Classifications

• • 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
  • C07F9/655—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms
  • C07F9/65515—Heterocyclic compounds, e.g. containing phosphorus as a ring hetero atom having oxygen atoms, with or without sulfur, selenium, or tellurium atoms, as the only ring hetero atoms the oxygen atom being part of a five-membered ring
• • 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
  • 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
  • C07F9/093—Polyol derivatives esterified at least twice by phosphoric acid groups
• • 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
  • 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
  • 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
  • C09B57/02—Coumarine dyes
• • 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
  • C09B69/101—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing an anthracene dye
  • C09B69/102—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing an anthracene dye containing a perylene 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
  • C09B69/103—Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds containing a diaryl- or triarylmethane 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

Definitions

• the present invention is directed to novel fluorescent or colored dyes and methods for their preparation and use in various analytical methods.
• Fluorescent and/or colored dyes are known to be particularly suitable for applications in which a highly sensitive detection reagent is desirable. Dyes that are able to preferentially label a specific ingredient or component in a sample enable the researcher to determine the presence, quantity and/or location of that specific ingredient or component. In addition, specific systems can be monitored with respect to their spatial and temporal distribution in diverse environments.
• Fluorescence and colorimetric methods are extremely widespread in chemistry and biology. These methods give useful information on the presence, structure, distance, orientation, complexation and/or location for biomolecules. In addition, time-resolved methods are increasingly used in measurements of dynamics and kinetics. As a result, many strategies for fluorescence or color labeling of biomolecules, such as nucleic acids and protein, have been developed.
• perylene derivatives have been used primarily as pigments and fluorescent dyes.
• Perylene dyes of various colors and light-absorbing properties have been reported. For example, Becker S. et al, Chem. Eur. J., 6,213,984, (2000), report the synthesis of thermotropic perylenedicarboximide chromophores that show a color change from blue to orange. Perylene and related chromophores have seen limited use as biomolecular probes, apparently due to the strongly hydrophobic character of these types of molecules and difficulties with regiospecific labeling of biomolecules with the same.
• 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. By appropriate selection of the dye, as described herein, visually detectable biomolecules of a variety of colors may be obtained.
• R 1 , R 2 , R 3 , R 4 , R 5 , L 1 , L 3 , L 4 , L 6 , L 7 , L 8 , M 1 , M 2 , q, w and n are as defined herein.
• 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:
• 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.
• 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.
• Sulfhydryl refers to the -SH 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), having from one to twelve carbon atoms (C 1 -C 12 alkyl), preferably one to eight carbon atoms (Ci-C 8 alkyl) or one to six carbon atoms (Ci-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, 2-methylhexyl, ethenyl, prop-l-enyl, but-l-enyl, pent-l-enyl, penta-l,4-dienyl
• 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.
• the points of attachment of the alkylene chain to the rest of the molecule and to the substituent group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, an alkylene chain may be 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. Unless stated otherwise specifically in the specification, an alkoxy group may be optionally substituted.
• Alkylamino refers to a group of the formula - HR a or - R 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 may be 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.
• PEG polyethylene glycol
• an alkylether group may be optionally substituted. For example, in some embodiments and alkylether is substituted with an alcohol or phosphate.
• 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 substituted.
• the -Oalkyl or -Oalkylether moiety (R b ) in a alkylphospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or
• Oalkylphospho is an alkylphospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkylphospho group may be optionally substituted.
• R b is -Oalkyl or -Oalkylether, wherein R c is a counter ion (e.g., Na+ and the like).
• an alkyletherphopsho group may be optionally substituted.
• alkyletherphospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl,
• Oalkyletherphospho is an alkyletherphospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkyletherphospho group may be optionally substituted.
• the -Oalkyl or -Oalkylether moiety in a alkythiophospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or
• Oalkylthiophospho is a alkylthiophospho group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Oalkylthiophospho group may be optionally substituted.
• an alkyletherthiophospho group may be optionally substituted.
• alkyletherthiophospho group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
• "Oalkyletherthiophospho is an
• alkyletherthiophospho group connected to the remainder of the molecule via an oxygen atom.
• Oalkyletherthiophospho group may be optionally substituted.
• Amide refers to the - R a R b radical, wherein R a and R b are independently H, alkyl or aryl. Unless stated otherwise specifically in the specification, an amide group may be optionally substituted.
• 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.
• 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 may be optionally substituted.
• Aralkyl refers to a group of the formula -R b -Rc where R 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 may be optionally substituted.
• Oaralkyl is an aralkyl group which is connected to the remainder of the molecule via an oxygen linkage.
• ODMT dimethoxytrityl linked to the rest of the molecule via an O atom. Unless stated otherwise specifically in the specification, an Oaralkyl group may be optionally substituted.
• Cyanoalkyl refers to an alkyl group comprising at least one cyano substituent.
• the one or more -CN substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a cyanoalkyl group may be 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,
• Cycloalkylalkyl refers to a group of the formula -R b R d where R is an alkylene chain as defined above and R d is a cycloalkyl group as defined above. Unless stated otherwise specifically in the specification, a cycloalkylalkyl group may be 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.
• 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.
• Haloalkyl refers to an alkyl group, as defined above, that is substituted by one or more halo groups, as defined above, e.g., trifluorom ethyl, difluoromethyl, trichloromethyl, 2,2,2-trifluoroethyl, 1,2-difluoroethyl, 3-bromo-2-fluoropropyl, 1,2-dibromoethyl, and the like. Unless stated otherwise specifically in the
• haloalkyl group may be optionally substituted.
• 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
• N-heterocyclyl refers to a heterocyclyl group as defined above containing at least one nitrogen and where the point of attachment of the heterocyclyl group to the rest of the molecule is through a nitrogen atom in the heterocyclyl group. Unless stated otherwise specifically in the specification, a N-heterocyclyl group may be optionally substituted.
• Heterocyclylalkyl refers to a group of the formula -R R e where R is an alkylene chain as defined above and Re is a heterocyclyl group as defined above, and if the heterocyclyl is a nitrogen-containing heterocyclyl, the heterocyclyl may be attached to the alkyl group at the nitrogen atom. Unless stated otherwise specifically in the specification, a heterocyclylalkyl group may be optionally substituted.
• 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,
• N-heteroaryl refers to a heteroaryl group as defined above containing at least one nitrogen and where the point of attachment of the heteroaryl group to the rest of the molecule is through a nitrogen atom in the heteroaryl group. Unless stated otherwise specifically in the specification, an N-heteroaryl group may be optionally substituted.
• Heteroarylalkyl refers to a group of the formula -3 ⁇ 4R f where R is an alkylene chain as defined above and R f is a heteroaryl group as defined above. Unless stated otherwise specifically in the specification, a heteroarylalkyl group may be optionally substituted.
• 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 may be 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 may be optionally substituted.
• phosphoalkylether or thiophosphoalkylether.
• "Ophosphoalkyl is a phosphoalkyl group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an ophosphoalkyl group may be optionally substituted.
• 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 - Oalkylether moiety in a phosphoalkylether group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
• "Ophosphoalkylether is a phosphoalkylether group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an ophosphoalkylether group may be optionally substituted.
• Sulfhydrylalkyl refers to an alkyl group comprising at least one sulfhydryl substituent.
• the one or more -SH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a sulfhydrylalkyl group may be optionally substituted.
• Sulfhydrylalkylether refers to an alkylether group comprising at least one sulfhydryl substituent.
• the one or more -SH substituents may be on a primary, secondary or tertiary carbon atom. Unless stated otherwise specifically in the specification, a sulfhydrylalkylether group may be optionally substituted.
• Sulfonate refers to the -OS(0)2R a group, wherein R a is alkyl or aryl. Unless stated otherwise specifically in the specification, a sulfonate group may be optionally substituted.
• Thioalkyl refers to a group of the formula -SR a where R a is an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, a thioalkyl group may be optionally substituted.
• a thiophosphoalkyl group may be optionally substituted.
• the -Oalkyl moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate,
• Othiophosphoalkyl is a thiophosphoalkyl group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Othiophosphoalkyl group may be optionally substituted.
• a thiophosphoalkylene group is optionally substituted.
• 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.
• a thiophosphoalkylether group may be optionally substituted.
• the -Oalkylether moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether.
• Othiophosphoalkylether is a thiophosphoalkylether group connected to the remainder of the molecule via an oxygen atom. Unless stated otherwise specifically in the specification, an Othiophosphoalkylether group may be optionally substituted.
• substituted means any of the above groups (i.e., alkyl, alkylene, aminoalkylene, alkoxy, alkylamino, alkylether, alkylenether, polyalkylenether, hydroxylpolyalkylenether, aminopolyalkylenether, alkylphospho, alkyletherphospho, alkylthiophospho, alkyletherthiophospho, amide, thioalkyl, aryl, aryloxy, aralkyl, Oaralkyl, cyanoalkyl, carbocyclic ring, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, N-heterocyclyl, heterocyclylalkyl, heteroaryl, N-heteroaryl, heteroarylalkyl, hydroxylalkyl, a hydroxylalkylene, aminoalkyl, hydroxylalkylether, phosphoalkyl
• sulfhydrylalkylether sulfonate, thiophosphoalkyl, thiophosphoalkylene, and/or thiophosphoalkylether
• 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 R 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.
• Conjugation refers to the overlap of one p-orbital with another p-orbital across an intervening sigma bond. Conjugation may occur in cyclic or acyclic compounds.
• a “degree of conjugation” refers to the overlap of at least one p-orbital with another p-orbital across an intervening double bond. For example, 1, 3-butadine has one degree of conjugation, while benzene and other aromatic compounds typically have multiple degrees of conjugation. Fluorescent and colored compounds typically comprise at least one degree of conjugation.
• 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.
• Cold 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.
• 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 i.e., compounds of structure (I) having a biomolecule linked thereto
• 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 a 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.
• perylene derivative is intended to include any substituted perylene that is visually detectable. However, the term is not intended to include perylene itself.
• anthracene derivative e.g., perylene, pyrene, anthracene or naphthalene derivative
• a derivative is an imide, bisimide or hydrazamimide derivative of perylene, anthracene, naphthalene, or pyrene.
• the visually detectable biomolecules 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 biomolecule.
• biological systems include cells, cell extracts, tissue samples, electrophoretic gels, assay mixtures, and hybridization reaction mixtures.
• Microparticle is a type of solid support and 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 beads.
• Base pairing moiety refers to a heterocyclic moiety capable of hybridizing with a complementary heterocyclic moiety via hydrogen bonds (e.g.,
• Base pairing moieties include natural and unnatural bases.
• Non-limiting examples of base pairing moieties are RNA and DNA bases such adenosine, guanosine, thymidine, cytosine and uridine and analogues thereof.
• the invention disclosed herein is 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
• 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).
• the compound has the following structure (I):
• M 1 and M 2 are, at each occurrence, independently a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
• L 1 , L 3 , L 4 L 6 , L 7 and L 8 are, at each occurrence, independently optional alkylene or heteroalkylene linkers;
• R 1 is, at each occurrence, independently H, alkyl or alkoxy
• R 2 is an electron pair, H, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho,
• R 3 is H, OH, SH, -NH 2 , alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, -Oaralkyl, phosphate, thiophosphate, alkylphospho, alkylthiophospho, -Oalkylphospho,
• R 2 is -L 9 -(L 10 ) Z -L U -Q or
• R 4 is, at each occurrence, independently O “ , S “ , OZ, SZ or N(R 6 ) 2 , where Z is a cation and each R 6 is independently H or alkyl;
• R 5 is, at each occurrence, independently oxo, thioxo or absent;
• L 9 and L 11 are, at each occurrence, independently an optional linker
• L 10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene,
• aminoalkylene hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
• Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
• n is an integer from 1 to 20; q and w are each independently 0 or 1 for each integral value of n, wherein q is 1 for at least two integral values of n, or wherein q and w are each independently one for at least one integral value of n; and
• z is an integer from 1 to 10,
• R 2 or R 3 is -L 9 -(L 10 ) Z -L U -Q or
• R 2 or R 3 is -L 9 -(L 10 ) Z -L U -Q. In other embodiments, at least one of R 2 or R 3 is
• q is 1 and w is 0 for each integral value of n.
• the compound has the following structure (la):
• M 1 is, at each occurrence, independently a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1 is a moiety comprising four or more aryl or heteroaryl rings, or combinations thereof;
• L 1 , L 7 and L 3 are, at each occurrence, independently optional alkylene or heteroalkylene linkers
• R 1 is, at each occurrence, independently H, alkyl or alkoxy
• R 2 is an electron pair, H, alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho,
• alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, or R 2 is -L 9 -(L 10 ) Z -L U -Q or -L 9 -(L 10 ) z -L 11 -S-S-L 11 -(L 10 )z-L 9 -I, where I represents, independently, a further compound of structure (I);
• R 3 is H, OH, SH, -NH 2 , alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, cyanoalkyl, -Oaralkyl, phosphate, thiophosphate, alkylphospho, alkylthiophospho, -Oalkylphospho,
• R 2 is -L 9 -(L 10 ) Z -L U -Q or
• R 4 is, at each occurrence, independently O “ , S “ , OZ, SZ or N(R 6 ) 2 , where Z is a cation and each R 6 is independently H or alkyl;
• R 5 is, at each occurrence, independently oxo, thioxo or absent;
• L 9 and L 11 are, at each occurrence, independently an optional linker
• L 10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene,
• aminoalkylene hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
• Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule;
• n is an integer from 1 to 10;
• z is an integer from 1 to 10,
• R 2 or R 3 is -L 9 -(L 10 ) Z -L U -Q or
• the compound has the following structure
• R 7 , R 8 , R 9 , R 10 , R 11 and R 12 are, at each occurrence, independently H or alkyl;
• x 1 , y 1 and z 1 are, at each occurrence, independently an integer from 0 to
• the compound has one of the following structures (Ic), (Id), (Ie) or (If):
• w is 1 for at least one integral value of n.
• the compound has the following structure (Ig):
• R , R°, R', R , R and R iZ are, at each occurrence, independently H or alkyl
• x 1 , x 2 , y 1 , y 2 , z 1 and z 2 are, at each occurrence, independently an integer from 0 to 5.
• R is oxo and R 4 is O " or OZ.
• R 2 is H or an electron pair
• R 3 is -L 9 - (L ) Z -L -Q.
• R 2 is hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl or sulfhydrylalkylether, and R is
• R 2 has one of the following structures:
• R 2a is -OH, - H 2 , or -SH
• a is an integer from 1 to 10.
• R 3 is -L 9 -(L 10 ) Z L U -Q
• R 2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R 2 is optionally substituted with a substituent selected from -OH, - H 2 and -SH.
• R 2 has one of the followin structures:
• R a is -OH, -SH, -NH 2 , phosphate or thiophosphate
• R 4a and R 4b are independently O “ , S " , OZ or SZ, where Z is a cation;
• R 5a and R 5b are independently oxo, or thioxo
• a, b and c are each independently integers from 1 to 10
• R 2 is -L 9 -(L 10 ) Z -L U -Q, and R is OH or phosphate
• R 2 is -L 9 -(L 10 ) Z -L U -Q
• R 3 is, phosphate, thiophosphate, phospho, thiophospho, -Oalkylphospho
• R 3 has one of the followin structures:
• R a is -OH, -SH, - H 2 , phosphate or thiophosphate
• R 4a and R 4b are independently O “ , S " , OZ or SZ, where Z is a cation;
• R 5a and R 5b are independently oxo, or thioxo
• b and c are each independently integers from 1 to 10.
• R 2 is -L 9 -(L 10 ) Z -L U -Q
• R 3 is OH or phosphate
• R 4a and R 4b are each O " and R 5a and R 5b are each oxo. In some other embodiments, R 4a and R 4b are each O " and R 5a and R 5b are each thioxo. In some different embodiments, R 4a and R 4b are each S " and R 5a and R 5b are each thioxo. In more different embodiments, R 4a and R 4b are each S " and R 5a and R 5b are each oxo.
• At least one of a, b or c is 2.
• each of a, b and c is 2.
• At least one of a, b or c is 6.
• each of a, b and c is 6.
• n is an integer from 1 to 5. In some embodiments, n is an integer from 2 to 15. In some different embodiments, n is an integer from 2 to 10. In some other embodiments, n is an integer from 2 to 5.
• Still other embodiments provide a compound having the following structure (II):
• M is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
• L 1 , L 3 , and L 7 are, at each occurrence, independently optional alkylene or heteroalkylene linkers; R 1 is, at each occurrence, independently H, alkyl or alkoxy;
• R 2 is an electron pair, H, phospho, thiophospho, alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether; or R 2 is
• R 3 is H, OH, SH, -NH 2 , alkyl, alkylether, hydroxylalkyl, aminoalkyl, hydroxylalkylether, sulfhydrylalkyl, sulfyhdrylalkylether, phosphate, thiophosphate, alkylphospho, alkylthiophospho, -Oalkylphospho, -Oalkylthiophospho,
• alkyletherphospho alkyletherphospho
• alkyletherthiophospho alkyletherthiophospho
• -Oalkyletherphospho alkyletherphospho
• R 3 is -L 9 -(L 10 ) Z -L U -Q or
• R 4 is, at each occurrence, independently O “ , S “ , OZ, SZ or N(R 6 ) 2 , where Z is a cation and each R 6 is independently H or alkyl;
• R 5 is, at each occurrence, independently oxo, thioxo or absent;
• L 9 and L 11 are, at each occurrence, independently an optional linker
• L 10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene,
• aminoalkylene hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
• Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
• n is an integer from 1 to 20;
• z is an integer from 1 to 10,
• R 2 or R 3 is -L 9 -(L 10 ) Z -L U -Q or
• At least one of R 2 or R 3 is -L 9 -(L 10 ) Z -L U -Q. In different embodiments, at least one of R 2 or R 3 is-L 9 -(L 10 ) z -L 11 -S-S-L 11 -(L 10 )z-L 9 -I, where I represents, independently, a further compound of structure (I). In other embodiments of the foregoing, R 3 is -L 9 -(L 10 ) Z -L U -Q, and R 2 is an electron pair or H.
• R 3 is -L 9 -(L 10 ) Z -L U -Q
• R 2 is alkylphospho, alkylthiophospho, alkyletherphospho, alkyletherthiophospho, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether, wherein R 2 is optionally substituted with a substituent selected from -OH, - H 2 and -SH.
• R 2 has one of the following structures:
• R 2a is -OH, -SH, - H 2 , phosphate or thiophosphate
• R 4a and R 4b are independently O “ , S " , OZ or SZ, where Z is a cation; R 5a and R 5b are independently oxo, or thioxo; and
• a, b and c are each independently integers from 1 to 10.
• R 2 is -L 9 -(L 10 ) Z -L U -Q
• R 3 is OH or phosphate.
• R 2 is -L 9 -(L 10 ) Z -L U -Q
• R 3 is, phosphate, thiophosphate, phospho, thiophospho, -Oalkylphospho, -Oalkylthiophospho,
• -Ophosphoalkylether, -Othiophosphoalkyl or -Othiophosphoalkylether optionally substituted with a substituent selected from -OH, - H 2 , and -SH.
• R 3 has one of the following structures:
• R a is -OH, -SH, - H 2 , phosphate or thiophosphate
• R 4a and R 4b are independently O “ , S " , OZ or SZ, where Z is a cation; R 5a and R 5b are independently oxo, or thioxo; and
• b and c are each independently integers from 1 to 10.
• R 4 is O " and R 5 is oxo at each occurrence.
• L 1 , L 3 and L 7 are each alkylene linkers.
• L 1 and L 3 are each alkylene linkers and L 7 is absent.
• alkylene is methylene.
• M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
• R 1 is H, alkyl or alkoxy;
• R 2 is H, an electron pair or a cation; or
• R 2 is -L 9 -(L 10 ) Z -L U -Q or -L 9 -(L 10 ) z -L 11 -S-S-L 11 -(L 10 )z-L 9 -I, where I represents, independently, a further compound of structure (I);
• R 3 is H, phosphate or OH; or R 3 is -L 9 -(L 10 ) Z -L U -Q or -L 9 -(L 10 ) z -L 11 -S-S-L 11 -(L 10 )z-L 9 -I, where I represents, independently, a further compound of structure (I);
• R 4 is O " , S " , OZ, SZ where Z is a cation
• R 5 is oxo or thioxo
• R 1 , R 8°, R 9', R 10 , R 11 and R 1 i 2 Z are, at each occurrence, independently H or alkyl;
• L 9 and L 11 are, at each occurrence, independently an optional linker
• L 10 is, at each occurrence, independently a bivalent functional group selected from the group consisting of polyalkylenether, hydroxylalkylene,
• aminoalkylene hydroxylpolyalkylenether, aminopolyalkylenether, phospho, thiophospho, phosphoalkylene or thiophosphoalkylene;
• Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
• x, y and z are, at each occurrence, independently an integer from 0 to 5.
• z is an integer from 1 to 10,
• R 2 or R 3 is -L 9 -(L 10 ) Z -L U -Q or
• At least one of R 2 or R 3 is
• R 2 or R 3 is
• x, y and z are each 1.
• x is 0 and y and z are each 1.
• M 1 is generally a visually detectable moiety or substance.
• M 1 is generally a visually detectable moiety or substance.
• M 1 may be visually detectable in the UV, visible or IR spectrum.
• M 1 is, at each occurrence, independently fluorescent or colored.
• M 1 is fluorescent.
• M 1 is not a purine or pyrimidine base, such as, but not limited to guanine, cytosine, thymidine and adenine.
• M 1 is not a orphyrin. .
• M 1 is not one of the followin :
• M 1 comprises three or more aryl or heteroaryl rings, or combinations thereof, for example four or more aryl or heteroaryl rings, or combinations thereof, or even five or more aryl or heteroaryl rings, or combinations thereof.
• M 1 comprises six aryl or heteroaryl rings, or combinations thereof.
• the rings are fused.
• M 1 comprises three or more fused rings, four or more fused rings, five or more fused rings, or even six or more fused rings.
• M 1 is cyclic.
• M 1 is carbocyclic.
• M 1 is heterocyclic.
• M 1 at each occurrence, independently comprises an aryl moiety.
• the aryl moiety is multi cyclic.
• the aryl moiety is a fused-multicyclic aryl moiety, for example which may comprise at least 3, at least 4, or even more than 4 aryl rings.
• M 1 at each occurrence, independently comprises at least one heteroatom.
• the heteroatom is nitrogen, oxygen or sulfur.
• M 1 at each occurrence, independently comprises at least one substituent.
• the substituent is a fluoro, chloro, bromo, iodo, amino, alkylamino, arylamino, hydroxy, sulfhydryl, alkoxy, aryloxy, phenyl, aryl, methyl, ethyl, propyl, butyl, isopropyl, t-butyl, carboxy, sulfonate, amide, or formyl group.
• M 1 at each occurrence, independently is a dimethylaminostilbene, quinacridone, fluorophenyl- dimethyl-BODIPY, his-fluorophenyl-BODIPY, acridine, terrylene, sexiphenyl, porphyrin, benzopyrene, (fluorophenyl-dimethyl-difluorobora-diaza-indacene)phenyl, (bis-fluorophenyl-difluorobora-diaza-indacene)phenyl, quaterphenyl, bi-benzothiazole, ter-benzothiazole, bi-naphthyl, bi-anthracyl, squaraine, squarylium, 9, 10- ethynyl anthracene or ter-naphthyl moiety.
• M 1 is, at
• M 1 is, at each occurrence, independently a coumarin dye, resorufin dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, energy transfer dye, thiazole orange dye, polymethine or N-aryl-l,8-naphthalimide dye.
• M 1 at each occurrence is the same. In other embodiments, each M 1 is different. In still more embodiments, one or more M 1 is the same and one or more M 1 is different.
• M 1 is pyrene, perylene, perylene monoimide or 6- FAM or derivative thereof. In some other embodiments, M 1 has one of the following structures:
• M 2 is selected from any one of the above described M 1 moieties. In some embodiments, M 1 and M 2 are the same. In other embodiments, M 1 and M 2 are different.
• At least one occurrence of M 2 is a base pairing moiety.
• each occurrence of M 2 is a base pairing moiety.
• the base pairing moiety is a purine, a pyrimidine, a dihydropyrimidine or a derivative thereof.
• the base pairin moiety has one of the following structures:
• n is an integer from 1 to 5.
• n is an integer from 2 to 10, or 2 to 5, such as 3.
• n is 1.
• n is 2.
• n is 3.
• n is 4.
• n is 5.
• n is 6.
• n is 7.
• n is 8.
• n is 9.
• n is 10.
• methylene spacer units i.e., x, y and z
• x is 0. In other embodiments x is 1. In more embodiments, x is 2. In some embodiments x is 3. In other embodiments x is 4. In more embodiments, x is 5.
• y is 0. In other embodiments y is 1. In more embodiments, y is 2. In some embodiments y is 3. In other embodiments y is 4. In more embodiments, y is 5.
• z is 1-5. In some embodiments z is 0. In other embodiments z is 1. In more embodiments, z is 2. In some embodiments z is 3. In other embodiments z is 4. In more embodiments, z is 5.
• x is 1, y is 0 and z is 1. In other embodiments, x is 0, y is 1 and z is 1.
• L 9 is present.
• L 9 is Ci-C 6 alkylene.
• L 10 is selected from the group consisting of polyalkylenether, phospho and phosphoalkylene.
• L 10 is selected from the group consisting of:
• a is an integer from 1 to 6 and b is an integer from 2 to 10.
• (L 10 ) z has one of the following structures:
• b is an integer from 2-10, for example 5.
• L 9 and L 11 are each independently a Ci-C 6 alkylene linker. In some embodiments, L 9 is a C 2 alkylene linker. In other words,
• L 11 is a C 6 alkylene linker.
• Q is a moiety capable of bonding with an analyte molecule or a solid support.
• Q provides a means of connecting the compound of structure (I) to an analyte molecule or a solid support (e.g., by a covalent bond).
• Q is a reactive group capable of forming a covalent bond with an analyte molecule or a solid support.
• the type of Q group and connectivity of the Q group to the remainder of the compound of structure (I) is not limited.
• the Q 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).
• Q is a nucleophilic reactive group, an electrophilic reactive group or a cycloaddition reactive group.
• Q 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.
• -SH can be readily conjugated to many analyte molecules, bifinctiponal linker groups and/or solid supports (e.g., by formation of a disulfide bond with a free sulfhydryl on the analyte molecule or solid support).
• 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 2 or R 3 is -L 9 -(L 10 ) Z -L U -Q or -L 9 -(L 10 ) Z -L 11 -S-S-L 11 -(L 10 ) Z -L 9 -I, where I represents, independently, a further compound of structure (I).
• Compound of structure (I) refers to any of the compounds described herein, which are encompassed by structure (I).
• the dimer may be formed between any one of R 2 or R 3 and another one of R 2 or R 3 .
• an exemplary dimer, wherein the dimer is formed between two R 2 groups is illustrated below (la'):
• R 1 , R 3 , R 4 , R 5 , L 1 , L 3 , L 7 , L 9 , L 10 , L 11 and z are each independently as defined for any of the foregoing embodiments.
• the dimers are also illustrated as follows (la'):
• the disulfide linker between the two compounds of structure (I), i.e., -L 9 (L 10 ) Z -L 11 -S-S-L 11 -(L 10 ) Z -L 9 -, can have various structures.
• -L 9 (L 10 ) Z -L 11 -S-S-L 11 -(L 10 ) Z -L 9 - can have various structures.
• -L 9 (L 10 ) Z -L 11 -S-S-L 11 -(L 10 ) Z -L 9 - has one of the following structures:
• Q 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.
• R , R , R , R and R when present, are each H.
• x 1 , y 1 and z 1 are each 1.
• each 0 and each y 1 and z 1 are 1. In some different embodiments, each x 2 is 1 and each y 2 and z 2 are 0. Other embodiments are directed to a compound having the following structure (IV):
• M 1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
• Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
• R 20 is, at each occurrence, independently H, phosphate, alkyl substituted with phosphate, Ci-C 6 alkyl or Ci-C 6 hydroxylalkyl;
• each x', y' and z' is independently an integer from 0 to 10.
• M 1 is as defined in any one of the foregoing embodiments.
• M 1 is perylene.
• Q is as defined in any one of the foregoing embodiments.
• Q is -SH.
• each y' is 0. In some different embodiments, each z' is 1. In yet more embodiments of the foregoing, each x' is independently an integer from 2-6.
• R 20 is phosphate, -CH 2 OP03 2 - or
• M 1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
• R 20 is, at each occurrence, independently H, phosphate, alkylphosphate, Ci-C 6 alkyl or Ci-C 6 hydroxylalkyl;
• each x', y' and z' is independently an integer from 0 to 10.
• M 1 is as defined in any one of the foregoing embodiments.
• M 1 is perylene.
• each y' is 0. In some different embodiments, each z' is 1. In yet more embodiments of the foregoing, each x' is independently an integer from 2-6.
• R 20 is phosphate, CH 2 OP0 3 2" or
• the disulfide dimer has the following structure:
• M 1 has the following structure:
• M 1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
• Q is a moiety capable of bonding with an analyte molecule or a solid support; or Q is an analyte molecule or solid support;
• R 20 is, at each occurrence, independently H, phosphate, alkyl substituted with phosphate, Ci-C 6 alkyl or Ci-C 6 hydroxylalkyl;
• each x', y' and z' is, at each occurrence, independently an integer from 0 to 10.
• M 1 is as defined in any one of the foregoing embodiments.
• M 1 is perylene.
• Q is as defined in any one of the foregoing embodiments.
• Q is -SH.
• each y' is 0. In some different embodiments, each z' is 1. In yet more embodiments of the foregoing, each x' is independently an integer from 2-6.
• R 20 is phosphate, CH 2 OPO 3 2" or
• the compound has the following structure:
• M 1 has the following structure:
• M 1 is a moiety comprising two or more double bonds and at least one degree of conjugation, and at least one occurrence of M 1 is a moiety comprising three or more aryl or heteroaryl rings, or combinations thereof;
• R 20 is, at each occurrence, independently H, phosphate, alkyl substituted with phosphate, Ci-C 6 alkyl or Ci-C 6 hydroxylalkyl;
• each x', y' and z' is, at each occurrence, independently an integer from 0 to 10.
• M 1 is as defined in any one of the foregoing embodiments.
• M 1 is perylene.
• each y' is 0. In some different embodiments, each z' is 1. In yet more embodiments of the foregoing, each x' is independently an integer from 2-6.
• R 20 is phosphate, CH 2 OPO 3 2" or
• the disulfide dimer has the following structure:
• M 1 has the following structure:
• compositions comprising any of the foregoing compounds and one or more biomolecules are provided in various other embodiments. In some embodiments, use of such compositions in analytical methods for detection of the one or more biomolecules are also provided.
• 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), wherein R 2 is -L 9 -(L 10 ) Z -L U -Q, Q is a moiety capable of bonding with an analyte molecule and R 3 is H, OH, phosphate, thiophosphate, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether in an amount sufficient to produce an optical response when said sample is illuminated at an appropriate wavelength.
• R 2 is a linker comprising a covalent linkage to a biomolecule.
• a biomolecule for example, 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.
• R 2 comprises a linker comprising a covalent linkage to 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 a biomolecule, comprising:
• Q is a moiety capable of bonding with the biomolecule and R 3 is H, OH, phosphate, thiophosphate, phosphoalkyl, phosphoalkylether, thiophosphoalkyl or thiophosphoalkylether;
• 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:
• any embodiment of the compounds of structure (I), as set forth above, and any specific choice set forth herein for a R 1 , R 2 , R 3 , R 4 , R 5 , L 1 , L 3 , L 4 , L 6 , L 7 , L 8 , M 1 , M 2 , q, w and n variable in the compounds of structure (I), as set forth above, may be independently combined with other embodiments and/or variables of the compounds of structure (I) to form embodiments of the inventions not specifically set forth above.
• 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.
• Reaction Scheme I illustrates and exemplary method for preparing compounds of structure I.
• R 2 ' and R 3 represent R 2 and R 3 moieties as defined herein, or precursors to R 2 and R 3 moieties or protected derivatives thereof which can be converted to the desired R 2 and R 3 moieties using techniques known in the art and provided in the examples below.
• compounds of structure a can be purchased or prepared by methods well-known to those of ordinary skill in the art.
• Reaction of a with M x -X, where x is a halogen such as bromo under Suzuki coupling conditions known in the art results in compounds of structure b.
• Compounds of structure b can be modified to obtain number of other compounds of structure I.
• compounds of structure b can be oligomerized to obtain other compounds of structure I (i.e., where n is greater than 1, such as 2-10).
• Exemplary methods for oligomerization include methods analogous to phosphoramadite-based solid-phase oligonucleotide synthesis, which is well known in the art.
• Reaction Scheme II illustrates an alternative method for preparation of compounds of structure I.
• R 2 ' and R 3 represent R 2 and R 3 moieties as defined herein, or precursors to R 2 and R 3 moieties or protected derivatives thereof which can be converted to the desired R 2 and R 3 moieties using techniques known in the art and provided in the examples below.
• a compound of structure c which can be purchased or prepared by well-known techniques, is reacted with M -Z to yield compounds of structure d.
• Y and Z represent function groups having
• Z may be pendant to M 1 or a part of the structural backbone of M, for example a cyclic anhydride.
• Y may be any number of functional groups, such as amino.
• the compounds of structure I are oligomers comprising from 2-10 repeating units.
• Such oligomers can be prepared using methods analogous to well-known automated DNA synthesis methods. 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
• DMT dimethoxytrityl
• 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.
• Preparation of the phosphoramidites used in the oligomerization methods is also well-known in the art.
• a primary alcohol e.g., R 3
• a secondary alcohol e.g., R 2
• R 3 a primary alcohol
• R 2 a secondary alcohol
• R 2 is then functionalized as a phosphoramidite by reaction with an appropriate reagent such as 2-cyanoethyl ⁇ , ⁇ -dissopropylchlorophosphoramidite.
• 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 CI 8 column (4.6mm x 100mm, 5 ⁇ particle size). Excitation and emission profiles experiments were recorded on a Cary Eclipse spectra photometer.
• oligomer 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 oligomers was the following: (i) detritylation, 3% trichloroacetic acid 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/pyridine/water, 10/10/1, v/v/v, 30 s.
• Example 1 exemplifies a water soluble dye substance, modified to contain an activated ester group (2 and 3), which can be conjugated to macromolecules having primary amine functional groups.
• a dye sequence (1) containing a disulfide linker is reduced with tris(2-carboxyethyl)phosphine (TCEP) to release two smaller dye sequences, each with a Fluor and a free thiol terminus.
• TCEP tris(2-carboxyethyl)phosphine
• ecoMPOUND 1 38.000 M-l cm-1
• VCOMPOUND I 3.88 mL
• Equation 3 was used to calculate the moles of TCEP required to achieve a 11.3 : 1 molar ratio of TCEP to COMPOUND 1.
• the HC1 salt of TCEP is acidic and reduction of the COMPOUND 1 needs to occur at slightly acidic to neutral pH (e.g. pH 6-7).
• the NaP0 4 buffer should be in approximately 5-fold or higher molar excess maintain a pH of 6.5. Since the molarity of 0.6 M NaP0 4 stock solution is 5.45-fold higher than the 0.111 M TCEP stock solution, an equal volume of the stock added to TCEP is sufficient to buffer the reaction.
• COMPOUND 1 products There are two reduced COMPOUND 1 products: the 5'-ECC-SH species which has an expected mass of 785 Daltons and the HS-CCE-3 ' species which has an expected mass of 865 Daltons.
• o A 0.1 M TEAA, 5% methanol in H 2 0
• a water soluble dye with a functional maleimide group was synthesized by reacting a water soluble dye containing a terminal primary amine (compound 4) with the N-Hydroxysuccinimidyl group of Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-l-carboxylate (Sulfo-SMCC).
• Sulfo-SMCC 2.765 ml of Sulfo-SMCC.
• Sulfo-SMCC is acidic and addition of the compound 4 should occur at slightly basic to neutral pH (e.g. pH 7.5-8.5).
• the NaP0 4 buffer should be
• the pH of the reaction was approximately 7.5 using litmus paper.
• Compound 5 was purified to an overall purity of 78% from the crude reaction mixture as follows:

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