolidinyl or N-pyrrolyl.
• R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 and R 2j are each independently H, halo, C 1 -C 6 alkoxy, aryloxy, amino, alkylamino, arylamino, aralklyamino, heterocyclyl, -L -(R 3 ) Z -L 2 -M or -L 1 -(R 3 ) z -L 2 -S-S-L 2 -(R 3 )z-L 1 -I, where I represents, independently, a further compound of structure (I).
• R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g are independently selected from the group consisting of R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g ,
• R 2h , R 2i or R 2j join with another one or more (e.g., one or two) of R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 or R 2 -" on the same ring to form a mono or fused bicyclic carbocyclic or heterocyclic ring and the remaining R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 2i and R 2j are each independently H, halo, C 1 -C 6 alkoxy, aryloxy, amino, alkylamino, arylamino, aralklyamino, heterocyclyl, -L -(R 3 ) Z -L 2 -M or -L 1 -(R 3 ) z -L 2 -S-S-L 2 -(R 3
• At least one of R A , R , R , R E , R 2F , R 2G , R 21 or R 2 -" is halo, alkoxy or aryloxy.
• at least one of R 2A , R 2B , R 2D , R 2E , R 2F , R 2G , R 2I or R 2J is halo.
• at least one of R 2A , R 2B , R 2D , R 2E , R 2F , R 2G , R 2I or R 2J is alkoxy.
• at least one of R 2A , R 2B , R 2D , R 2E , R 2F , R 2G , R 21 or R 2J is aryloxy.
• At least one of R 2A , R 2B , R 2d R 2e R 2f R 2g R 2i Qr R 3 ⁇ 4 ig H For example; in some embodiments each of R 2A , R 2B ,
• R LA , R LB , R LC , R LD , R LE and R LF are each independently absent, H, halo, nitro, C 1 -C 6 alkyl, -SO 3 " ,
• R is C 1 -C 6 alkoxy, aryloxy or C 1 -C 6 alkylcarbonyloxy. In some of these embodiments, C 1 -C 6 alkoxy is methoxy. In other of the foregoing embodiments, at least one of R A , R , R C , R , R LE or R LF is amino, alkylamino, arylamino or aralklyamino. In some of these embodiments, alkylamino is dimethylamino.
• At least one of R LA , R LB , R LC , R LD , R LE or R LF is halo or nitro.
• At least one of R LA , R LB , R LC , R LD , R LE or R LF is -SO 3 " or -S0 3 alkyl.
• At least one of R LA , R LB , R LC , R LD , R LE or R LF is C 1 -C 6 alkyl or aryl. In some of these embodiments, C 1 -C 6 alkyl is methyl or ethyl.
• one of R LA , R LB , R LC , R LD , R LE or R LF joins with another one of R LA , R LB , R LC , R LD , R LE or R LF to form a carbocyclic or heterocyclic ring and the remaining R LA , R LB , R LC , R LD , R LE and R LF are each independently absent, H, halo, nitro, C 1 -C 6 alkyl, -OSO 2 " ,
• -OS0 2 alkyl C 1 -C 6 alkoxy, aryl, aryloxy, C 1 -C 6 alkylcarbonyl, C 1 -C 6 alkylcarbonyloxy, arylcarbonyl, arylcarbonyloxy, amino, alkylamino, arylamino, aralklyamino,
• the compound has one of the following structures:
• L 1 is present.
• L 1 is C 1 -C 6 alkylene.
• L 1 is C 1 -C 6 heteroalkylene.
• L 2 is present.
• L 2 is C 1 -C 6 alkylene.
• L 2 is C 1 -C 6 heteroalkylene.
• L 2 comprises a cyclic linking moiety.
• R 3 is selected from the group consisting of polyalkylether, phosphate, phospho and phosphoalkyl.
• R 3 is selected from the group consistin of:
• n is an integer from 1 to 6 and m is an integer from 2 to 10.
• -(R 3 ) z -L 2 -M has one of the following
• R 3 is phosphoramidite and M is absent. In other embodiments, M is absent or H.
• M is a moiety capable of bonding with an analyte molecule or a solid support.
• M provides a means of connecting the compound of structure (I) to an analyte molecule or a solid support (e.g., by a covalent bond).
• M is a reactive group capable of forming a covalent bond with an analyte molecule or a solid support.
• the type of M group and connectivity of the M group to the remainder of the compound of structure (I) is not limited.
• the M is a moiety which is not susceptible to hydrolysis under aqueous conditions, but is sufficiently reactive to form a bond with a corresponding group on an analyte molecule or solid support (e.g., an amine).
• compounds of structure (I) comprises M groups commonly employed in the field of bioconjugati on. For example in some
• M is a nucleophilic reactive group, an electrophilic reactive group or a cycloaddition reactive group.
• M is sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, a-haloamide, biotin, amino or a maleimide.
• the activated ester is an N-succinimide ester, imidoester or polyflourophenyl ester.
• the alkyne is an alkyl azide or acyl azide.
• a compound of structure (I) wherein M is -SH since -SH can be readily conjugated to many analyte molecules and/or solid supports (e.g., by formation of a disulfide bond with a free sulfhydryl on the analyte molecule or solid support).
• -SH can be readily conjugated to many analyte molecules and/or solid supports (e.g., by formation of a disulfide bond with a free sulfhydryl on the analyte molecule or solid support).
• At least one of R la , R lb , R lc , R ld , R le , R lf , R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 or R 2j is
• the dimer may be formed between any one of R la , R lb , R lc , R ld , R le , R lf , R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 or R 2j and another one of R la , R lb , R lc , R ld , R le ,
• R la , R lb , R lc , R ld , R le , R lf , R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 21 , R 2j , R 3 , L 1 , L 2 , x, y and z are each independently as defined for any of the foregoing embodiments.
• the dimers are also illustrated as follows ( ⁇ ):
• the dimers have the following structure (la'):
• the dimers have the following structure (lb'):
• ) ( ) - can have various structures.
• ) ( ) - has one of the following structures:
• M is an analyte molecule or solid support.
• the analyte molecule is a biomolecule.
• the biomolecule is a nucleic acid, amino acid or a polymer thereof.
• the biomolecule is a nucleic acid, peptide, carbohydrate, lipid, enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer, antigen or prion.
• the analyte molecule is a drug, vitamin or small molecule.
• the structure of the compound of structure (I) is typically selected to optimize the excitation and or emission wavelengths. Accordingly, in various embodiments the compound of structure (I) has a maximum excitation wavelength ranging from about 390 nm to about 430 nm, for example from about 400 nm to about 420 nm. In other embodiments, the compound of structure (I) has a maximum emission wavelength ranging from about 510 nm to about 550 nm, for example, from about 520 to about 540 nm. For example, in certain embodiment the dyes have a maximum excitation wavelength at about 410 nm and a maximum emission wavelength at about 533 nm.
• the compound of structure (I) has one of the followin structures:
• M is a moiety capable of bonding with an analyte molecule or a solid support; or M is an analyte molecule or solid support, such as a microparticle, covalently linked via an optional linker.
• M is -SH.
• compositions comprising any of the disclosed compounds and one or more biomolecules are provided in various other embodiments.
• use of such compositions in analytical methods for detection of the one or more biomolecules is also provided as described in more detail below.
• Suitable protecting groups include hydroxy, amino, mercapto and carboxylic acid.
• Suitable protecting groups for hydroxy include trialkylsilyl or diarylalkylsilyl (for example, t-butyldimethylsilyl, t-butyldiphenylsilyl or trimethylsilyl), tetrahydropyranyl, benzyl, and the like.
• Suitable protecting groups for amino, amidino and guanidino include t-butoxycarbonyl, benzyloxycarbonyl, and the like.
• Suitable protecting groups for mercapto include -C(0)-R" (where R" is alkyl, aryl or arylalkyl), /?-methoxybenzyl, trityl and the like.
• Suitable protecting groups for carboxylic acid include alkyl, aryl or arylalkyl esters.
• Protecting groups may be added or removed in accordance with standard techniques, which are known to one skilled in the art and as described herein. The use of protecting groups is described in detail in Green, T.W. and P.G.M. Wutz, Protective Groups in Organic Synthesis (1999), 3rd Ed., Wiley.
• the protecting group may also be a polymer resin such as a Wang resin, Rink resin or a 2-chlorotrityl-chloride resin.
• all compounds of the invention ⁇ e.g., compounds of structure (I)) which exist in free base or acid form can be converted to their salts by treatment with the appropriate inorganic or organic base or acid by methods known to one skilled in the art. Salts of the compounds of the invention can be converted to their free base or acid form by standard techniques.
• R la , R lb , R lc , R ld , R le , R lf , R 2a , R 2b , R 2c , R 2d , R 2e , R 2f , R 2g , R 2h , R 2i , R 2j , x and y are as defined herein.
• starting components may be obtained from sources such as Sigma Aldrich, Lancaster Synthesis, Inc., Maybridge, Matrix Scientific, TCI, and Fluorochem USA, etc. or synthesized according to sources known to those skilled in the art (see, for example, Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th edition (Wiley, December 2000)) or prepared as described in this invention.
• Reaction Scheme I
• Reaction Scheme I illustrates an exemplary method for preparing an exemplary compound of structure (I).
• compounds of structure A and B can be purchased or prepared by methods well-known to those of ordinary skill in the art.
• Treatment of 2 equivalents of A with a strong base, such as n- butyl lithium, followed by reaction with B results in compounds of structure C.
• Compounds of structure C can be further functionalized by reaction with 9-BBN and an appropriate precursor to linking moiety L 1 to produce compounds of structure D.
• General Reaction Scheme I depicts preparation of symmetrical (i.e., identical phenyl groups) compounds of structure (I), it will be readily apparent to one of ordinary skill in the art that other, non-symmetrical, compounds of structure (I) can be prepared by similar methods (e.g., stepwise reaction of differently substituted phenyls). It should also be noted that General Reaction Scheme I illustrates a compound of structure (I) wherein L 1 is an alkylene linker, but other compounds of structure (I) with different linking moieties or no linking moiety are prepare via analogous methods.
• compounds of structure (I) obtained by the above methods can be further modified to obtain different compounds of structure (I).
• phosphoramidite E is further functionalized using common techniques (e.g., techniques analogous to solid-phase DNA synthesis) to obtain compounds of structure (I) comprising various R 3 moieties.
• Reactive moieties (M) are attached to the R 3 moiety using techniques known in the art and described in more detail in the examples.
• Analyte molecules e.g., biomolecules
• embodiments of the compounds of structure (I) include M groups capable of forming covalent bonds with a functional group on an analyte molecule as a means for attaching analyte molecules.
• M groups include, but are not limited to activated phosphorus compounds (e.g., phosphoramidites), activated esters, amines, alcohols, and the like. Methods for preparation of such compounds and reacting the same with an analyte molecule to form a covalent bond are well-known in the art.
• the compounds of structure (I) comprise a covalent bond to an oligonucleotide.
• bonds may be formed by including a phosphoramidite moiety in the compound of structure (I) and reacting the same with an oligomer (or phosphoramidite monomer) under standard DNA synthesis conditions.
• DNA synthesis methods are well-known in the art. Briefly, two alcohol groups are functionalized with a dimethoxytrityl (DMT) group and a 2-cyanoethyl-N,N- diisopropylamino phosphoramidite group, respectively.
• DMT dimethoxytrityl
• 2-cyanoethyl-N,N- diisopropylamino phosphoramidite group respectively.
• the phosphoramidite group is coupled to an alcohol group, typically in the presence of an activator such as tetrazole, followed by oxidation of the phosphorous atom with iodine.
• the dimethoxytrityl group can be removed with acid (e.g., chloroacetic acid) to expose the free alcohol, which can be reacted with a phosphoramidite group.
• the 2-cyanoethyl group can be removed after oligomerization by treatment with aqueous ammonia.
• a primary alcohol can be protected as a DMT group by reaction with DMT-C1.
• a secondary alcohol is then functionalized as a phosphoramidite by reaction with an appropriate reagent such as 2-cyanoethyl N,N- dissopropylchlorophosphoramidite.
• Methods for preparation of phosphoramidites and their oligomerization are well-known in the art and described in more detail in the examples.
• the compounds are useful in various analytical methods.
• the disclosure provides a method of staining a sample, the method comprising adding to said sample a compound of structure (I) in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
• M is an analyte molecule such as a biomolecule.
• the biomolecule is nucleic acid, amino acid or a polymer thereof (e.g., polynucleotide or polypeptide).
• the biomolecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
• M is a microparticle.
• the microparticle is a polymeric bead or nonpolymeric bead.
• said optical response is a fluorescent response.
• said sample comprises cells, and some embodiments further comprise observing said cells by flow cytometry.
• the method further comprises distinguishing the fluorescence response from that of a second fluorophore having detectably different optical properties.
• the disclosure provides a method for visually detecting an analyte molecule, comprising:
• the biomolecule is a nucleic acid, amino acid or a polymer thereof (e.g., polynucleotide or polypeptide).
• the biomolecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.
• a method for visually detecting a biomolecule comprising:
• the compound admixed with the one or more biomolecules will be a compound of structure (I) wherein M is a reactive moiety, and in further embodiments the reactive moiety forms a covalent bond or other strong association with the biomolecule.
• certain embodiments of the compounds of structure (I) comprise an analyte molecule (e.g., biomolecule) or a ligand attached (conjugated) thereto. Attachment may be, for example, by covalent bonding, ionic bonding, dated bonding, hydrogen bonding, and other forms of molecular bonding.
• useful conjugated substrates of the invention include, but are not limited to, compounds of structure (I) comprising an analyte molecule attached thereto (also referred to herein as a "conjugated substrate"), the analyte molecule being selected from antigens, small molecules, steroids, vitamins, drugs, haptens, metabolites, toxins, environmental pollutants, amino acids, peptides, proteins, photosensitizers, nucleotides, oligonucleotides, nucleic acids, carbohydrates, lipids, ion-complexing moieties and non-biological polymers.
• the conjugated substrate is a natural or synthetic amino acid, a natural or synthetic peptide or protein, or an ion-complexing moiety.
• exemplary peptides include, but are not limited to protease substrates, protein kinase substrates, phosphatase substrates, neuropeptides, cytokines, and toxins.
• Exemplary protein conjugates include enzymes, antibodies, lectins, glycoproteins, histones, alumin, lipoproteins, avidin, streptavidins, protein A, protein G, casein, phycobiliproteins, other fluorescent proteins, hormones, toxins, growth factors, and the like.
• the point of attachment of the analyte molecule to the remainder of the compound of structure (I) can and will vary depending upon the embodiment. Further, some embodiments include a linker (L 2 ) between the analyte molecule and the remainder of the compound of structure (I), although use of the linker is optional and not required in all embodiments. It is also envisioned that the compound of structure (I) may comprise more than one analyte molecule. For example, two, three or more than three analyte molecules may be conjugated to the naphthyl and/or phenyl rings of compound (I).
• a compound of the disclosure may include a covalent bond to DNA or RNA via one or more purine or pyrimidine bases through an amide, ester, ether, or thioether bond; or is attached to the phosphate or carbohydrate by a bond that is an ester, thioester, amide, ether, or thioether.
• a compound of structure (I) may be bound to the nucleic acid by chemical post-modification, such as with platinum reagents, or using a photoactivatable molecule such as a conjugated psoralen.
• the compounds of the invention are useful in many applications including those described for other dyes in U.S. Pat. Nos. 7, 172,907; 5,268,486; and U.S. Patent Application Nos. 20040014981; and 20070042398, all of which are incorporated herein by reference in their entireties.
• fluorescent dyes such as those described herein, may be used in imaging with techniques such as those based on fluorescence detection, including but not limited to fluorescence lifetime, anisotropy, photoinduced electron transfer, photobleaching recovery, and non-radioactive transfer.
• the compounds of structure (I), as such may be utilized in all fluorescent-based imaging, microscopy, and spectroscopy techniques including variations on such.
• fluorescence detection techniques include those that involve detecting fluorescence generated within a system. Such techniques include, but are not limited to, fluorescence microscopy, fluorescence activated cell sorting (FACS), fluorescent flow cytometry, fluorescence correlation spectroscopy (FCS), fluorescence in situ
• FISH hybridization
• FIONA free radical initiated peptide sequencing
• SHRF P second harmonic retinal imaging of membrane potential
• the compounds of structure (I) can be used as markers or tags to track dynamic behavior in living cells.
• fluorescence recovery after photobleaching FRAP
• FRAP fluorescence recovery after photobleaching
• Variants of FRAP include, but are not limited to, polarizing FRAP (pFRAP), fluorescence loss in photo-bleaching (FLIP), and fluorescence localization after photobleaching (FLAP).
• FRAP and variants of FRAP can be used to determine kinetic properties, including the diffusion coefficient, mobile fraction, and transport rate of the fluorescently labeled molecules.
• Methods for such photo-bleaching based techniques are described in Braeckmans, K. et al., Biophysical Journal 85: 2240-2252, 2003; Braga, J. et al., Molecular Biology of the Cell 15: 4749- 4760, 2004; Haraguchi, T., Cell Structure and Function 27: 333-334, 2002; Gordon, G. W. et al., Biophysical Journal 68: 766-778, 1995, which are all incorporated herein by reference in their entireties.
• fluorescence imaging techniques are based on non-radioactive energy transfer reactions that are homogeneous luminescence assays of energy transfer between a donor and an acceptor.
• Such techniques that may employ the use of the subject fluorescent dyes include, but are not limited to, FRET, FET, FP, HTRF, BRET, FLIM, FLI, TR-FRET, FLIE, smFRET, and SHREK. These techniques are all variations of FRET.
• the subject compounds may be used as biosensors such as a Ca 2+ ion indicator; a pH indicator; a phosphorylation indicator, or an indicator of other ions, e.g., magnesium, sodium, potassium, chloride and halides.
• biosensors such as a Ca 2+ ion indicator; a pH indicator; a phosphorylation indicator, or an indicator of other ions, e.g., magnesium, sodium, potassium, chloride and halides.
• biochemical processes frequently involve protonation and deprotonation of biomolecules with concomitant changes in the pH of the milieu.
• Substitution at the meso-position with different pH-sensitive groups generates a variety of NIR fluorescent pH sensors with different pKa's.
• the substituents at the meso-position will be in extended ⁇ -conjugation with the fluorophore core to effect marked spectral changes in response to different pH environments.
• the compounds are used as colorants or dyes in various applications.
• the substituents on the napthalene and/or phenyl moieties are not particularly limited provided the compound maintains its desired color and/or absorbance and/or emission properties. Selection of appropriate substituents for this purpose is within the skill of one of ordinary skill in the art.
• the compounds disclosed herein find utility as a dye or colorant in textiles, plastics, paints and/or safety devices ⁇ e.g., reflective materials, emergency lights, glow sticks, etc.)
• safety devices e.g., reflective materials, emergency lights, glow sticks, etc.
• Phosphoramidites and precursor molecules were analyzed using an Agilent Infinity 1260 UHPLC system with a diode array detector and High Performance Autosampler using an Aapptec SpiritTM Peptide C18 column (4.6mm x 100mm, 5 ⁇ particle size). Molecular weights for monomer intermediates were obtained using tropylium cation infusion enhanced ionization. 1 Excitation and emission profiles experiments were recorded on a Cary Eclipse spectra photometer.
• oligonucleotide dyes were synthesized on an ABI 394 DNA synthesizer using standard protocols for the phosphoramidite based coupling approach.
• the chain assembly cycle for the synthesis of oligonucleotide phosphoramidates was the following: (i) detritylation, 3% trichloroaceticacid in dichloromethane, 1 min; (ii) coupling, 0.1 M phosphoramidite and 0.45 M tetrazole in acetonitrile, 10 min; (iii) capping, 0.5 M acetic anhydride in THF/lutidine, 1/1, v/v 15 s; (iv) oxidation, 0.1 M iodine in THF/pyri dine/water, 10/10/1, v/v/v, 30 s.
• NMR and mass spectral properties are determined using techniques known in the art, including those described above.

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