POLYMERIC DYES HAVING A BACKBONE COMPRISING ORGANOPHOSPHATE UNITS
BACKGROUND

Technical Field

The present invention is generally directed to polymeric fluorescent or colored dyes, and methods for their preparation and use in various analytical methods.

Description of the Related Art

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. Since analysis of biomolecules typically occurs in an aqueous environment, the focus has been on development and use of water soluble dyes.

Highly fluorescent or colored dyes are desirable since use of such dyes increases the signal to noise ratio and provides other related benefits. Accordingly, attempts have been made to increase the signal from known fluorescent and/or colored moieties. For example, dimeric and polymeric compounds comprising two or more fluorescent and/or colored moieties have been prepared in anticipation that such compounds would result in brighter dyes. However, as a result of intramolecular fluorescence quenching, the known dimeric and polymeric dyes have not achieved the desired increase in brightness.

There is thus a need in the art for dyes having an increased molar brightness. Ideally, such dyes and biomarkers should be intensely colored or fluorescent and should be available in a variety of colors and fluorescent wavelengths. The present invention fulfills this need and provides further related advantages.

BRIEF SUMMARY

In brief, embodiments of the present invention are generally directed to compounds useful as water soluble, fluorescent and/or colored dyes and/or probes that enable visual detection of analyte molecules, such as biomolecules, as well as reagents for their preparation. Methods for visually detecting analyte molecules using the dyes are also described.

Embodiments of the presently disclosed dyes include two or more fluorescent and/or colored moieties covalently linked by linkers ( e.g ., Lla, Llb, L2, L3, L4, L5, L6 and L7). In contrast to previous reports of dimeric and/or polymeric dyes, the present dyes are significantly brighter than the corresponding monomeric dye compound. While, not wishing to be bound by theory, it is believed that the linker moiety provides sufficient spatial separation between the fluorescent and/or colored moieties such that intramolecular fluorescence quenching is reduced and/or eliminated.

The water soluble, fluorescent or colored dyes of embodiments 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 analyte molecules of a variety of colors may be obtained.

In one embodiment, compounds having the following structure (I) are provided:

or a stereoisomer, tautomer or salt thereof, wherein R1, R2, R3, R4, R5, Lla, Llb, L2, L3, L4, L5, L6, L7, M1, M2, q, w, m and n are as defined herein. Compounds of structure (I) find utility in a number of applications, including use as fluorescent and/or colored dyes in various analytical methods.

In another embodiment, a method for staining a sample is provided, the method comprises 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.

In still other embodiments, the present disclosure provides a method for visually detecting an analyte molecule, comprising:

(a) providing a compound of structure (I); and

(b) detecting the compound by its visible properties.

Other disclosed methods include a method for visually detecting a biomolecule, the method comprising:

(a) admixing a compound of structure (I) with one or more biomolecules; and

(b) detecting the compound by its visible properties.

Other embodiments provide a method for visually detecting an analyte, the method comprising:

(a) providing a compound as disclosed herein, wherein R1 or R2 comprises a linker comprising a covalent bond to a targeting moiety having specificity for the analyte;

(b) admixing the compound and the analyte, thereby associating the targeting moiety and the analyte; and

(c) detecting the compound by its visible properties.

Other embodiments are directed to a composition comprising a compound of structure (I) and one or more analyte molecule, such as a biomolecule.

Use of such compositions in analytical methods for detection of the one or more biomolecules is also provided.

These and other aspects of the invention will be apparent upon reference to the following detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

In the figures, identical reference numbers identify similar elements.

The sizes and relative positions of elements in the figures are not necessarily drawn to scale and some of these elements are enlarged and positioned to improve figure legibility. Further, the particular shapes of the elements as drawn are not intended to convey any information regarding the actual shape of the particular elements, and have been solely selected for ease of recognition in the figures.

FIG. 1 shows fluorescence intensity for an polymer compound comprising Alexa Fluor 488 moieties (3c, 5x and lOx, respectively).

FIGS. 2A-B show spectral intensity and a PAGE readout for Alexa Fluor 350 moieties (3c, 5 and lOx, respectively).

FIGS. 3 A-B depict spectral intensity and a PAGE readout for Pacific Orange moieties (3c, 5 and lOx, respectively); the PAGE readout provides a comparison to fluorescein.

FIG. 4 illustrates a comparison between polymer compounds comprising fluorescein and Alexa Fluor 700 (each at 3x, 5 and lOx) using 254 nm, 365 nm and white light, respectively.

FIG. 5 shows representative flow cytometry readouts for samples prepared with a conjugates of UCHT-l and Pacific Orange or Compound 1-4 having a degree of labeling ("DOL") ranging from 3.3 to 4.76.

FIG. 6 is a plot of the stain index against the micrograms per test for a sample prepared using a Pacific Orange control and Compound 1-4 having a DOL ranging from 3.3 to 4.76.

FIG. 7 shows populations of granulocytes, monocytes and lymphocytes and a representative plotting of signal to noise.

FIG. 8 illustrates the stain index correlation to a signal to noise reading for samples prepared using Compound 1-4 (calculated from readings shown in FIG. 5).

FIG. 9 shows an average stain index for samples prepared with

Compound 1-4 with DOL ranging from 3.3 to 4.76 compared to samples prepared with Pacific Orange alone.

FIG. 10 is a plot of noise for samples prepared using Pacific Orange compared to Compound 1-4 with DOL ranging from 3.3 to 4.76.

FIG. 11 is a plot of signal for samples prepared with Pacific Orange compared to Compound 1-4 with DOL ranging from 3.3 to 4.76.

FIG. 12 shows flow cytometry readouts for samples prepared with a conjugates of UCHT-l and Alexa Fluor 488 and Compound 1-5 having a DOL ranging from 3.46 to 4.40.

FIG. 13 is a plot of the stain index against the micrograms per test for an samples prepared with Alexa Fluor 488 alone and Compound 1-5 having a DOL ranging from 3.46 to 4.40.

FIG. 14 illustrates the stain index correlation to a signal to noise reading for samples prepared using Compound 1-5 (calculated from readings shown in FIG. 5).

FIG. 15 is a plot of the stain index against the micrograms per test for samples prepared with Alexa Fluor 488 alone versus Compound 1-5 having a DOL ranging from 3.46 to 4.40.

FIG. 16 is a plot of noise for samples prepared using Alexa Fluor 488 compared to Compound 1-5 with DOL ranging from 3.3 to 4.76.

FIG. 17 is a plot of signal for samples prepared with Alexa Fluor 488 compared to Compound 1-5 with DOL ranging from 3.3 to 4.76.

FIG. 18 depicts flow cytometry data acquired from samples prepared with conjugates of UCHT-l and Compound 1-6 having a DOL ranging from 3.54 to 4.6.

FIG. 19 shows flow cytometry readouts for samples prepared with conjugates of UCHT-l and Alexa Fluor 350, Compound 1-1, Compound 1-2 and Compound 1-6 having a DOL of 3.54, respectively.

FIG. 20 shows a plot of stain index against micrograms per test for samples prepared with Alexa Fluor 350 control and Compound 1-6 having a DOL ranging from 3.54 to 4.6.

FIG. 21 shows a plot of average stain index against micrograms per test for samples prepared with Compound 1-6 having a DOL ranging from 3.54 to 4.6, Compound 1-2 having a DOL ranging from 3.05 to 3.31, Compound 1-1 having a DOL ranging from 3.28 to 3.57 and a control sample of Alexa Fluor 350 alone.

FIG. 22 shows a plot of stain index correlated to a signal to noise reading for samples prepared with Compound 1-6 (calculated from readings shown in FIG. 18).

FIG. 23 shows noise for samples prepared using Compound 1-6,

Compound 1-2, Compound 1-1 and Alexa Fluor 350, respectively.

FIG. 24 shows signal for samples prepared using Compound 1-6, Compound 1-2, Compound 1-1 and Alexa Fluor 350, respectively.

FIG. 25 shows additional representative flow cytometry readouts for samples prepared with a conjugates of UCHT-l and Pacific Orange or Compound 1-4 having a DOL ranging from 3.3 to 4.76.

FIG. 26 is an additional representative plot of the stain index against the micrograms per test for a Pacific Orange control and Compound 1-4 having a DOL ranging from 3.3 to 4.76.

FIG. 27 illustrates the stain index correlation to a signal to noise reading for Compound 1-4 (calculated from readings shown in FIG. 25).

DETAILED DESCRIPTION

In the following description, certain specific details are set forth in order to provide a thorough understanding of various embodiments of the invention.

However, one skilled in the art will understand that the invention may be practiced without these details.

Unless the context requires otherwise, throughout the present specification and claims, the word "comprise" and variations thereof, such as,

"comprises" and "comprising" are to be construed in an open, inclusive sense, that is, as "including, but not limited to".

Reference throughout this specification to "one embodiment" or "an embodiment" means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Thus, the appearances of the phrases "in one embodiment" or "in an embodiment" in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics may be combined in any suitable manner in one or more embodiments.

"Amino" refers to the -NH2 group.

"Carboxy" refers to the -C02H group.

"Cyano" refers to the -CN group.

"Formyl" refers to the -C(=0)H group.

"Hydroxy" or "hydroxyl" refers to the -OH group.

"Imino" refers to the =NH group.

"Nitro" refers to the -N02 group.

"Oxo" refers to the =0 group.

"Sulfhydryl" refers to the -SH group.

"Thioxo" refers to the =S group.

"Alkyl" refers to a straight or branched hydrocarbon chain group consisting solely of carbon and hydrogen atoms, containing no unsaturation, having from one to twelve carbon atoms (C|-C | 2 alkyl), one to eight carbon atoms (Ci-C8 alkyl) or one to six carbon atoms (Ci-C6 alkyl), and which is attached to the rest of the molecule by a single bond, e.g ., methyl, ethyl, «-propyl, l-methylethyl (Ao-propyl), «-butyl, «-pentyl, l,l-dimethylethyl (/-butyl), 3-methylhexyl, 2-methylhexyl, and the like. Unless stated otherwise specifically in the specification, alkyl groups are optionally substituted.

"Alkylene" or "alkylene chain" refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing no unsaturation, 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 bond and to the radical group through a single bond. The points of attachment of the alkylene chain to the rest of the molecule and to the radical group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, alkylene is optionally substituted.

"Alkenylene" or "alkenylene chain" refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing at least one carbon-carbon double bond and having from two to twelve carbon atoms, e.g. , ethenylene, propenylene, «-butenylene, and the like. The alkenylene chain is attached to the rest of the molecule through a single bond and to the radical group through a double bond or a single bond. The points of attachment of the alkenylene chain to the rest of the molecule and to the radical group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, alkenylene is optionally substituted.

"Alkynylene" or "alkynylene chain" refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing at least one carbon-carbon triple bond and having from two to twelve carbon atoms, e.g. , ethenylene, propenylene, «-butenylene, and the like. The alkynylene chain is attached to the rest of the molecule through a single bond and to the radical group through a double bond or a single bond. The points of attachment of the alkynylene chain to the rest of the molecule and to the radical group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, alkynylene 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-carbon bond. The carbon-oxygen-carbon 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-carbon bond, but may include more than one. For example, polyethylene glycol (PEG) is included within the meaning of alkylether. Unless stated otherwise specifically in the specification, an alkylether group is optionally substituted. For example, in some embodiments an alkylether is substituted with an alcohol or

-OP(=Ra)(Rb)Rc, wherein each of Ra, Rb and Rc is as defined for compounds of structure (I).

"Alkoxy" refers to a group of the formula -ORa where Ra is an alkyl group as defined above containing one to twelve carbon atoms. Unless stated otherwise specifically in the specification, an alkoxy group is optionally substituted.

"Alkoxyalkylether" refers to a group of the formula -ORaRb where Ra is an alkylene group as defined above containing one to twelve carbon atoms, and Rb is an alkylether group as defined herein. Unless stated otherwise specifically in the specification, an alkoxyalkylether group is optionally substituted, for example substituted with an alcohol or -OP(=Ra)(Rb)Rc, wherein each of Ra, Rb and Rc is as defined for compounds of structure (I).

"Heteroalkyl" refers to an alkyl group, as defined above, comprising at least one heteroatom ( e.g ., N, O, P or S) within the alkyl group or at a terminus of the alkyl group. In some embodiments, the heteroatom is within the alkyl group (i.e., the heteroalkyl comprises at least one carbon-[heteroatom]x-carbon bond, where x is 1, 2 or 3). In other embodiments, the heteroatom is at a terminus of the alkyl group and thus serves to join the alkyl group to the remainder of the molecule (e.g., Ml-H-A), where

Ml is a portion of the molecule, H is a heteroatom and A is an alkyl group). Unless stated otherwise specifically in the specification, a heteroalkyl group is optionally substituted. Exemplary heteroalkyl groups include ethylene oxide (e.g, polyethylene oxide), optionally including phosphorous-oxygen bonds, such as phosphodiester bonds. "Heteroalkoxy" refers to a group of the formula -ORa where Ra is a heteroalkyl group as defined above containing one to twelve carbon atoms. ETnless stated otherwise specifically in the specification, a heteroalkoxy group is optionally substituted.

"Heteroalkylene" refers to an alkylene group, as defined above, comprising at least one heteroatom ( e.g ., Si, N, O, P or S) within the alkylene chain or at a terminus of the alkylene chain. In some embodiments, the heteroatom is within the alkylene chain (i.e., the heteroalkylene comprises at least one carbon-[heteroatom]-carbon bond, where x is 1, 2 or 3). In other embodiments, the heteroatom is at a terminus of the alkylene and thus serves to join the alkylene to the remainder of the molecule (e.g., M1-H-A-M2, where Ml and M2 are portions of the molecule, H is a heteroatom and A is an alkylene). ETnless stated otherwise specifically in the specification, a heteroalkylene group is optionally substituted. Exemplary

heteroalkylene groups include ethylene oxide (e.g, polyethylene oxide) and the "C," "HEG," and "PEG 1K" linking groups illustrated below:

'PEG 1K linker’

Multimers of the above C-linker, HEG linker and/or PEG 1K linker are included in various embodiments of heteroalkylene linkers. In some embodiments of the PEG 1K linker, n ranges from 19-25, for example n is 19, 20, 21, 22, 23, 24, or 25. Multimers may comprise, for example, the following structure:

wherein x is 0 or an integer greater than 0, for example, x ranges from 0-100 ( e.g ., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10).

"Heteroalkenylene" is a heteroalkylene, as defined above, comprising at least one carbon-carbon double bond. Unless stated otherwise specifically in the specification, a heteroalkenylene group is optionally substituted.

"Heteroalkynylene" is a heteroalkylene comprising at least one carbon-carbon triple bond. Unless stated otherwise specifically in the specification, a heteroalkynylene group is optionally substituted.

"Heteroatomic" in reference to a "heteroatomic linker" refers to a linker group consisting of one or more heteroatoms. Exemplary heteroatomic linkers include single atoms selected from the group consisting of O, N, P and S, and multiple heteroatoms for example a linker having the formula -P(0-)(=0)0- or -0P(0-)(=0)0-and multimers and combinations thereof.

"Phosphate" refers to the -OP(=0)(Ra)Rb group, wherein Ra is OH, O- or ORc; and R¾ is OH, O-, ORc, a thiophosphate group or a further phosphate group, wherein Re is a counter ion (e.g., Na+ and the like).

"Phosphoalkyl" refers to the -OP(=0)(Ra)Rb group, wherein Ra is OH,

O- or ORc; and Rb is -Oalkyl, wherein Rc is a counter ion (e.g, Na+ and the like).

Unless stated otherwise specifically in the specification, a phosphoalkyl group is optionally substituted. For example, in certain embodiments, the -Oalkyl moiety in a phosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl,

phosphoalkylether, thiophosphoalkylether or -OP(=Ra)(Rb)Rc, wherein each of Ra, Rb and Rc is as defined for compounds of structure (I).

"Phosphoalkylether" refers to the -OP(=0)(Ra)Rb group, wherein Ra is OH, O- or ORc; and Rb is -Oalkylether, wherein Rc is a counter ion (e.g, Na+ and the like). Unless stated otherwise specifically in the specification, a phosphoalkylether

group is optionally substituted. For example, in certain embodiments, the -Oalkylether moiety in a phosphoalkylether group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl,

thiophosphoalkyl, phosphoalkylether, thiophosphoalkylether or -OP(=Ra)(Rb)Rc, wherein each of Ra, Rb and Rc is as defined for compounds of structure (I).

"Thiophosphate" refers to the -OP(=Ra)(Rb)Rc group, wherein Ra is O or S, Rb is OH, O-, S-, ORd or SRd; and Rc is OH, SH, O-, S-, ORd, SRd, a phosphate group or a further thiophosphate group, wherein Rd is a counter ion (e.g, Na+ and the like) and provided that: i) Ra is S; ii) Rb is S- or SR¾ iii)Rc is SH, S- or SR¾ or iv) a combination of i), ii) and/or iii).

"Thiophosphoalkyl" refers to the -OP(=Ra)(Rb)Rc group, wherein Ra is O or S, Rb is OH, O-, S-, ORd or SRd; and Rc is -Oalkyl, wherein Rd is a counter ion (e.g, Na+ and the like) and provided that: i) Ra is S; ii) Rb is S- or SRd; or iii)Ra is S and Rb is S- or SRd. Unless stated otherwise specifically in the specification, a thiophosphoalkyl group is optionally substituted. For example, in certain embodiments, the -Oalkyl moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl,

thiophosphoalkyl, phosphoalkylether, thiophosphoalkylether or -OP(=Ra)(Rb)Rc, wherein each of Ra, Rb and Rc is as defined for compounds of structure (I).

"Thiophosphoalkylether" refers to the -OP(=Ra)(Rb)Rc group, wherein Ra is O or S, Rb is OH, O-, S-, ORd or SRd; and Rc is -Oalkylether, wherein Rd is a counter ion (e.g, Na+ and the like) and provided that: i) Ra is S; ii) Rb is S- or SR¾ or iii)Ra is S and Rb is S- or SRd. Unless stated otherwise specifically in the specification, a thiophosphoalkylether group is optionally substituted. For example, in certain embodiments, the -Oalkylether moiety in a thiophosphoalkyl group is optionally substituted with one or more of hydroxyl, amino, sulfhydryl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether, thiophosphoalkylether or

-OP(=Ra)(Rb)Rc, wherein each of Ra, Rb and Rc is as defined for compounds of structure

(I)·

"Carbocyclic" refers to a stable 3- to l8-membered aromatic or non-aromatic ring comprising 3 to 18 carbon atoms. Unless stated otherwise specifically in the specification, a carbocyclic ring may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems, and may be partially or fully saturated. Non-aromatic carbocyclyl radicals include cycloalkyl, while aromatic carbocyclyl radicals include aryl. Unless stated otherwise specifically in the specification, a carbocyclic 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 cyclocalkyls include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. Polycyclic cycloalkyls include, for example, adamantyl, norbornyl, decalinyl, 7,7-dimethyl-bicyclo-[2.2. l]heptanyl, and the like. Unless stated otherwise specifically in the specification, a cycloalkyl group is optionally substituted.

"Aryl" refers to a ring system comprising at least one carbocyclic aromatic ring. In some embodiments, an aryl comprises from 6 to 18 carbon atoms.

The aryl ring may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems. Aryls include, but are not limited to, aryls derived from aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, chrysene, fluoranthene, fluorene, as-indacene, s-indacene, indane, indene, naphthalene, phenalene, phenanthrene, pleiadene, pyrene, and triphenylene. Unless stated otherwise specifically in the specification, an aryl group is optionally substituted.

"Heterocyclic" refers to a stable 3- to l8-membered aromatic or non-aromatic ring comprising one to twelve carbon atoms and from one to six heteroatoms selected from the group consisting of nitrogen, oxygen and sulfur. Unless stated otherwise specifically in the specification, the heterocyclic ring 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 heterocyclic ring may be optionally oxidized; the nitrogen atom may be optionally quaternized; and the heterocyclic ring may be partially or fully saturated. Examples of aromatic heterocyclic rings are listed below in the definition of heteroaryls (i.e., heteroaryl being a subset of heterocyclic). Examples of non-aromatic heterocyclic rings 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, pyrazolopyrimidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trioxanyl, trithianyl, triazinanyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl,

l-oxo-thiomorpholinyl, and l,l-dioxo-thiomorpholinyl. ETnless stated otherwise specifically in the specification, a heterocyclic group is optionally substituted.

"Heteroaryl" refers to a 5- to l4-membered ring system 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. For purposes of certain embodiments of this invention, the heteroaryl radical 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 radical may be optionally oxidized; the nitrogen atom may be optionally quaternized. Examples include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzthiazolyl, benzindolyl, benzodioxolyl, benzofuranyl, benzooxazolyl, benzothiazolyl, benzothiadiazolyl, benzo[b][l,4]dioxepinyl, l,4-benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl), benzotriazolyl,

benzo[4,6]imidazo[l,2-a]pyridinyl, benzoxazolinonyl, benzimidazolthionyl, carbazolyl, cinnolinyl, dibenzofuranyl, dibenzothiophenyl, furanyl, furanonyl, isothiazolyl, imidazolyl, indazolyl, indolyl, indazolyl, isoindolyl, indolinyl, isoindolinyl, isoquinolyl, indolizinyl, isoxazolyl, naphthyridinyl, oxadiazolyl, 2-oxoazepinyl, oxazolyl, oxiranyl, l-oxidopyridinyl, l-oxidopyrimidinyl, l-oxidopyrazinyl, l-oxidopyridazinyl,

1 -phenyl- lH-pyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl,

pteridinyl, pteridinonyl, purinyl, pyrrolyl, pyrazolyl, pyridinyl, pyridinonyl, pyrazinyl, pyrimidinyl, pryrimidinonyl, pyridazinyl, pyrrolyl, pyrido[2,3-d]pyrimidinonyl, quinazolinyl, quinazolinonyl, quinoxalinyl, quinoxalinonyl, quinolinyl, isoquinolinyl, tetrahydroquinolinyl, thiazolyl, thiadiazolyl, thieno[3,2-d]pyrimidin-4-onyl, thieno[2,3-d]pyrimidin-4-onyl, triazolyl, tetrazolyl, triazinyl, and thiophenyl (i.e. thienyl). Unless stated otherwise specifically in the specification, a heteroaryl group is optionally substituted.

The suffix "-ene" refers to a particular structural feature (e.g, alkyl, aryl, heteroalkyl, heteroaryl) attached to the rest of the molecule through a single bond and attached to a radical group through a single bond. In other words, the suffix "-ene" refers to a linker having the structural features of the moiety to which it is attached.

The points of attachment of the "-ene" chain to the rest of the molecule and to the radical group can be through one atom of or any two atoms within the chain. For example, a heteroarylene refers to a linker comprising a heteroaryl moiety as defined herein.

"Fused" refers to a ring system comprising at least two rings, wherein the two rings share at least one common ring atom, for example two common ring atoms. When the fused ring is a heterocyclyl ring or a heteroaryl ring, the common ring atom(s) may be carbon or nitrogen. Fused rings include bicyclic, tricyclic, tertracyclic, and the like.

The term "substituted" used herein means any of the above groups (e.g, alkyl, alkylene, alkenylene, alkynylene, heteroalkyl ene, heteroalkenylene,

heteroalkynylene, alkoxy, alkylether, phosphoalkyl, phosphoalkylether,

thiophosphoalkyl, thiophosphoalkylether, carbocyclic, cycloalkyl, aryl, heterocyclic and/or heteroaryl) wherein at least one hydrogen atom (e.g, 1, 2, 3 or all hydrogen atoms) is replaced by a bond to a non-hydrogen atoms such as, but not limited to: a halogen atom such as F, Cl, 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, dialkylarylsilyl groups, alkyldiarylsilyl groups, and triarylsilyl groups; and other heteroatoms in various other 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. For example, "substituted" includes any of the above groups in which one or more hydrogen atoms are replaced with -NRgRh,

-NRgC(=0)Rh, -NRgC(=0)NRgRh, -NRgC(=0)0Rh, -NRgS02Rh, -0C(=0)NRgRh, -ORg, -SRg, -SORg, -S02Rg, -0S02Rg, -S020Rg, =NS02Rg, and -S02NRgRh.

"Substituted also means any of the above groups in which one or more hydrogen atoms are replaced with -C(=0)Rg, -C(=0)0Rg, -C(=0)NRgRh, -CH2S02Rg,

-CH2S02NRgRh. In the foregoing, Rg and Rh are the same or different and

independently hydrogen, alkyl, alkoxy, alkylamino, thioalkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, haloalkyl, heterocyclyl, /V-heterocyclyl, heterocyclylalkyl, heteroaryl, A-heteroaryl and/or heteroaryl alkyl. "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, /V-heterocyclyl, heterocyclylalkyl, heteroaryl, /V-heteroaryl and/or heteroarylalkyl group. In addition, 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 sigma bond. For example, 1, 3-butadiene 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.

"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.

The term "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. In some embodiments of the disclosure, exemplary conjugates (e.g., compounds of structure (I) having a biomolecule linked thereto) are prepared, as further described herein, by contacting a biomolecule with a compound having a reactive 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.

A "reactive group" is a moiety capable of reacting with a second reactive groups (e.g, a "complementary reactive group") to form one or more covalent bonds, for example by a displacement, oxidation, reduction, addition or cycloaddition reaction. Exemplary reactive groups are provided in Table 1, and include for example, nucleophiles, electrophiles, dienes, dienophiles, aldehyde, oxime, hydrazone, alkyne, amine, azide, acylazide, acylhalide, nitrile, nitrone, sulfhydryl, disulfide, sulfonyl halide, isothiocyanate, imidoester, activated ester, ketone, a,b-unsaturated carbonyl, alkene, maleimide, a-haloimide, epoxide, aziridine, tetrazine, tetrazole, phosphine, biotin, thiirane and the like.

"Bio-conjugation" or "bio-conjugate" and related variations refer to a chemical reaction strategy for forming a stable covalent bond between two molecules. The term "bio-conjugation" is generally used when one of the molecules is a

biomolecule ( e.g ., an antibody), but can be used to describe forming a covalent bond with a non-biomolecule (e.g., a polymeric resin). The product or compound resulting from such a reaction strategy is a "conjugate," "bio-conjugate" or a grammatical equivalent.

The terms "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 compounds 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.

For purposes of embodiments of this disclosure, 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. Preferably, 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. Non-limiting 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.

As used herein, the term "perylene derivative" is intended to include any substituted perylene that is visually detectable. However, the term is not intended to include perylene itself. The terms "anthracene derivative", "naphthalene derivative", and "pyrene derivative" are used analogously. In some preferred embodiments, a derivative ( e.g ., perylene, pyrene, anthracene or naphthalene derivative) is an imide, bisimide or hydrazamimide derivative of perylene, anthracene, naphthalene, or pyrene.

The visually detectable molecules of various embodiments of the invention are useful for a wide variety of analytical applications, such as biochemical and biomedical applications, in which there is a need to determine the presence, location, or quantity of a particular analyte (e.g., biomolecule). In another aspect, therefore, 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. For purposes of the invention, 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. For example, 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. As used herein, the term "biological

system" is used to refer to any solution or mixture comprising one or more

biomolecules in addition to the visually detectable biomolecule. Nonlimiting examples of such biological systems include cells, cell extracts, tissue samples, electrophoretic gels, assay mixtures, and hybridization reaction mixtures.

"Solid support" or "solid support residue" refers to any solid substrate known in the art for solid-phase support of molecules, for example a "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, non-polymeric beads, and the like. In certain embodiments, a microparticle comprises polystyrene beads.

A "targeting moiety" is a moiety that selectively binds or associates with a particular target, such as an analyte molecule. "Selectively" binding or associating means a targeting moiety preferentially associates or binds with the desired target relative to other targets. In some embodiments the compounds disclosed herein include linkages to targeting moieties for the purpose of selectively binding or associating the compound with an analyte of interest (i.e., the target of the targeting moiety), thus allowing detection of the analyte. Exemplary targeting moieties include, but are not limited to, antibodies, antigens, nucleic acid sequences, enzymes, proteins, cell surface receptor antagonists, and the like. In some embodiments, the targeting moiety is a moiety, such as an antibody, that selectively binds or associates with a target feature on or in a cell, for example a target feature on a cell membrane or other cellular structure, thus allowing for detection of cells of interest. Small molecules that selectively bind or associate with a desired analyte are also contemplated as targeting moieties in certain embodiments. One of skill in the art will understand other analytes, and the

corresponding targeting moiety, that will be useful in various embodiments.

"Base pairing moiety" refers to a heterocyclic moiety capable of hybridizing with a complementary heterocyclic moiety via hydrogen bonds ( e.g ., Watson-Crick base pairing). 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.

Embodiments disclosed herein are also meant to encompass all compounds being isotopically-labelled by having one or more atoms replaced by an atom having a different atomic mass or mass number. Examples of isotopes that can be incorporated into the disclosed compounds include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine, and iodine, such as 2H, 3H, UC, 13C, 14C, 13N, 15N, 150, 170, 180, 31P, 32P, 35S, 18F, 36Cl, 123I, and 125I, 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.

"Stable 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.

"Optional" or "optionally" means that the subsequently described event or circumstances may or may not occur, and that the description includes instances where said event or circumstance occurs and instances in which it does not. For example, "optionally substituted alkyl" means that the alkyl group may or may not be substituted and that the description includes both substituted alkyl groups and alkyl groups having no substitution.

"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- lO-sulfonic acid, capric acid, caproic acid, caprylic acid, carbonic acid, cinnamic acid, citric acid, cyclamic acid, dodecylsulfuric acid, ethane- l,2-disulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, formic acid, fumaric acid, galactaric acid, gentisic acid, glucoheptonic acid, gluconic acid, glucuronic acid, glutamic acid, glutaric acid, 2-oxo-glutaric acid, glycerophosphoric acid, glycolic acid, hippuric acid, isobutyric acid, lactic acid, lactobionic acid, lauric acid, maleic acid, malic acid, malonic acid, mandelic acid, methanesulfonic acid, mucic acid,

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, p-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.

Crystallizations may produce a solvate of the compounds described herein. Embodiments of the present invention include all solvates of the described compounds. As used herein, the term "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.

Alternatively, the solvent may be an organic solvent. Thus, 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.

Embodiments of the compounds of the disclosure ( e.g ., compounds of structure I), or their salts, tautomers or solvates may contain one or more stereocenters 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 (I))- or (/.)- for amino acids. Embodiments of the present invention are meant to include all such possible isomers, as well as their racemic and optically pure forms. Optically active (+) and (-), (R)- and (S)-, or (I))- and (/.)- 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). When the compounds described herein contain olefmic double bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers. Likewise, all tautomeric forms are also intended to be included.

A "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 non-superimposable 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.

The chemical naming protocol and structure diagrams used herein are a modified form of the I.ET.P.A.C. nomenclature system, using the ACD/Name Version

9.07 software program and/or ChemDraw Ultra Version 11.0 software naming program (CambridgeSoft). Common names familiar to one of ordinary skill in the art are also used.

Compounds

As noted above, in one embodiment of the present invention, compounds useful as fluorescent and/or colored dyes in various analytical methods are provided. In other embodiments, compounds useful as synthetic intermediates for preparation of compounds useful as fluorescent and/or colored dyes are provided. In general terms, embodiments of the present invention are directed to dimers and higher polymers of fluorescent and/or colored moieties. The fluorescent and or colored moieties are linked by a linking moiety. Without wishing to be bound by theory, it is believed the linker helps to maintain sufficient spatial distance between the fluorescent and/or colored moieties such that intramolecular quenching is reduced or eliminated, thus resulting in a dye compound having a high molar "brightness" ( e.g ., high fluorescence emission).

Accordingly, in some embodiments the compounds have the following structure (A):

wherein L is a linker (e.g., heteroalkyl ene) sufficient to maintain spatial separation between one or more (e.g, each) M1 group so that intramolecular quenching is reduced or eliminated, and R1, R2, Lla, Llb, L2, L3, M1 and n are as defined for structure (I). In some embodiments of structure (A), L is a linker comprising one or more ethylene glycol or polyethylene glycol moieties.

In different embodiments the compounds have the following structure

(B):

wherein L is a linker ( e.g ., heteroalkyl ene) sufficient to maintain spatial separation between one or more (e.g., each) M2 group so that intramolecular quenching is reduced or eliminated, and R , R , R , L , L , L , L , M and n are as defined for structure (I).

In some embodiments of structure (B), L is a linker comprising one or more ethylene glycol or polyethylene glycol moieties.

In other embodiments is provided a compound having the following structure (I):

or a stereoisomer, salt or tautomer thereof, wherein:

M1 and M2 are, at each occurrence, independently a fluorescent or colored moiety comprising two or more double bonds and at least one degree of conjugation;

Lla is, at each occurrence, independently a heteroalkylene or heteroarylene linker;

Llb, L2, L3, L5, L6 and L 7 are, at each occurrence, independently optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linkers;

L4 is, at each occurrence, independently an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linker;

R1 and R2 are each independently H, OH, SH, alkyl, alkoxy, alkylether, heteroalkyl, -OP(=Ra)(Rb)Rc, Q, or a protected form thereof, or L';

R3 is, at each occurrence, independently H, alkyl or alkoxy;

R4 is, at each occurrence, independently OH, SH, O , S , ORd or SRd;

R5 is, at each occurrence, independently oxo, thioxo or absent;

Ra is O or S;

Rb is OH, SH, O , S , ORd or SRd;

Rc is OH, SH, O , S , ORd, OL', SRd, alkyl, alkoxy, heteroalkyl, heteroalkoxy, alkylether, alkoxyalkylether, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether;

Rd is a counter ion;

Q is, at each occurrence, independently a moiety comprising a reactive group, or protected form thereof, capable of forming a covalent bond with an analyte molecule, a targeting moiety, a solid support or a complementary reactive group Q';

L1 is, at each occurrence, independently a linker comprising a covalent bond to Q, a linker comprising a covalent bond to a targeting moiety, a linker comprising a covalent bond to an analyte molecule, a linker comprising a covalent bond to a solid support, a linker comprising a covalent bond to a solid support residue, a linker comprising a covalent bond to a nucleoside or a linker comprising a covalent bond to a further compound of structure (I);

m is, at each occurrence, an integer of one or greater;

n is an integer of one or greater;

q and w are, at each occurrence, independently 0 or 1 provided that q and w are not both 0 at each occurrence; and

at least one occurrence of M1 or M2 have one of the following structures:
The various linkers and substituents ( e.g ., M1, M2, Q, R1, R2, R3, Rc, Lla, Llb, L2, L3, L4, L5, L6 and L7) in the compound of structure (I) are optionally substituted with one more substituent. For example, in some embodiments the optional substituent is selected to optimize the water solubility or other property of the compound of structure (I). In certain embodiments, each chromophore, alkyl, alkoxy, alkylether, heteroaryl ene, heteroalkyl, alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, heteroalkynylene, alkoxyalkylether, phosphoalkyl, thiophosphoalkyl, phosphoalkylether and thiophosphoalkylether in the compound of structure (I) is optionally substituted with one more substituent selected from the group consisting of hydroxyl, alkoxy, alkylether , alkoxyalkylether, sulfhydryl, amino, alkylamino,

carboxyl, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether and thiophosphoalkylether. In certain embodiments the optional substituent is -OP(=Ra)(Rb)Rc, where Ra, Rb and Rc are as defined for the compound of structure (I).

In some embodiments, at least one occurrence of Lla is an optionally substituted 5-7 membered heteroarylene linker. In some more specific embodiments, Lla is, at each occurrence independently an optionally substituted 5-7 membered heteroarylene linker. In some embodiments, Lla is a 6-membered heteroarylene. In some embodiments, Lla comprises two N atoms and two O atoms. In certain embodiments, Lla is, at each occurrence, substituted. In some related embodiments, Llb is substituted, for example, Llb is substituted with oxo, alkyl (e.g., methyl, ethyl, etc.) or combinations thereof. In more specific embodiments, Lla is, at each occurrence, substituted with at least one oxo. In some embodiments, Lla has one of the following structures:

In some embodiments, Llb is, at each occurrence, independently an optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene, heteroalkynylene, alkyleneheteroarylenealkylene, alkyleneheterocyclylenealkylene, alkylenecarbocyclylenealkylene, heteroalkyleneheteroarylenealkylene,

heteroalkyleneheterocyclylenealk lene, heteroalkylenecarbocyclylenealkylene, heteroalkyleneheteroaryleneheteroalkylene,

heteroalkyleneheterocyclyleneheteroalkylene,

heteroalkylenecarbocyclyleneheteroalkylene, alkyleneheteroaryleneheteroalkylene, alkyleneheterocyclyleneheteroalkylene, alkylenecarbocyclyleneheteroalkylene, heteroarylene, heterocyclylene, carbocyclylene, alkyleneheteroarylene,

alkyleneheterocyclylene, heteroarylenealkylene, alkylenecarbocyclylene,

carb ocy cly 1 enealky 1 ene, heteroalkyl eneheteroary 1 ene, heteroalkyl eneheterocy cly 1 ene, heteroaryleneheteroalkylene, heteroalkylenecarbocyclylene,

carbocyclyleneheteroalkylene or heteroatomic linker. In some embodiments, Llb is an optionally substituted heteroalkenylene linker.

In some embodiments, at least one occurrence of Llb is substituted. In certain embodiments, Llb is substituted at each occurrence. In some more specific embodiments, Llb is substituted with oxo.

In other embodiments, Llb is at each occurrence, independently a linker comprising a functional group capable of formation by reaction of two complementary reactive groups ( e.g ., triazolyl, amide, etc.), for example a Q group.

The optional linkers Llb and L 7 can be used as a point of attachment of the M1 and M2 moieties to the remainder of the compound. For example, in some embodiments a synthetic precursor to the compound of structure (I) is prepared, and the M1 and M2 moieties are attached to the synthetic precursor using any number of facile methods known in the art, for example methods referred to as "click chemistry." For this purpose any reaction which is rapid and substantially irreversible can be used to attach M1 and M2 to the synthetic precursor to form a compound of structure (I).

Exemplary reactions include the copper catalyzed reaction of an azide and alkyne to form a triazole (Huisgen 1, 3-dipolar cycloaddition), reaction of a diene and dienophile (Diels- Alder), strain-promoted alkyne-nitrone cycloaddition, strain-promoted cycloalkyne-azide cycloaddition (Cu-free click), reaction of a strained alkene with an azide, tetrazine or tetrazole, alkene and azide [3+2] cycloaddition, alkene and tetrazine inverse-demand Diels-Alder, alkene and tetrazole photoreaction and various displacement reactions, such as displacement of a leaving group by nucleophilic attack on an electrophilic atom. Exemplary displacement reactions include reaction of an amine with: an activated ester; an N-hydroxysuccinimide ester; an isocyanate; an isothioscyanate or the like. In some embodiments the reaction to form Llb or L7 may be performed in an aqueous environment.

Accordingly, in some embodiments Llb or L7 are at each occurrence, independently a linker comprising a functional group capable of formation by reaction of two complementary reactive groups, for example a functional group which is the product of one of the foregoing "click" reactions. In various embodiments, for at least one occurrence of Llb or L7, the functional group can be formed by reaction of an aldehyde, oxime, hydrazone, alkyne, amine, azide, acylazide, acylhalide, nitrile, nitrone, sulfhydryl, disulfide, sulfonyl halide, isothiocyanate, imidoester, activated ester ( e.g ., N-hydroxysuccinimide ester), ketone, a,b-unsaturated carbonyl, alkene, maleimide, a-haloimide, epoxide, aziridine, tetrazine, tetrazole, phosphine, biotin or thiirane functional group with a complementary reactive group, for example, via a reaction of an amine with an N-hydroxysuccinimide ester or isothiocyanate.

In other embodiments, for at least one occurrence of Llb or L7, the functional group can be formed by reaction of an alkyne and an azide. In other embodiments, for at least one occurrence of Llb or L7, the functional group can be formed by reaction of an amine (e.g., primary amine) and an N-hydroxysuccinimide ester or isothiocyanate.

In more embodiments, for at least one occurrence of Llb or L7, the functional group comprises an alkene, ester, amide, thioester, disulfide, carbocyclic, heterocyclic or heteroaryl group. In more embodiments, for at least one occurrence of Llb or L7, the functional group comprises an alkene, ester, amide, thioester, thiourea, disulfide, carbocyclic, heterocyclic or heteroaryl group. In other embodiments, the functional group comprises an amide or thiourea. In some more specific embodiments, for at least one occurrence of Llb or L7, Llb or L7 are linkers comprising a triazolyl functional group. In some related embodiments, Llb or L7, at each occurrence, independently comprises a triazolyl functional group. While in other embodiments, at least one occurrence of Llb or L7 is a linker comprising an amide or thiourea functional group.

In still other embodiments, for at least one occurrence of Llb, Llb-M' has the following structure:

wherein Llc and Lld are each independently optional linkers.

In different embodiments, for at least one occurrence of Llb, Llb-M' has the following structure:

wherein Llc and Lld are each independently optional linkers.

In various embodiments of the foregoing, Llc or Lld, or both, is absent.

In other embodiments, Llc or Lld, or both, is present.

In some embodiments Llc and Lld, when present, are each independently alkylene or heteroalkylene. For example, in some embodiments Llc and Lld, when present, independently have one of the following structures:

In still other embodiments, for at least one occurrence of L7, L7-M2 has the following structure:

wherein L le If

and L11 are each independently optional linkers.

In different embodiments, for at least one occurrence of L7, L7-M2 has the following structure:

wherein Lle and Llf are each independently optional linkers.

In various embodiments of the foregoing, Lle or Llf, or both, is absent.

In other embodiments, Lle or Llf, or both, is present.

In some embodiments Lle and Llf, when present, are each independently alkylene or heteroalkylene. For example, in some embodiments Lle and Llf, when present, independently have one of the following structures:

In still other different embodiments of structure (I), Llb is at each occurrence, independently an optional alkylene or heteroalkylene linker. In certain embodiments, Llb has one of the following structures:

In some embodiments, at least one occurrence of L7 is an optionally substituted heteroalkylene linker. In certain embodiments, L7 is, at each occurrence, independently an optionally substituted heteroalkylene. In more specific embodiments, L7 comprises an amide or a triazolyl functional group.

In still other different embodiments of structure (I), L7 is at each occurrence, independently an optional alkylene or heteroalkylene linker. In certain embodiments, at least one occurrence of L7 has one of the following structures:

In some related embodiments, each occurrence of L7 has one of the following structures:

In some embodiments, at least one occurrence of L7 has the following structure:

In some related embodiments, each occurrence of L7 has the following structure:

In some embodiments, at least one occurrence of Llb and/ or L7 has one of the following structures:

wherein

a, b, and c are each independently an integer ranging from 1-6.

In some embodiments, each occurrence of Llb and / or L 7 has one of the following structures:

wherein

a, b, and c are each independently an integer ranging from 1-6.

In some embodiments, at least one occurrence of Llb and/ or L 7 has one of the following structures:

In still other different embodiments of structure (I), Llb and / or L 7 is at each occurrence, independently an optional alkylene or heteroalkylene linker. In certain embodiments, Llb and/ or L 7 has one of the following structures:

In some embodiments, at least one occurrence of L3 is an alkylene linker. In some embodiments, at least one occurrence of L3 is an alkylene linker. In more specific embodiments, L3 or is an alkylene linker at each occurrence. In certain embodiments, the alkylene linker is a methylene linker.

In some embodiments, at least one occurrence of L2 is absent. In more specific embodiments, L2 is absent at each occurrence.

In certain embodiments, at least one occurrence of L5 or L6 is, independently a heteroalkyl ene linker. In some more specific embodiments, L5 is a heteroalkylene linker at each occurrence and at least one occurrence of L6 is absent. In some embodiments, at least one occurrence of L4 comprises alkylene oxide. In some embodiments, at least one occurrence of L5 or L6 independently comprises alkylene oxide. In some of the foregoing embodiments, the alkylene oxide is ethylene oxide, for example, polyethylene oxide. In certain embodiments, at least one occurrence of L5 or L6 is an alkylene linker ( e.g ., methylene). In some more specific embodiments, L5 or L6 is an alkylene linker at each occurrence (e.g., methylene).

In certain embodiments, at least one occurrence of L5 is a heteroalkylene linker. In some more specific embodiments, L5 is a heteroalkylene linker at each occurrence. In some embodiments, at least one occurrence of L5 comprises alkylene oxide, for example, ethylene oxide (e.g, polyethylene oxide). In certain embodiments, at least one occurrence of L5 is an alkylene linker (e.g., methylene). In some more specific embodiments, L5 is an alkylene linker at each occurrence (e.g, methylene). In certain embodiments, at least one occurrence of L5 is absent. In some more specific embodiments, L5 is absent at each occurrence.

In certain embodiments, at least one occurrence of L6 is a heteroalkylene linker. In some more specific embodiments, L6 is a heteroalkylene linker at each

occurrence. In some embodiments, at least one occurrence of L6 comprises alkylene oxide. In some of the foregoing embodiments, the alkylene oxide is ethylene oxide, for example, polyethylene oxide. In certain embodiments, at least one occurrence of L6 is an alkylene linker ( e.g ., methylene). In some more specific embodiments, L6 is an alkylene linker at each occurrence (e.g., methylene). In certain embodiments, at least one occurrence of L6 is absent. In some more specific embodiments, L6 is absent at each occurrence.

In certain embodiments, at least one occurrence of L5 or L6 comprises a phosphodiester moiety. In more specific embodiments, each occurrence of L5 or L6 comprises a phosphodiester moiety. In more embodiments, L2, L3, L4 or L6 are, at each occurrence, independently Ci-C6 alkylene, C2-C6 alkenylene or C2-C6 alkynylene.

In some embodiments, at least one occurrence of L5 is heteroalkylene. In some embodiments, L5 is heteroalkylene at each occurrence, for example, a

heteroalkylene comprising one of the following structures:

In some embodiments, at least one occurrence of L6 is heteroalkylene. In some embodiments, L6 is heteroalkylene at each occurrence, for example, a

heteroalkylene comprising one of the following structures:

In some of the foregoing embodiments, a heteroalkylene (e.g, L3, L4, L5 or L6) comprises the following structure:

wherein

z is an integer ranging from 20 to 30. In certain embodiments, the average z is 23. In certain embodiments, the average z is 24. In certain embodiments, the average z is 25. In certain embodiments, the average z is 26. In certain

embodiments, the average z is 27. In some embodiments, the average z is 21, 22, 23, 24 or 25. In some embodiments, z is 24 or 25. In some embodiments, the average z is 21, 22, 23, 24, 25, 26 or 27.

In some embodiments, at least one occurrence of L5 or L6 independently comprises the following structure:

wherein

q' is an integer from 1-20; and

z is an integer from 1-100.

In some of the foregoing embodiments, z is an integer from 3 to 6. In some embodiments, z is an integer from 22 to 26, for example 22, 23, 24, 25, or 26. In some more specific embodiments, the average z is 23 or 24. In some embodiments, z is 24 or 25. In some embodiments, the average z is 21, 22, 23, 24, 25, 26 or 27.

In some of the foregoing embodiments, q' is 1. In other embodiments, q' is from 2 to 9.

In some embodiments, at least one occurrence of R3 is H. In more specific embodiments, R3 is H at each occurrence.

In some embodiments of structure (I), at least one occurrence of q is 0. In some embodiments of structure (I), q is 0 at each occurrence. In some related embodiments, the the compound has the following structure (la):

In some other embodiments, the compound has one of the following structures

wherein:

Llb is, at each occurrence, independently an optionally substituted alkylene or an optionally substituted heteroalkylene linker.

In some embodiments, the compound has one of the following structures

wherein:

z is an integer from 1 to 100.

In some embodiments, z is 24 or 25. In some embodiments, the average z is 21, 22, 23, 24, 25, 26 or 27.

In some embodiments, Llb, at each occurrence, independently comprises an amide functional group or a triazolyl functional group.

In some embodiments of structure (I), at least one occurrence of m is 0. In some embodiments of structure (I), m is 0 at each occurrence. In some related embodiments, the compound has one of the following structures (If):

In some more specific embodiments, the compound has one of the following structures (Ig) or (Ih):

In some more specific embodiments, the compound has one of the following structures (Ij) or (Ik):

wherein

z is, at each occurrence, independently an integer from 1 to 100; and p is, at each occurrence, independently an integer of zero or greater.

In some embodiments of structures (Ij) or (Ik), at least one occurrence of z ranges from 3 to 6. In some more specific embodiments of structures (Ij) or (Ik), z ranges from 3 to 6 at each occurrence. For example, in some of the foregoing embodiments, z is 3 or z is 6. In some embodiments, z is 24 or 25. In some

embodiments, the average z is 21, 22, 23, 24, 25, 26 or 27.

In some embodiments of structures (Ij) or (Ik), at least one occurrence of p ranges from 1 to 20. In some more specific embodiments of structures (Ij) or (Ik), p ranges from 1 to 20 at each occurrence. For example, in some of the foregoing embodiments, p is 2, 3, 4, 5, 6, 7, 8, 9 or 10.

In some of the foregoing embodiments of structures (If), (Ig), (Ih), (Ij) or

(Ik), at least one occurrence of L comprises one of the following structures:

In some more specific embodiments of structures (If), (Ig), (Ih), (Ij) or

(Ik), each occurrence of L6 comprises one of the following structures:

In some embodiments of structure (I), at least one occurrence of w is 0. In some embodiments of structure (I), w is 0 at each occurrence. In some related embodiments, the compound has one of the following structures (Im):

In some more specific embodiments, the compound has the following structure (In):

wherein:

s is, at each occurrence, independently an integer of 0 or greater;

z is, at each occurrence, independently an integer from 1 to 100;

p is, at each occurrence, independently an integer of zero or greater; and L 7 is, at each occurrence, independently an optionally substituted heteroalkylene linker.

In some embodiments, z is 6 and p is 3. In some embodiments, the average z ranges from 21 to 25, for example 21, 22, 23, 24, or 25. In some

embodiments, z is 3. In some embodiment, z is 24 or 25. In some embodiments, the average z is 21, 22, 23, 24, 25, 26 or 27. In some embodiments, z is 25 and s is 4. In some embodiments, z is 25 s is 4 and n is 1.

In some of the foregoing embodiments, L6 is absent, for example, at each occurrence. In some of the foregoing embodiments of structures (Im) or (In), at least one occurrence of L6 comprises one of the following structures:

In some more specific embodiments of structures (Im) or (In), each occurrence of L6 comprises one of the following structures:

In different embodiments of structures (Im) or (In), at least one occurrence of L6 is alkylene, for example, methylene. In some related embodiments of structures (Im) or (In), L6 is alkylene at each occurrence, for example, methylene.

In some embodiments of the structures (In) or (Io), at least one occurrence of L6 is heteroalkylene. In some embodiments of the structures (In) or (Io), L6 is heteroalkylene at each occurrence, for example, a heteroalkylene comprising one of the following structures:

In some of the foregoing embodiments of structures (Im) or (In), at least one occurrence of L5 comprises one of the following structures:

O O

- s-o-p II-o^s- s II s

fo-P-o-b

O or O

In some more specific embodiments of structures (Im) or (In), each occurrence of L5 comprises one of the following structures:

O O

* 11 s II s

- °-P-0^ fo-P-o-b

O or O

In different embodiments of structures (Im) or (In), at least one occurrence of L5 is alkylene, for example, methylene. In some related embodiments of structures (Im) or (In), L5 is alkylene at each occurrence, for example, methylene.

In some embodiments of the structures (In) or (Io), at least one occurrence of L5 is heteroalkylene. In some embodiments of the structures (In) or (Io), L5 is heteroalkylene at each occurrence, for example, a heteroalkylene comprising one of the following structures:

In some of the foregoing embodiments, L6 is absent.

In some of the foregoing embodiments of the structures (In) or (Io), a heteroalkylene ( e.g . , L3, L4, L5 or L6) comprises the following structure:

wherein

z is an integer ranging from 20 to 30. In certain embodiments, the average z is 24 or 25. In some embodiments, the average z is 21, 22, 23, 24, 25, 26 or 27.

In still other embodiments of any of the compounds of structures (I),

(la), (lb), (Ic), (Id), (Ie), (If), (Ig), (Ih), (Ij), (Ik), (Im). (In) or (Io), R5 is, at each occurrence, independently OH, O or ORd· It is understood that "ORd" and "SRd" are intended to refer to O and S associated with a cation. For example, the disodium salt of a phosphate group may be represented as:

where Rd is sodium (Na+).

In other embodiments of any of the compounds of structures (I), (la),

(lb), (Ic), (Id), (Ie), (If), (Ig), (Ih), (Ij), (Ik), (Im). (In) or (Io) at least one occurrence of R4 is oxo. In other embodiments of any of the compounds of structure (I), R4 is, at each occurrence, oxo.

In other various embodiments, R1 and R2 are each independently OH or -OP(=Ra)(Rb)Rc· In some different embodiments, R1 or R2 is OH or -OP(=Ra)(Rb)Rc, and the other of R1 or R2 is Q or a linker comprising a covalent bond to Q.

In still more different embodiments of any of the foregoing compounds of structures (I), (la), (lb), (Ic), (Id), (Ie), (If), (Ig), (Ih), (Ij), (Ik), (Im). (In) or (Io) R1 and R2 are each independently -OP(=Ra)(Rb)Rc· In some of these embodiments, Rc is OL'.

In other embodiments, R1 and R2 are each independently -OP(=Ra)(Rb)OL', and L' is an alkylene or heteroalkylene linker to: Q, a targeting moiety, an analyte ( e.g ., analyte molecule), a solid support, a solid support residue, a nucleoside or a further compound of structure (I).

The linker L' can be any linker suitable for attaching Q, a targeting moiety, an analyte ( e.g ., analyte molecule), a solid support, a solid support residue, a nucleoside or a further compound of structure (I) to the compound of structure (I). Advantageously certain embodiments include use of L' moieties selected to increase or optimize water solubility of the compound. In certain embodiments, L' is a

heteroalkylene moiety. In some other certain embodiments, L' comprises an alkylene oxide or phosphodiester moiety, or combinations thereof.

In certain embodiments, L' has the following structure:

wherein:

m" and n" are independently an integer from 1 to 10;

Re is H, an electron pair or a counter ion;

L" is Re or a direct bond or linkage to: Q, a targeting moiety, an analyte (e.g., analyte molecule), a solid support, a solid support residue, a nucleoside or a further compound of structure (I).

In some embodiments, m" is an integer from 4 to 10, for example 4, 6 or 10. In other embodiments n" is an integer from 3 to 6, for example 3, 4, 5 or 6. In some embodiments, n" is an integer from 18-28, for example, from 21-23.

In some other embodiments, L" is an alkylene, alkyleneheterocyclylene, alkyleneheterocyclylenealkylene, alkylenecyclylene, alkylenecyclylenealkylene, heteroalkylene, heteroalkyleneheterocyclylene,

heteroalkyleneheterocyclyleneheteroalkylene, heteroalkylenecyclylene, or

heteroalkylenecycleneheteroalkylene moiety. In some other certain embodiments, L" comprises an alkylene oxide, phosphodiester moiety, sulfhydryl, disulfide or maleimide moiety or combinations thereof.

In certain of the foregoing embodiments, the targeting moiety is an antibody or cell surface receptor antagonist.

In other more specific embodiments of any of the foregoing compounds of structure (I), R1 or R2 has one of the following structures:

In other more specific embodiments of any of the foregoing compounds of structure (I), R1 or R2 has one of the following structures:

Certain embodiments of compounds of structure (I) can be prepared according to solid-phase synthetic methods analogous to those known in the art for preparation of oligonucleotides. Accordingly, in some embodiments, L' is a linkage to a solid support, a solid support residue or a nucleoside. Solid supports comprising an activated deoxythymidine (dT) group are readily available, and in some embodiments can be employed as starting material for preparation of compounds of structure (I). Accordingly, in some embodiments R1 or R2 has the following structure:

One of skill in the art will understand that the dT group depicted above is included for ease of synthesis and economic efficiencies only, and is not required.

Other solid supports can be used and would result in a different nucleoside or solid support residue being present on L', or the nucleoside or solid support residue can be removed or modified post synthesis.

In still other embodiments, Q is, at each occurrence, independently a moiety comprising a reactive group capable of forming a covalent bond with an analyte molecule or a solid support. In other embodiments, Q is, at each occurrence, independently a moiety comprising a reactive group capable of forming a covalent bond with a complementary reactive group Q'. For example, in some embodiments, Q' is present on a further compound of structure (I) ( e.g ., in the R1 or R2 position), and Q and Q' comprise complementary reactive groups such that reaction of the compound of structure (I) and the further compound of structure (I) results in covalently bound dimer of the compound of structure (I). Multimer compounds of structure (I) can also be prepared in an analogous manner and are included within the scope of embodiments of the invention.

The type of Q group and connectivity of the Q group to the remainder of the compound of structure (I) is not limited, provided that Q comprises a moiety having appropriate reactivity for forming the desired bond.

In certain embodiments, 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, azide or alkyne).

Certain embodiments of compounds of structure (I) comprise Q groups commonly employed in the field of bioconjugation. For example in some

embodiments, Q comprises a nucleophilic reactive group, an electrophilic reactive group or a cycloaddition reactive group. In some more specific embodiments, Q comprises a sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, a-haloamide, biotin, amino or maleimide functional group. In some embodiments, the activated ester is an N-succinimide ester, imidoester or polyflourophenyl ester. In other embodiments, the alkyne is an alkyl azide or acyl azide.

The Q groups can be conveniently provided in protected form to increase storage stability or other desired properties, and then the protecting group removed at the appropriate time for conjugation with, for example, a targeting moiety or analyte.

Accordingly, Q groups include "protected forms" of a reactive group, including any of the reactive groups described above and in the Table 1 below. A "protected form" of Q refers to a moiety having lower reactivity under predetermined reaction conditions relative to Q, but which can be converted to Q under conditions, which preferably do not degrade or react with other portions of the compound of structure (I). One of skill in the art can derive appropriate protected forms of Q based on the particular Q and desired end use and storage conditions. For example, when Q is SH, a protected form of Q includes a disulfide, which can be reduce to reveal the SH moiety using commonly known techniques and reagents.

Exemplary Q moieties are provided in Table 1 below.

TableJ . Exemplary Q Moieties

It should be noted that in some embodiments, wherein Q is SH, the SH moiety will tend to form disulfide bonds with another sulfhydryl group, for example on another compound of structure (I). Accordingly, some embodiments include compounds of structure (I), which are in the form of disulfide dimers, the disulfide bond being derived from SH Q groups.

Also included within the scope of certain embodiments are compounds of structure (I), wherein one, or both, of R1 and R2 comprises a linkage to a further compound of structure (I). For example, wherein one or both of R1 and R2 are

-OP(=Ra)(Rb)Rc, and Rc is OL', and L' is a linker comprising a covalent bond to a further compound of structure (I). Such compounds can be prepared by preparing a first compound of structure (I) having for example about 10 "M1" and/or "M2" moieties (i.e., n = 10) and having an appropriate "Q" for reaction with a complementary Q' group on a second compound of structure (I). In this manner, compounds of structure (I), having any number of "M1" and/or "M2" moieties, for example 100 or more, can be prepared without the need for sequentially coupling each monomer. Exemplary embodiments of such compounds of structure (I) have the following structure (G):

wherein:

each occurrence of R1, R2, R3, R4, R5, Lla, Llb, L2, L3, L4, L5, L6, L7, M1,

M1, q, m, w and n are independently as defined for a compound of structure (I);

L" is a linker comprising a functional group resulting from reaction of a Q moiety with a corresponding Q' moiety; and

a is an integer greater than 1, for example from 1 to 100, or 1 to 10. Compounds of structure (G) are derivable by those of ordinary skill in the art, for example by dimerizing or polymerizing compounds of structure (I) provided herein.

In other embodiments, the Q moiety is conveniently masked ( e.g ., protected) as a disulfide moiety, which can later be reduced to provide an activated Q moiety for binding to a desired analyte molecule or targeting moiety. For example, the Q moiety may be masked as a disulfide having the following structure:

wherein R is an optionally substituted alkyl group. For example, in some embodiments, Q is provided as a disulfide moiety having the following structure:

where n is an integer from 1 to 10.

In some other embodiments, one of R1 or R2 is OH or -OP(=Ra)(Rb)Rc, and the other of R1 or R2 is a linker comprising a covalent bond to an analyte molecule or a linker comprising a covalent bond to a solid support. For example, in some embodiments the analyte molecule is a nucleic acid, amino acid or a polymer thereof.

In other embodiments, the analyte molecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion. In some embodiments, the targeting moiety is an antibody or cell surface receptor antagonist. In still different embodiments, the solid support is a polymeric bead or non-polymeric bead.

The fluorescence intensity can also be tuned by selection of different values of the variables n, m, q, p, s and w. In certain embodiments, n is an integer from 1 to 100. In other embodiments, n is an integer from 1 to 10. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some

embodiments, n is 4. In some embodiments, n is 5. In some embodiments, n is 6. In some embodiments, n is 7. In some embodiments, n is 8. In some embodiments, n is 9. In some embodiments, n is 10.

In certain embodiments, m is an integer from 1 to 100. In other embodiments, m is an integer from 7 to 12. In some embodiments, m is an integer from 20 to 26. In some embodiments, m is an integer from 3 to 6. In some embodiments, m is 3. In some embodiments, m is 4. In some embodiments, m is 5. In some

embodiments, m is 6. In some embodiments, m is 7. In some embodiments, m is 8. In

some embodiments, m is 9. In some embodiments, m is 10. In some embodiments, m is 11.

In certain embodiments, w is an integer from 1 to 100. In other embodiments, w is an integer from 7 to 12. In some embodiments, w is an integer from 20 to 26. In some embodiments, w is an integer from 3 to 6. In some embodiments, w is 3. In some embodiments, w is 4. In some embodiments, w is 5. In some

embodiments, w is 6. In some embodiments, w is 7. In some embodiments, w is 8. In some embodiments, w is 9. In some embodiments, w is 10. In some embodiments, w is 11

In certain embodiments, p is an integer from 1 to 100. In other embodiments, p is an integer from 7 to 12. In some embodiments, p is an integer from 20 to 26. In some embodiments, p is an integer from 3 to 6. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In some embodiments, p is 6. In some embodiments, p is 7. In some embodiments, p is 8. In some

embodiments, p is 9. In some embodiments, p is 10. In some embodiments, p is 11.

In certain embodiments, s is an integer from 1 to 100. In other embodiments, s is an integer from 7 to 12. In some embodiments, s is an integer from 20 to 26. In some embodiments, s is an integer from 3 to 6. In some embodiments, s is 3. In some embodiments, s is 4. In some embodiments, s is 5. In some embodiments, s is 6. In some embodiments, s is 7. In some embodiments, s is 8. In some

embodiments, s is 9. In some embodiments, s is 10. In some embodiments, s is 11.

In certain embodiments, q is an integer from 1 to 100. In other embodiments, q is an integer from 7 to 12. In some embodiments, q is an integer from 20 to 26. In some embodiments, q is an integer from 3 to 6. In some embodiments, q is 3. In some embodiments, q is 4. In some embodiments, q is 5. In some embodiments, q is 6. In some embodiments, q is 7. In some embodiments, q is 8. In some

embodiments, q is 9. In some embodiments, q is 10. In some embodiments, q is 11.

M1 and M2 are selected based on the desired optical properties, for example based on a desired color and/or fluorescence emission wavelength. In some embodiments, M1 and M2 are the same at each occurrence; however, it is important to note that each occurrence of M1 and M2 need not be an identical M1 and M2, and certain embodiments include compounds wherein M1 and M2 are not the same at each occurrence. For example, in some embodiments each M1 and M2 are not the same and the different M1 and M2 moieties are selected to have absorbance and/or emissions for use in fluorescence resonance energy transfer (FRET) methods. For example, in such embodiments the different M1 and M2 moieties are selected such that absorbance of radiation at one wavelength causes emission of radiation at a different wavelength by a FRET mechanism. Exemplary M1 and M2 moieties can be appropriately selected by one of ordinary skill in the art based on the desired end use. Exemplary M1 and M2 moieties for FRET methods include fluorescein and 5-TAMRA (5-carboxytetramethylrhodamine, succinimidyl ester) dyes.

M1 or M2 may be attached to the remainder of the molecule from any position ( i.e ., atom) on M1 or M2, respectively. One of skill in the art will recognize means for attaching M1 or M2 to the remainder of molecule. Exemplary methods include the "click" reactions described herein.

In some embodiments, M1 and M2 are, at each occurrence, independently a fluorescent or colored moiety ( e.g ., a chromophore). Any fluorescent and/or colored moiety may be used, for examples those known in the art and typically employed in colorimetric, UV, and/or fluorescent assays may be used. Examples of M1 and M2 moieties which are useful in various embodiments of the invention include, but are not limited to: Xanthene derivatives (e.g., fluorescein, rhodamine, Oregon green, eosin or Texas red); Cyanine derivatives (e.g, cyanine, indocarbocyanine, oxacarbocyanine, thiacarbocyanine or merocyanine); Squaraine derivatives and ring-substituted squaraines, including Seta, SeTau, and Square dyes; Naphthalene derivatives (e.g, dansyl and prodan derivatives); Coumarin derivatives; oxadiazole derivatives (e.g, pyridyloxazole, nitrobenzoxadiazole or benzoxadi azole); Anthracene derivatives (e.g, anthraquinones, including DRAQ5, DRAQ7 and CyTRAK Orange); Pyrene derivatives such as cascade blue; Oxazine derivatives (e.g, Nile red, Nile blue, cresyl violet, oxazine 170); Acridine derivatives (e.g, proflavin, acridine orange, acridine yellow); Arylmethine derivatives: auramine, crystal violet, malachite green; and Tetrapyrrole derivatives ( e.g ., porphin, phthalocyanine or bilirubin). Other exemplary M1 and M2 moieties include: Cyanine dyes, xanthate dyes (e.g., Hex, Vic, Nedd, Joe or Tet);

Yakima yellow; Redmond red; tamra; texas red and alexa fluor® dyes.

In still other embodiments of any of the foregoing, M1 or M2 at one or more occurrences independently 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. In some embodiments, M1 and M2 at one or more occurrences independently comprise six aryl or heteroaryl rings, or combinations thereof. In further embodiments, the rings are fused. For example in some embodiments, M1 and M2 at one or more occurrences independently comprise three or more fused rings, four or more fused rings, five or more fused rings, or even six or more fused rings.

In some embodiments, M1 or M2 are, at one or more occurrences, independently cyclic. For example, in some embodiments M1 and M2 are, at one or more occurrences, independently carbocyclic. In other embodiment, M1 and M2 are, at one or more occurrences, independently heterocyclic. In still other embodiments of the foregoing, M1 and M2 are, at one or more occurrences, independently comprises an aryl moiety. In some of these embodiments, the aryl moiety is multicyclic. In other more specific examples, the aryl moiety is a fused-multicyclic aryl moiety, for example which may comprise at least 2, at least 3, at least 4, or even more than 4 aryl rings.

In other embodiments of any of the foregoing compounds of structure (I), (la), (lb), (Ic), (Id), (Ie), (If), (Ig), (Ih), (Ij), (Ik), (Im), (In) or (G), M1 or M2 at one or more occurrences, independently comprises at least one heteroatom. For example, in some embodiments, the heteroatom is nitrogen, oxygen or sulfur.

In still more embodiments of any of the foregoing, M1 and M2, at one or more occurrences, independently comprise at least one substituent. For example, in some embodiments 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.

In some even more specific embodiments of the foregoing, M1 or M2, at one or more occurrences, 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, lO-ethynylanthracene or ter-naphthyl moiety. In other embodiments, M1 and M2 are, at one or more occurrences, independently p-terphenyl, perylene, azobenzene, phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, or perylene amide or a derivative thereof. In still more embodiments, M1 and M2 are, at one or more occurrences, independently a coumarin dye, resorufm dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, energy transfer dye, thiazole orange dye, polymethine or N-aryl-l,8-naphthalimide dye.

In still more embodiments of any of the foregoing, M1 and M2 at one or more occurrences are the same. In other embodiments, each M1 and M2 are different.

CLAIMS

What is claimed is:

1. A compound having the following structure (I):

or a stereoisomer, salt or tautomer thereof, wherein:

M1 and M2 are, at each occurrence, independently a fluorescent or colored moiety comprising two or more double bonds and at least one degree of conjugation;

Lla is, at each occurrence, independently a heteroalkylene or

heteroarylene linker;

Llb, L2, L3, L5, L6 and L7 are, at each occurrence, independently optional alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linkers;

L4 is, at each occurrence, independently an alkylene, alkenylene, alkynylene, heteroalkylene, heteroalkenylene or heteroalkynylene linker;

R1 and R2 are each independently H, OH, SH, alkyl, alkoxy, alkylether, heteroalkyl, -OP(=Ra)(Rb)Rc, Q, or a protected form thereof, or L';

R3 is, at each occurrence, independently H, alkyl or alkoxy;

R4 is, at each occurrence, independently OH, SH, O , S , ORd or SRd;

R5 is, at each occurrence, independently oxo, thioxo or absent;

Ra is O or S;

Rb is OH, SH, O , S , ORd or SRd;

Rc is OH, SH, O , S , ORd, OL', SRd, alkyl, alkoxy, heteroalkyl, heteroalkoxy, alkylether, alkoxyalkylether, phosphate, thiophosphate, phosphoalkyl, thiophosphoalkyl, phosphoalkylether or thiophosphoalkylether;

Rd is a counter ion;

Q is, at each occurrence, independently a moiety comprising a reactive group, or protected form thereof, capable of forming a covalent bond with an analyte molecule, a targeting moiety, a solid support or a complementary reactive group Q';

L1 is, at each occurrence, independently a linker comprising a covalent bond to Q, a linker comprising a covalent bond to a targeting moiety, a linker comprising a covalent bond to an analyte molecule, a linker comprising a covalent bond to a solid support, a linker comprising a covalent bond to a solid support residue, a linker comprising a covalent bond to a nucleoside or a linker comprising a covalent bond to a further compound of structure (I);

m is, at each occurrence, an integer of one or greater;

n is an integer of one or greater;

q and w are, at each occurrence, independently 0 or 1 provided that q and w are not both 0 at each occurrence; and

at least one occurrence of M1 or M2 has one of the following structures:

2. The compound of claim 1, wherein at least one occurrence of L7 is an optionally substituted heteroalkylene linker.

3. The compound of any one of claims 1-2, wherein L7 is, at each occurrence, independently an optionally substituted heteroalkylene.

4. The compound of any one of claims 1-3, wherein L7 comprises an amide or a triazolyl functional group.

5. The compound of any one of claims 1-4, wherein at least one occurrence of L7 has one of the following structures:

6 The compound of any one of claims 1-5, wherein each occurrence of L7 has one of the following structures:

7. The compound of any one of claims 1-6, wherein at least one occurrence of L7 has the following structure:

8. The compound of any one of claims 1-7, wherein each occurrence of L7 has the following structure:

9. The compound of any one of claims 1-8, wherein at least one occurrence of L5 or L6 is, independently a heteroalkylene linker.

10. The compound of any one of claims 1-9, wherein at least one occurrence ofL5 or L6 independently comprises alkylene oxide.

11. The compound of any one of claims 1-10, wherein at least one occurrence of L5 comprises alkylene oxide.

12. The compound of any one of claims 10 or 11, wherein the alkylene oxide is ethylene oxide.

13. The compound of any one of claims 1-12, wherein at least one occurrence of L5 or L6 independently comprises the following structure:

wherein

q' is an integer from 1-20; and

z is an integer from 1-100.

14. The compound of claim 13, wherein z is an integer from 3 to 6.

15. The compound of claims 13, wherein z is an integer from 22 to

26.

16. The compound of any one of claims 13 or 15, wherein the average z is 23 or 24.

17. The compound of any one of claims 13-16, wherein q' is 1.

18. The compound of any one of claims 13-16, wherein q' is from 2 to 9.

19. The compound of any one of claims 1-17, wherein at least one occurrence of R3 is H.

20. The compound of any one of claims 1-19, wherein the compound has the following structure (Im):

21. The compound of any one of claims 1-20, wherein the compound has one of the following structures (In) or (Io):

wherein:

s is, at each occurrence, independently an integer of 0 or greater;

z is, at each occurrence, independently an integer from 1 to 100;

p is, at each occurrence, independently an integer of zero or greater; and

L 7 is, at each occurrence, independently an optionally substituted heteroalkylene linker.

22. The compound of any one of claims 1-21, wherein L6 is absent.

23. The compound of any one of claims 1-22, wherein R5 is, at each occurrence, independently OH, O or OR4.

24. The compound of any one of claims 1-23, wherein R4 is, at each occurrence, oxo.

25. The compound of any one of claims 1-24, wherein R1 and R2 are each independently OH or -OP(=Ra)(Rb)Rc.

26. The compound of any one of claims 1-24, wherein one of R1 or R2 is OH or -OP(=Ra)(Rb)Rc, and the other of R1 or R2 is Q or a linker comprising a covalent bond to Q.

27. The compound of any one of claims 1-24, wherein R1 and R2 are each independently -OP(=Ra)(Rb)Rc.

28. The compound of any one of claims 25-27, wherein Re is OL'.

29. The compound of claim 28, wherein L' is a heteroalkylene linker to: Q, a targeting moiety, an analyte molecule, a solid support, a solid support residue, a nucleoside or a further compound of structure (I).

30. The compound of claim 29, wherein L' comprises an alkylene oxide or phosphodiester moiety, or combinations thereof.

31. The compound of claim 30, wherein L' has the following structure:

wherein:

m" and n" are independently an integer from 1 to 10;

Re is H, an electron pair or a counter ion;

L" is Re or a direct bond or linkage to: Q, a targeting moiety, an analyte molecule, a solid support, a solid support residue, a nucleoside or a further compound of structure (I).

32. The compound of claim 29-31, wherein the targeting moiety is an antibody or cell surface receptor antagonist.

33. The compound of any one of claims 1-31, wherein R1 or R2 has one of the following structures:

34. The compound of any one of claims 1-33, wherein R1 or R2 has the following structure:

35. The compound of any one of claims 1-31, wherein Q comprises a nucleophilic reactive group, an electrophilic reactive group or a cycloaddition reactive group.

36. The compound of claim 35, wherein Q comprises a sulfhydryl, disulfide, activated ester, isothiocyanate, azide, alkyne, alkene, diene, dienophile, acid halide, sulfonyl halide, phosphine, a-haloamide, biotin, amino or maleimide functional group.

37. The compound of claim 36, wherein the activated ester is an N-succinimide ester, imidoester or polyflourophenyl ester.

38. The compound of claim 36, wherein the azide is an alkyl azide or acyl azide.

39. The compound of any one of claims 1-31, wherein Q is a moiety selected from Table 1.

40. The compound of any one of claims 1-24, wherein one of R1 or R2 is OH or -OP(=Ra)(Rb)Rc, and the other of R2 or R3 is a linker comprising a covalent bond to an analyte molecule, a linker comprising a covalent bond to a targeting moiety or a linker comprising a covalent bond to a solid support.

41. The compound of claim 40, wherein the analyte molecule is a nucleic acid, amino acid or a polymer thereof.

42. The compound of claim 40, wherein the analyte molecule is an enzyme, receptor, receptor ligand, antibody, glycoprotein, aptamer or prion.

43. The compound of claim 40, wherein the targeting moiety is an antibody or cell surface receptor antagonist.

44. The compound of claim 40, wherein the solid support is a polymeric bead or non-polymeric bead.

45. The compound of any one of claims 1-44, wherein n is an integer from 1 to 100.

46. The compound of any one of claims 1-45, wherein n is an integer from 1 to 10.

47. The compound of any one of claims 1-46, wherein q is an integer from 3 to 15.

48. The compound of any one of claims 1-46, wherein q is an integer from 2 to 12.

49. The compound of any one of claims 1-48, wherein M1 and M2 are, at one or more occurrences, independently a moiety comprising four or more aryl or heteroaryl rings, or combinations thereof.

50. The compound of any one of claims 1-49, wherein M1 and M2 are, at one or more occurrences, independently fluorescent or colored.

51. The compound of claim 50, wherein M1 and M2 are fluorescent.

52. The compound of any one of claims 1-51, wherein M1 and M2 are, at one or more occurrences, independently comprise a fused-multicyclic aryl or heteroaryl moiety comprising at least four fused rings.

53. The compound of any one of claims 1-52, wherein M1 and M2 are, at one or more occurrences, independently 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, lO-ethynylanthracene or ter-naphthyl moiety.

54. The compound of any one of claims 1-52, wherein M1 and M2 are, at one or more occurrences, independently p-terphenyl, perylene, azobenzene,

phenazine, phenanthroline, acridine, thioxanthrene, chrysene, rubrene, coronene, cyanine, perylene imide, or perylene amide or derivative thereof.

55. The compound of any one of claims 1-52, wherein M1 and M2 are, at one or more occurrences, independently a coumarin dye, resorufm dye, dipyrrometheneboron difluoride dye, ruthenium bipyridyl dye, energy transfer dye, thiazole orange dye, polymethine or N-aryl-l,8-naphthalimide dye.

56. The compound of any one of claims 1-52, wherein M1 and M2 are, at one or more occurrences, independently pyrene, perylene, perylene monoimide or 6-FAM or derivative thereof.

57. The compound of any one of claims 1-52, wherein M1 and M2, at each occurrence, independently have one of the following structures:

58. The compound of any one of claims 1-52, wherein M1 and M2, at one or more occurrences, independently have one of the following structures
59. A compound selected from Table 2.

60. A method of staining a sample, comprising adding to the sample the compound of any one of claims 1-59 in an amount sufficient to produce an optical response when the sample is illuminated at an appropriate wavelength.

61. The method of claim 60, wherein the optical response is a fluorescent response.

62. The method of any one of claims 60-61, wherein the sample comprises cells.

63. The method of claim 62, further comprising observing the cells by flow cytometry.

64. The method of claim 63, further comprising distinguishing the fluorescence response from that of a second fluorophore having detectably different optical properties.

65. A method for visually detecting an analyte molecule, the method comprising:

(a) providing the compound of claim 1, wherein R1 or R2 is a linker comprising a covalent bond to the analyte molecule; and

(b) detecting the compound by its visible properties.

66. A method for visually detecting an analyte molecule, the method comprising:

(a) admixing the compound of claim 1, wherein R1 or R2 is Q or a linker comprising a covalent bond to Q, with the analyte molecule;

(b) forming a conjugate of the compound and the analyte molecule; and

(c) detecting the conjugate by its visible properties.

67. A method for visually detecting an analyte, the method comprising:

(a) providing the compound of claim 1, wherein R1 or R2 comprises a linker comprising a covalent bond to a targeting moiety having specificity for the analyte;

(b) admixing the compound and the analyte, thereby associating the targeting moiety and the analyte; and

(c) detecting the compound by its visible properties.

68. A composition comprising the compound of any one of claims 1-59 and one or more analyte molecules.

69. Use of the composition of claim 68 in an analytical method for detection of the one or more analyte molecules.