WO2008091378A2

WO2008091378A2 - High throughput ligand binding assays and reagents

Info

Publication number: WO2008091378A2
Application number: PCT/US2007/074322
Authority: WO
Inventors: Neal Woodbury
Original assignee: The Arizona Board Of Regents, A Body Corporate Of The State Of Arizona Acting For And On Behalf Of Arizona State University
Priority date: 2006-07-25
Filing date: 2007-07-25
Publication date: 2008-07-31
Also published as: WO2008091378A3

Abstract

The present invention provides methods, compositions, and computer readable storage media for multiplex detection of ligand binding.

Description

High Throughput Ligand Binding Assays and Reagents

Cross Reference This application claims priority to U.S. Provisional Patent Application Serial

No. 60/833,019 filed July 25, 2006, incorporated by reference herein in its entirety.

Background of the invention

In many applications of both nucleic acid hybridization and especially protein binding to arrays, it would be very desirable to test multiple targets simultaneously on one array. For example, if one is profiling 100 different samples for binding characteristics, lower cost, greater speed and a more precise comparison of binding/hybridization could be performed if all of these samples could be analyzed simultaneously on an array. Currently, there are commercially available array reading instruments that have as many as about 16 channel wavelength read-outs and multiple excitation lasers. With such an instrument and the proper choice of fluorescent molecules or particles for labeling the probe samples, up to about 10 samples can be measured simultaneously. This is especially true if quantum dots are used as the label on the probing samples. It is possible to purchase at least ten different quantum dots with ten distinct fluorescence spectra, (e.g., see, for example, the Invitrogen web site probes.invitrogen.com/products/qdot/ and the Evident Technologies web site evidenttech.com/nanomaterials/evidots/quantum-dot-emission-absorption.php) Further, quantum dots can be obtained that can all be excited at the same wavelength. Thus, currently available array readers and labels will allow one to simultaneously determine the relative amounts of up to approximately ten different fluorescing species at any point on the array being measured, but not many more.

Summary of the invention

In a first aspect, the present invention provides methods for detection of ligand binding, comprising

(a) providing a plurality of addressable arrays of molecules to be assessed for ligand binding, wherein the addressable arrays each comprise identical species of molecules to be assessed for ligand binding and/or different molecules to be assessed for ligand binding that bind to the same ligand, (b) providing a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable;

(c) providing a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between one or more ligands in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample;

(d) contacting at least a first addressable array with the first ligand sample and contacting at least a second addressable array with the second ligand sample under conditions to promote ligand binding to molecules to be assessed on the addressable arrays;

(e) detecting signal from the detectable labels associated with ligands bound to molecules on the addressable arrays; and

(f) identifying ligand bound to molecules on the addressable arrays based on the signals detected. In a second aspect, the present invention provides computer readable storage media. In one embodiment, the computer readable storage media comprise a set of instructions for causing a device to execute procedures comprising:

(a) detecting signal from detectable labels associated with ligands bound to molecules on one or more addressable array, wherein the ligands comprise (i) a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable; and (ii) a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between at least one ligand in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample; and (b) identifying ligand bound to molecules on the addressable arrays based on the signals detected.

In a further embodiment, the computer readable storage media comprise a set of instructions for causing a device to execute procedures comprising:

(a) detecting signal from detectable labels associated with ligands bound to molecules on one or more addressable array; (b) forming a set of equations selected from the group consisting of i) I = f{β, C); ii) I = f(δ,β,C) ; iii) / = /(«, δ, β,C); and n iv) /„* = ∑ «_ta δφ^ C_11n ; and m=\

(c) solving the system of equations to determine a measure relating to the relative occupancy of at least one addressable array position by at least one ligand species or set of ligand species. In a further embodiment, the computer readable storage media comprises a set of instructions for causing the device to execute procedures for carrying out the first and/or fourth aspects of the invention. The invention further provides devices incorporating the computer readable storage media of the invention.

In a third aspect, the present invention provides compositions, comprising: (a) a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, and wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signals generated from different ligand groups or secondary labels in the first ligand sample are distinguishable one from the other; and

(b) a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable one from the other; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between one or more ligands in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample.

In a fourth aspect, the present invention provides methods for detection of ligand binding, comprising (a) providing an addressable array of molecules to be assessed for ligand binding;

(b) contacting the addressable array with a first ligand sample comprising a plurality of ligand groups under conditions to promote ligand binding to molecules on the addressable array, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable;

(c) detecting signal from the detectable labels associated with ligands from the first ligand sample bound to molecules on the addressable array;

(d) removing bound ligand from the addressable array; (e) contacting the addressable array with a second ligand sample comprising a plurality of ligand groups under conditions to promote ligand binding to molecules on the addressable array, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between one or more ligands in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample;

(f) detecting signal from the detectable label associated with ligands from the second ligand sample bound to molecules on the addressable array; and

(g) identifying ligand bound to molecules on the addressable array based on the signals detected .

Brief Description of the Figures Figure 1. An exemplary three color embodiment of the invention. By using three colors and two arrays, nine different proteins targets can be analyzed. Protein A will be red on both arrays, protein B will be red and green, etc. This could be expanded to at least a ten by ten array and in principle extended into the third (1O x 1O x 10) or even fourth (1O x 10 x 10 x 10) dimensions.

Description of the Invention

In one aspect, the present invention provides methods for detection of ligand binding, comprising (a) providing a plurality of addressable arrays of molecules to be assessed for ligand binding, wherein the addressable arrays each comprise identical species of molecules to be assessed for ligand binding and/or different molecules to be assessed for ligand binding that bind to the same ligand;

(b) providing a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable;

(c) providing a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between one or more ligands in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample; (d) contacting at least a first addressable array with the first ligand sample and contacting at least a second addressable array with the second ligand sample under conditions to promote ligand binding to molecules to be assessed on the addressable arrays; (e) detecting signal from the detectable labels associated with ligands bound to molecules on the addressable arrays; and

(f) identifying ligand bound to molecules on the addressable arrays based on the signals detected.

As used herein, the term "ligand" refers to any entity, including but not limited to compounds, cells, molecular complexes, molecular assemblies, organelles, membrane systems, crystals, nanoparticles, beads, virus and phage particles, which can bind in a selective or differential manner to molecules on an addressable array, and which can be detectably labeled, either directly or via a secondary label. In various preferred embodiments, the ligand comprises polypeptides, nucleic acids, lipids, carbohydrates, synthetic polymers, metabolites, groups of molecules created as binding agents, drugs or diagnostics, or combinations (including complexes) of any of the foregoing. In one embodiment, the ligand comprises polypeptides or nucleic acids. As used herein "nucleic acids" are any and all forms of alternative nucleic acid containing modified bases, sugars, and backbones. These include, but are not limited to DNA, RNA, peptide nucleic acids ("PNA"), 2'-5' DNA, and locked nucleic acids ("LNA"). The term "polypeptide" is used in its broadest sense to refer to a polymer of subunit amino acids, amino acid analogs, or peptidomimetics, including proteins and peptoids. The polypeptides may be naturally occurring full length proteins or fragments thereof, processed forms of naturally occurring polypeptides (such as by enzymatic digestion), chemically synthesized polypeptides, or recombinantly expressed polypeptides. The polypeptides may comprise D- and/or L-amino acids, as well as any other synthetic amino acid subunit, and may contain any other type of suitable modification, including but not limited to peptidomimetic bonds and reduced peptide bonds, As used herein, the "molecules to be assessed for binding to a ligand" can be any compound, molecule, molecular complex, substance, or surface variation that can bind in a selective or differential manner to ligands on an addressable array. In various preferred embodiments, the molecules to be assessed comprise polypeptides, nucleic acids, lipids, carbohydrates, other polymers, or any synthetic molecular system that either be created or placed in any way (for example, by printing) on a surface to provide a chemically diverse pattern. In a most preferred embodiment, the molecules to be assessed for ligand binding comprise polypeptides or nucleic acids. The "binding" may comprise any detectable interaction of a ligand with a molecule to be assessed, including without limitation a covalent bond, ionic bond, salt bridge, hydrogen bond, van der Waals interaction, hydrophobic / hydrophilic interaction, electrostatic interaction, steric interaction, other associations, or any combination of any of the foregoing. As will be understood by those of skill in the art, array interactions do not require chemical binding. As used herein, an addressable array may be any arrangement or disposition of the species of molecules to be assessed in association with one or more substrates and/or substrate loci, permitting measurement of the labeled ligand associated with each specie of molecules to be assessed. In one embodiment, the addressable array may consist of a single "spot" (ie: region from which signal is to be detected) in which many molecules (ie: at least 20, more preferably 100, 500, 1000, 10,000, or more molecules) to be assessed for ligand binding are pooled. In another embodiments, the addressable array comprises a plurality of spots on which one or more molecules to be assessed for ligand binding; in various embodiments, each addressable array comprises at least 2, 5, 10, 20, 50, 100, 1000, 5000 or more spots on which one or more (2, 5, 10, 50, 100, 1000, or more) molecules to be assessed for ligand binding are present. In one embodiment, the molecules are at specific and identifiable spots on the addressable array. Those of skill in the art will recognize that many such permutations of the molecules on the addressable array are possible. In one non-limiting embodiment, a single spot on the addressable array may comprise a plurality of members of a genus of molecules to be assessed for ligand binding, which have slight variation between them (ie: polypeptides with single amino acid difference, or similar amino acid sequences in different states, such as different protonation or conformation). In another non- limiting embodiment, each spot on the addressable array comprises a distinct molecule to be assessed for ligand binding. As will be clear to those of skill in the art based on the disclosure herein, many other permutations are also possible.

As used herein, the term "substrate" refers to any type of solid support to which the molecules to be assessed for binding to the ligand can be attached. Examples of such substrates include, but are not limited to, microarrays, beads, columns, optical fibers, wipes, nitrocellulose, nylon, glass, quartz, diazotized membranes (paper or nylon), silicones, polyformaldehyde, cellulose, cellulose acetate, paper, ceramics, metals, metalloids, semiconductive materials, coated beads, magnetic particles; plastics such as polyethylene, polypropylene, and polystyrene; and gel- forming materials, such as proteins (e.g., gelatins), lipopolysaccharides, silicates, agarose, polyacrylamides, methylmethracrylate polymers; sol gels; porous polymer hydrogels; nanostructured surfaces; nanotubes (such as carbon nanotubes), and nanoparticles (such as gold nanoparticles or quantum dots). In one exemplary embodiment, the substrate comprises a substrate suitable for use in a "dipstick" device, such as one or more of the substrates disclosed above. When bound to a substrate, the molecules to be assessed for binding to the ligand can be directly linked to the support, or attached to the surface via a linker. Thus, the solid substrate and/or the molecules can be derivatized using methods known in the art to facilitate binding of the molecules to be assessed to the solid support, so long as the derivitization does not eliminate detection of binding between the molecules and their relevant ligand. Other molecules, such as reference or control molecules, can be optionally immobilized on the solid surface as well. Methods for immobilizing various types of molecules on a variety of solid surfaces are well known to those of skill in the art. A wide variety of materials can be used for the solid surface. A variety of different materials may be used to prepare the support to obtain various properties. For example, proteins (e.g., bovine serum albumin) or mixtures of macromolecules (e.g., Denhardt's solution) can be used to minimize non-specific binding, simplify covalent conjugation, and/or enhance signal detection. If covalent bonding between a molecule and the substrate surface is desired, the surface of the substrate will usually be functionalized or capable of being functionalized. Functional groups which may be present on the substrate surface and used for linking include, but are not limited to, carboxylic acids, aldehydes, amino groups, cyano groups, ethylenic groups, hydroxyl groups, and thiol groups. In addition, strong, but noncovalent, interactions may be used for affixing the molecules to the substrate surface (e.g., attachment via a biotin/avidin linkage). Methods for linking a wide variety of compounds to various solid surfaces are well known to those of skill in the art.

As used herein, the term "plurality" means at least two. Thus, in various embodiments 2, 3, 4, 5, 6, 7, 8, 9, 10, or more different addressable arrays can be used with the methods of the invention. There is no theoretical limit on the number of substrates that can be used, so long as enough mathematically independent group assignments (see below) are designated.

As used herein, the phrase "the addressable arrays each comprise identical species of molecules to be assessed" means that each addressable array used in the methods of the invention include all or a subset of the same set of molecules to be assessed for binding to the ligands. Where a subset of the molecules to be assessed for ligand binding are different on the different addressable arrays, the different molecules to be assessed for ligand binding bind to the same ligand. For example, if there are two antibodies for a particular protein, one can be used as a molecule to be assessed on the first addressable array and the other antibody can be used as a molecule to be assessed on the second addressable array. As will be apparent to those of skill in the art, this embodiment can comprise the use of any type of different molecules on the different addressable arrays. This embodiment provides a powerful way to improve performance (decrease false positives) without substantially increasing the associated expense or assay time. Different addressable arrays can also include additional molecules, etc. that are not identical to each addressable array, including but not limited to control molecule/locations on the addressable array, orientation sites, etc. Other variables that can be modified from addressable array to addressable array include, but are not limited to, changes in: amount of molecule attached per unit area; the density of features per unit area; the length of a linker to the surface; and the nature of the attachment chemistry.

In some embodiments, it may be beneficial to include one or more control molecules on the addressable arrays. By comparing the intensity of binding between the control molecules and their ligands with the binding of the molecules to be assessed with their ligands certain variables that might otherwise cause overall signal changes between addressable arrays or from measurement to measurement can be removed. This includes the effects of intrinsic fluorophore yields under the conditions of the measurements, changes in fluorophore labeling efficiency from measurement to measurement, small variations due to incubation time or temperature during the binding process, normalization between different fluorophores used for the different ligand groups and other experiment-associated normalization issues known in the art. As used herein, the phrase "plurality of ligand groups" means at least 2 different ligand groups. Thus, each ligand sample contains at least two different ligand groups. Furthermore, at least one ligand group in each ligand sample comprises at least two different ligands; each ligand in a given ligand group is labeled (directly or indirectly) with an indistinguishable detectable label. In various embodiments, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% of the ligand groups in each ligand sample comprise at least two different ligands. As used herein, "indistinguishable" means capable of simultaneous detection without distinguishing the identification of the specific ligand, and does not mean that the different detectable labels could never be distinguished under any assay conditions. Thus, detection of ligands in a given ligand group does not necessarily result in identification of the specific ligand, but does identify which ligand group the detectable signal is generated by. Ligands in different ligand groups in a ligand sample are labeled with distinguishable detectable labels (directly or indirectly), and thus detection of signal from a single ligand sample distinguishes which ligand group a bound ligand belongs to, while not necessarily specifically identifying which ligand is bound.

There are at least two such ligand samples, and at least two different ligand groups within each ligand sample. In various embodiments, there are 3, 4, 5, 6, 7, 8, 9, 10, or more ligand samples and/or ligand groups. In various further embodiments, each ligand group has at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more ligands. There is no theoretical limit on the number of ligand samples, ligand groups, and/or ligands that can be used, so long as enough mathematically independent labeled groups (see below) are available. When additional ligand groups are utilized, one or more of such additional ligand groups may comprise only a single ligand type. Thus, for example, where 5 ligand groups are used, at least 1 of the ligand groups comprise a plurality of ligands; in various further embodiments, 2, 3, 4, or 5 of the ligand groups comprise at least two different ligands, each ligand in a given ligand group labeled (directly or indirectly) with an indistinguishable detectable label. Those of skill in the art will understand that many such permutations of the ligand groups are possible.

As noted above, the ligands in the second ligand sample (as well as ligands in any further ligand samples) comprise a plurality of the same ligands as in the first labeled ligand sample; in various embodiments, at least 50%, 60%, 70%, 89%, 90%, or more of the ligands in the second (or further) ligand samples are the same as those in the first ligand sample. In a further embodiment, the ligands in the second ligand sample (as well as ligands in any further ligand samples) comprise the same ligands as in the first labeled ligand sample. This embodiment does not require that the set of ligand species comprised in each of the ligand samples are identical, as additional ligands or other compounds can be added to the second, third, and further ligand samples, such as control ligands, different detectable labels, etc.

As used herein, "group assignment" means the determination of which labels are to be associated with which ligand species in the ligand sample to be applied to a given addressable array. Detectable labels are varied between the ligands in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample. Such "mathematically independent group assignments" mean variation of the labels associated with the ligand species in the various ligand samples relative to each other so that signals from the detectable labels on the different addressable arrays can be used to identify the specific ligand(s) involved in binding events on the addressable array(s). The mathematically independent group assignments may be group assignments that are orthogonal, or may be group assignments that are not fully orthogonal but that are sufficiently independent to allow identification of at least one ligand species involved in binding to at least one species of molecule to be assessed on the addressable array(s)

The group assignments of the ligands applied to one addressable array are different than the group assignments used on the second addressable array. If three (or more) addressable arrays are to be used, than the group assignments are different for all of the addressable arrays. Each ligand species may be thought of as having associated with it a group assignment code, which may be expressed as the set of labels assigned to each ligand species in the ligand samples to be applied to each of the addressable arrays, ordered in the same way that the addressable arrays are ordered. For example, if ligand species X is labeled with label 1 in the ligand sample to be applied to the first addressable array, and ligand species X is labeled with label 2 in the ligand sample to be applied to the second addressable array, its group assignment code would be (1, 2). In one embodiment, group assignments are made in such a way that each ligand species has a group assignment code that differs from all other ligand species present in the ligand sample. If group assignments are made in such a way that all ligand species do not have unique group assignment codes, then, in general, the information that can be extracted regarding interaction of ligands with molecules on the addressable arrays may be reduced. For example, if two ligand species have the same group assignments, it may only be possible to determine their combined interaction with the molecules of the addressable array, rather than their individual interactions; such information may nevertheless be useful in some applications. In various embodiments, group assignments are made such that at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent of the ligand species present in a ligand sample have unique group assignment codes.

Further ligand samples would have their ligands assigned to ligand groups in such a way that at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more ligands have mathematically independent group assignments.

Various aspects of the invention are exemplified in Figure 1, using only nine different ligands (noted in this example as proteins) and three different detectable labels (noted in this example as fluorescent tags (quantum dots)). One first splits the nine proteins (9 ligand species in the first labeled ligand sample) into three groups of three (3 ligand groups) and labels each group of three with a different quantum dot (each protein in a ligand group with the same quantum dot (indistinguishable)); ligand species in different ligand groups are labeled with different quantum dots (distinguishable)). One then repeats this with a second protein sample (second labeled ligand sample with the same 9 ligands) but this time uses three different ligand groupings (mathematically independent group assignments relative to the first set of groupings).

First labeled ligand sample: Ligand group 1 : A, B, C Quantum Dot: Red

Ligand group 2: D, E, F Quantum Dot: Green

Ligand Group 3: G, H, I Quantum Dot: Blue

Second labeled ligand sample: Ligand group 1 : A, D, G Quantum Dot: Red

Ligand group 2: B, E, H Quantum Dot: Green

Ligand Group 3: C, F, I Quantum Dot: Blue

Two identical addressable arrays are probed. The first addressable array is probed with the first ligand sample; the second addressable array is probed with the second ligand sample. Following binding and any optional steps to remove unbound ligand, fluorescence detection of signal patterns from the detectable labels on ligand bound to molecules on the addressable array is carried out, but the detection only requires distinguishing between three different colors. By comparing the signal patterns from the two addressable arrays, one can tell which specific protein (ligand) bound to which molecule on the addressable array. In the example shown in Figure 1 , we can deduce, for example, that if the spot is blue on the first addressable array and green on the second addressable array, ligand H was bound to the spot.

Table 1 provides a full set of results based on signals that could be obtained from a spot on the two addressable array in this example.

Table 1:

In a further example where two labeled ligand samples each contain 5 detectably labeled ligand groups, 5 different labels can be used to identify 25 detectably labeled ligands, as exemplified below:

First labeled ligand sample:

Ligand group 1 : A, B, C, D, E Quantum Dot: Red

Ligand group 2: F, G, H, I, J Quantum Dot: Green Ligand Group 3 : K, L, M, N, O Quantum Dot: Blue Ligand Group 4: P, Q, R, S, T Quantum Dot: Orange Ligand Group 5 : U, V, W, X, Y Quantum Dot: Yellow

Second labeled ligand sample:

Ligand group 1 : A, F, K, P, U Quantum Dot: Red Ligand group 2: B, G, L, Q, V Quantum Dot: Green

Ligand Group 3 : C, H, M, R, W Quantum Dot: Blue Ligand Group 4: D, I, N, S, X Quantum Dot: Orange Ligand Group 5 : E, J, O, T, Y Quantum Dot: Blue

Table 2 provides a full set of results based on signal patterns that could be obtained from the two addressable arrays in this example.

Table 2:

In a further example where three labeled ligand samples each contain 3 labeled ligand groups, 3 different labels can be used to identify 27 detectably labeled ligands, as exemplified below:

First labeled ligand sample:

Ligand group 1 : A, B, C, D, E, F, G, H, I Quantum Dot: Red

Ligand group 2: J, K, L, M, N, O, P, Q, R Quantum Dot: Green

Ligand Group 3 : S, T, U, V, W, X, Y, Z, AA Quantum Dot: Blue

Second labeled ligand sample:

Ligand group 1 : A, J, S, B, K, T, C, L, U Quantum Dot: Red

Ligand group 2: D, M, V, E, N, W, F, O, X Quantum Dot: Green

Ligand Group 3 : G, P, Y, H, Q, Z, I, R, AA Quantum Dot: Blue

Third labeled ligand sample:

Ligand group 1 : A, J, S, D, M, V, G, P, Y Quantum Dot: Red

Ligand group 2: B, K, T, E, N, W, H, Q, Z Quantum Dot: Green

Ligand Group 3 : C, L, U, F, O, X, I, R, AA Quantum Dot: Blue

Table 3 provides a full set of results based on signal patterns that could be obtained from the three addressable arrays in this example.

Table 3

As will be apparent to those of skill in the art based on the teachings herein, there is no theoretical limit to the number of detectably labeled ligands that can be assessed for binding using the methods of the invention. For example, 100 different ligands can be labeled, in groups often (10 different ligand groups), with ten different quantum dots (10 different ligands per ligand group), or other detectable labels. An array reader that can distinguish between the ten detectable labels can then be used to compare the signal patterns from two addressable arrays to determine which ligands bound to which molecules on the addressable arrays, all in a single experiment. In a further embodiment, the method is scalable to higher dimensions. For example, if three arrays can be compared, it would be possible to simultaneously decode the arrays for 1000 (10 x 10 x 10) ligand samples by grouping and detectably labeling 3 different ligand samples in three mathematically independent ways. Using 4 different labeled ligand samples in this example permits identification of 10,000 ligand samples in this example. As noted above, there is no theoretical upper limit to the number of different ligand samples (and thus ligands) that can be assessed for binding to molecule(s) of interest, so long as each ligand sample comprises ligands that can be detectably labeled (directly or indirectly) in mathematically independent group assignments with respect to the other ligand samples. In some applications it is useful to consider intensity of fluorescence from spots on the addressable array and/or multiple ligand binding to a particular molecule to be assessed on the addressable array. Furthermore, various experimental issues may reduce the amount of information that can be obtained from measuring binding of the labeled ligands to the addressable arrays. Such issues include labeling efficiency, variations in the number of labeling sites between different ligand species, variations in fluorescence yield of the label associated with the ligand, use of different labels having different extinction coefficients for light absorption and/or different inherent fluorescence yields. In addition, there can be variation in the amount of molecules to be assessed present in a given spot or array position, and there may be experiment-to-experiment variation in the amount of a particular ligand that binds to a particular spot. Thus, in some embodiments it may be useful (but is not necessary) to take some or all of these variables into account. It is possible to consider these and other measurement issues quantitatively. In one embodiment, the label intensity measured at a particular point in an array may be expressed as:

/ = /(/?, C) where I is a signal intensity from a particular reporter attached to ligands bound to a particular position of a particular addressable array which has associated with it molecules to be assessed, C is the concentration of a ligand bound to a particular position in a particular addressable array, and β is a representation of an assignment code determining which ligand is associated with which labeled ligand group and used on which particular addressable array.

In a further embodiment, the label intensity measured at a particular point in an array may be expressed as: I = f(δ,β,C) where I, β, C are as defined above, while δ represents corrections due to both the production and detection of signals from the different reporters used in the labeling of the ligand groups including, but not limited to, variations in the detector efficiency for different labels and efficiency of signal generation by different labels. In a further embodiment, the label intensity measured at a particular point in an array may be expressed as:

I = f(a,δ,β,C) where I, β, C and δ are as defined above, while α represents any corrections needed due to any variations in labeling of the ligand groups including, but not limited to, variations that depend on the reporter used and the ligand molecule being labeled.

In a further embodiment, the label intensity measured at a particular point in an array may be expressed as: n

* ijk ^~ 2—₁ ^km^k P km] ^ im m=\ where I_y is the fluorescence intensity at the position (spot) i on addressable array j for label k. The possible positions or addressable spots on the substrate are assumed to be present in some order given by the index i; the order may be arbitrary provided that the ith spot in all the addressable arrays comprises the same species of molecules to be assessed. There may be a correspondence between the index i and a physical position on the substrate, the code for a bead in an encoded bead system, or other indicia or feature by which the array is made addressable. The index j denotes which addressable array is being referred to. The index k denotes the label species (or, in general, which reporter molecule or reporter system) to which the intensity I corresponds. It is assumed that the intensity attributable to each label species can be determined or estimated. This can simply be the total steady state fluorescence intensity of the fluorescent labels, or could be a quantity that includes in it polarization, fluorescent lifetime, wavelength or other measurable properties of the fluorescence. It is also possible to label the ligands with reporter molecules other than fluorescent labels, so long as the signal from the different labels can be distinguished one from the other, which may be accomplished either by direct measurement, by suitable estimation techniques, and/or by computational analysis.

In the expression given, C_im is the quantity of ligand species m which is bound at position i. The index m denotes which ligand species is being considered. In a preferred embodiment where the quantity and species of molecules to be assessed present at spot i are the same on each addressable array, and the conditions under which the ligand samples are applied to each addressable array are kept uniform, C_im should be the same for each addressable array. It will be apparent to persons having ordinary skill in the art that to the extent that the composition of spot i is varied from one addressable array to another, and/or the conditions under which the ligand samples applied are varied, additional corrections may be employed. In the expression given, the specific affinity (or the binding constant or the dissociation constant) for the ligand species m to the molecules to be assessed at position i is not explicitly considered. Determination of the quantity of each ligand species bound at a particular position does not return a binding constant per se, though it may be possible to estimate a binding constant from the results of this analysis. Thus C_im is simply a measure of the quantity of ligand m bound at spot i.

In this embodiment, αk_m corrects for the average number of labels of type k associated to ligand m and provides a means of taking into account labeling efficiency, site occupancy, and/or any effect that coupling of the dye molecule to ligand m has on the fluorescence intensity of the dye. It is also possible to practice the methods disclosed herein with two or more different dye molecules assigned to any particular ligand group. In principle, if the same coupling chemistry is used, then α_km should be the same for each label species, and α_km then reduces to α_m. In practice, there may be some variation due to different labels coupling with different efficiencies; this can often be alleviated by attaching the label via a linker molecule which is common between labels. In this embodiment, δk corrects for the average fluorescent yield or other signal yield of label k and the detection efficiency of fluorescence or other signal from label k by the measurement instrument (or more generally, the detection efficiency of the signal from the reporter molecule). This term can be removed by normalizing the intensities measured to a standard intensity run on each array. In this embodiment, βkm, has the value of either zero or one, depending on whether ligand m is labeled with dye k in the grouping of ligands applied to substrate j. Thus, βk_mj maps the group assignment code for each ligand into the above expression for intensity.

The above expression for intensity represents one embodiment of a system of equations that can be simultaneously solved for each molecule to be assessed in the addressable array. In general, it is unnecessary to separate α_m from C_im and thus it is the product of these values that will result from the solution to the equations, δk can be removed by normalization to a control as pointed out above (it does not depend on the ligand molecule) and β_km, is known. In this embodiment, the total number of equations is equal to the product of the number of addressable array positions/spots times the number of label species times the number of addressable arrays. This system of equations may or may not completely determine all the (α_m x C_im) terms, depending on the conditions. In an embodiment using fluorescent labels that all couple to approximately the same extent to a particular ligand, where each addressable array can be well normalized via control probes and each ligand has a different assignment code, the (α_m x C_im) values can be entirely determined. It will be apparent to persons having ordinary skill in the art that many embodiments and variations are possible, resulting in systems of equations that may be completely or partially determined and that useful information regarding the interaction of ligand species with molecules to be assessed may be extracted in all such embodiments.

Thus, in further embodiments of each of the embodiments disclosed for the methods of the first aspect of the invention (and the fourth aspect disclosed below), the method comprises detecting the signal attributable to each label species with respect to each addressable array position for each addressable array; forming a set of equations selected from the group consisting of a) I = f{β, C); b) I = f(δ,β,C) ; c) / = /(«, δ, β,C); and n d) I_≠ = ∑ a _km δj^ C_11n ; and m=l solving the system of equations to determine a measure relating to the relative occupancy of at least one addressable array position by at least one ligand species or set of ligand species Thus, for example, in embodiments where ligand species are assigned to label groups such that at least one ligand species has a group assignment that differs from that of at least one other ligand species, the system of equations is solved to determine a measure relating to the relative occupancy of at least one addressable array position by at least one ligand species or set of ligand species. In another embodiment where ligand species are assigned to label groups such that at least 1, 2, 3, 4, 5, or more ligand species has a group assignment that differs from that of all other ligand species, the system of equations is solved to determine a measure relating to the relative occupancy of at least one addressable array position by at least one ligand species. In a further example where ligand species are assigned to label groups such that all ligand species have unique group assignments, the system of equations is solved for C_im or α_m C_im. or determining another measure relating to the relative occupancy of at least one addressable array position by at least one ligand species. Determining suitable conditions to promote binding of specific ligand types to molecules on the addressable array is well within the level of those of skill in the art. Thus, the methods of the invention are not limited by any specific type of binding conditions employed. Such conditions will vary depending on the type of ligand, the type of molecules arrayed on the addressable array, the type of substrate, the density of the molecules arrayed on the substrate, desired stringency of the binding interaction, and nature of the competing materials in the binding solution. In a preferred embodiment, the conditions comprise a step to remove unbound ligand from the addressable array. Determining the need for such a step, and appropriate conditions for such a step, are well within the level of skill in the art.

Any type of detectable label can be used in the methods of the present invention, including but not limited to radioisotope labels, fluorescent labels, luminescent labels, and electrochemical labels (ie: ligands labels with different electrode mid-point potential, where detection comprises detecting electric potential of the label). In a preferred embodiment, fluorescent or electrochemical labels are used. Detection of signal from detectable labels is well within the level of skill in the art. For example, fluorescent array readers are well known in the art, as are instruments to record electric potentials on a substrate (For electrochemical detection see, for example, J. Wang (2000) Analytical Electrochemistry, Vol., 2nd ed., Wiley - VCH, New York). In a further preferred embodiment, the detectable labels comprise quantum dots, which are commercially available from a number of sources, such as Invitrogen web site probes.invitrogen.com/products/qdot/) and Evident Technologies (web site evidenttech. com/nanomaterials/evidots/quantum-dot-emission- absorption.php). While any set of fluorophores with desirable absorbance and fluorescence properties (based on the user's needs) can be used, quantum dots have the advantage that they have narrow fluorescence spectra, so that up to at least 10 can be distinguished with a commercially available reader and some can be excited at the same wavelength. Quantum dots are specifically capable of absorbing energy from either a particle beam or an electromagnetic radiation source (of broad or narrow bandwidth), and are capable of emitting detectable electromagnetic radiation in a narrow wavelength band when so excited. Quantum dots may be grown in a core/shell configuration wherein a first semiconductor nanocrystal forms a core, and then shells of other semiconductors having controlled thickness of several monolayers are grown surrounding the core. See U.S. Pat. No. 6,333,110. In addition, quantum dots may be passivated with an inorganic coating, or "shell," uniformly deposited thereon, which can result in an increase in the quantum yield of the fluorescence emission, depending on the nature of the inorganic coating. The particular wavelength band emitted from a particular core/shell quantum dot then can be adjusted according to both the size and composition of the core and shell layers, and the number of shell layers surrounding the core. Labeling of the ligands with quantum dots thus advantageously permits simultaneous use of a plurality of differently colored quantum dots to be used in a single assay without significant spectral overlap in wavelengths of emitted light. Examples of quantum dots known in the art have a core selected from nanocrystals of Group II, VI semiconductors, such as MgS, MgSe, MgTe, CaS, CaSe, CaTe, SrS, SrSe, SrTe, BaS, BaSe, BaTe, ZnS, ZnSe, ZnTe, CdS, CdSe, CdTe, HgS, HgSe, and HgTe as well as mixed compositions thereof, and nanocrystals of Group III, V semiconductors such as GaAs, InGaAs, InP, and InAs and mixed compositions thereof, which nanocrystals are capable of emitting electromagnetic radiation upon excitation. See U.S. Pat. No. 6,207,392. The use of Group IV semiconductors such as germanium or silicon, and the use of organic semiconductors, may also be feasible under certain conditions. The semiconductor nanocrystals can also include alloys comprising two or more semiconductors selected from the groups described previously, and combinations thereof. Methods for making quantum dots are known in the art, as are methods for linking them (directly or indirectly, via linkers) to ligands. See, for example, US Patent Nos. 6630307; 6326144; 7079214, and US published application no. 2003148379, each incorporated by reference herein in their entirety.

In one embodiment, secondary labels can be used, including but not limited to secondary antibodies or ligands that bind to the ligands.

In one embodiment, the methods are used for finding oligonucleotide sequences or peptide sequences, arrayed on a substrate, that bind to specific protein ligands. The methods of the invention permit the use of a small number of addressable arrays (thus greatly reducing cost) to conduct, for example, high throughput screening of a very large number of potential binding partners for detectably labeled ligands of interest, looking for those with specific binding properties. As will be clear to those of skill in the art based on the teachings herein, the methods of the invention are also applicable, for example, to a variety of molecular evolution and library screening technologies, proteomics and metabolomics measurements, and large scale DNA hybridization assays to test many different samples on one addressable array. As will further be apparent to those of skill in the art, there are many variations on this theme including DNA/DNA, DNA/protein, DNA/RNA, RNA/protein, peptide/DNA, peptide/protein, protein/protein, and small molecule/peptide binding assays that could be performed according to the methods of the invention.

In a further embodiment, the ligands can be created on a substrate in the proper groupings, released and bound to a different set of addressable arrays as described above. This would be a way to store the ligands, as well as to search for peptide/peptide interactions, for example. This is also a good way to label specific groups of ligands, particularly if the ligands can be synthesized in situ on the surface. Methods for making the various ligands and addressable array of molecules to be assessed for binding to a ligand are well known in the art.

Methods for detecting signal from the ligand bound to the molecules on the addressable arrays are known in the art. In one embodiment, an imaging scheme comprising an excitation source, a monochromator (or any device capable of spectrally resolving the image, or a set of narrow band filters) and a detector array is used. In one embodiment, the apparatus consists of a blue or UV source of light, of a wavelength shorter than that of the luminescence detected. This may be a broadband UV light source, such as a deuterium lamp with a filter in front; the output of a white light source such as a xenon lamp or a deuterium lamp after passing through a monochromator to extract out the desired wavelengths; or any of a number of continuous wave (cw) gas lasers, including but not limited to any of the Argon Ion laser lines (457, 488, 514, etc. nm), a HeCd laser; solid state diode lasers in the blue such as GaN and GaAs (doubled) based lasers or the doubled or tripled output of YAG or YLF based lasers; or any of the pulsed lasers, to name a few. In a further embodiment, signals from the quantum dots may be passed through an imaging subtracting double monochromator, two single monochromators with the second one reversed from the first, or a computer controlled color filter wheel where each filter is a narrow band filter centered at the wavelength of emission of one of the dots. A CCD camera or some other two dimensional detector can be used to record the images, and software color codes that image to the wavelength chosen above.

In another embodiment, a scanning detection system is used, where the sample to be analyzed is scanned with respect to a microscope objective. The luminescence is put through a single monochromator or a grating or prism to spectrally resolve the colors. The detector is a diode array that then records the colors that are emitted at a particular spatial position. The software then ultimately recreates the scanned image and decodes it. As will be understood by those of skill in the art, readers using scanning systems and CCD camera detectors are commercially available (Princeton Instruments, Trenton, NJ 08619, Diagnostic Instruments Sterling Heights, MI 48314). Any one or all of the steps of the method can be automated or semi-automated, using automated synthesis methods, robotic handling of addressable arrays, microfluidics, and automated signal detection and analysis hardware (such as fluorescence detection hardware) and software.

In a second aspect, the present invention provides computer readable storage media. In one embodiment, the computer readable storage media comprise a set of instructions for causing a device to execute procedures comprising:

(a) detecting signal from detectable labels associated with ligands bound to molecules on one or more addressable array, wherein the ligands comprise

(i) a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable; and (ii) a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between at least one ligand in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample; and (c) identifying ligand bound to molecules on the addressable arrays based on the signals detected.

In a further embodiment, the plurality of ligand groups in the first and second ligand samples comprise a plurality of different ligands. In another embodiment, each ligand group in the first and second ligand samples comprise a plurality of different ligands. In a still further embodiment, detectable labels are varied between a plurality of ligands in the second ligand sample relative to the first ligand sample. In a further embodiment, detectable labels are varied between each ligand in the second ligand sample relative to the first ligand sample.

(a) detecting signal from detectable labels associated with ligands bound to molecules on one or more addressable array;

(b) forming a set of equations selected from the group consisting of i) / = /(/?, C); ii) I = f(δ,β,C) ; iii) / = /(«, δ, β,C); and

; and

(c) solving the system of equations to determine a measure relating to the relative occupancy of at least one addressable array position by at least one ligand species or set of ligand species.

In a further embodiment, the computer readable storage media comprises a set of instructions for causing the device to execute procedures for carrying out the first and/or fourth aspects of the invention.

The definitions and all embodiments disclosed in the first aspect apply to this second aspect, including but not limited to definitions for "ligands," "ligand groups," "detectable labels," "indistinguishable" and "mathematically independent group assignment," and any other terms in this third aspect that were previously defined and exemplified in the first aspect of the invention.

The computer readable storage medium can include, but is not limited to, magnetic disks, optical disks, organic memory, and any other volatile (e.g., Random Access Memory ("RAM")) or non-volatile (e.g., Read-Only Memory ("ROM")) mass storage system readable by a central processing unit ("CPU"). The computer readable storage medium includes cooperating or interconnected computer readable medium, which can exist exclusively on the processing system of the device or be distributed among multiple interconnected processing systems that may be local or remote to the device.

The invention further provides devices incorporating the computer readable storage media of the invention. The device can be any device capable of detecting signal and carrying out the analysis of the methods of the invention. In one embodiment the procedures are executed by a signal detection device or array reader comprising a processing device (such as a computer), where the processing device is either integrated into the device or is remote from the device.

In a third aspect, the present invention provides compositions, comprising:

(a) a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, and wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signals generated from different ligand groups or secondary labels in the first ligand sample are distinguishable one from the other; and

(b) a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable one from the other; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between one or more ligands in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample. The definitions and all embodiments disclosed in the first aspect apply to this third aspect, including but not limited to definitions for "ligands," "ligand groups," "detectable labels," "indistinguishable" and "mathematically independent group assignment," and any other terms in this third aspect that were previously defined and exemplified in the first aspect of the invention. The composition can be present in solution, lyophilized, or attached to a substrate, such as those substrates described above for the first aspect of the invention.

In a further embodiment of this third aspect, there are at least 2 ligand samples, each with at least 2 detectably labeled (directly or indirectly) ligand groups of at least 2 detectably labeled ligands each. In further preferred embodiments, there are at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or more ligand samples, each with 2, 3, 4, 5, 6, 7, 8, 9, 10, or more detectably labeled (directly or indirectly) ligand groups of 2, 3, 4, 5, 6, 7, 8, 9, 10, or more ligand species each. There is no theoretical limit on the number of ligand samples, labeled ligand groups, and/or ligands that can be used, so long as enough mathematically independent group assignments (see above) can be made. The compositions of the invention can be used, for example, in the methods of first aspect of the invention.

In a fourth aspect, the present invention provides methods for detection of ligand binding, comprising

(a) providing an addressable array of molecules to be assessed for ligand binding;

(b) contacting the addressable array with a first ligand sample comprising a plurality of ligand groups under conditions to promote ligand binding to molecules on the addressable array, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable; (c) detecting signal from the detectable labels associated with ligands from the first ligand sample bound to molecules on the addressable array;

(d) removing bound ligand from the addressable array;

(e) contacting the addressable array with a second ligand sample comprising a plurality of ligand groups under conditions to promote ligand binding to molecules on the addressable array, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between at least one ligand in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample;

(f) detecting signal from the detectable label associated with ligands from the second ligand sample bound to molecules on the addressable array; and (g) identifying ligand bound to molecules on the addressable array based on the signals detected .

The definitions and all embodiments disclosed in the first aspect apply to this fourth aspect, including but not limited to definitions for "ligands," "ligand groups," "detectable labels," "indistinguishable" and "mathematically independent group assignments," and any other terms in this fourth aspect that were previously defined and exemplified in the first aspect of the invention.

It will be apparent to persons having ordinary skill in the art that many variations and/or equivalents of various aspects of the invention disclosed herein could be employed, and the disclosure hereof is intended to extend to all operable variations and/or equivalents. Examples and illustrative embodiments disclosed herein are intended to be non-limiting. Unless otherwise expressly stated, none of the specific choices or instances reflected in any of such examples or illustrative embodiments or any subpart, step, or component thereof is intended to give rise to any inference that any of such specific choices or instances is a required feature or aspect of the invention disclosed herein.

Claims

I claim

1. A method for detection of ligand binding, comprising

(a) providing a plurality of addressable arrays of molecules to be assessed for ligand binding, wherein the addressable arrays each comprise identical species of molecules to be assessed for ligand binding and/or different molecules to be assessed for ligand binding that bind to the same ligand;

(b) providing a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable; (c) providing a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between at least one ligand in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample;

(e) detecting signal from the detectable labels associated with ligands bound to molecules on the addressable arrays; and (f) identifying ligand bound to molecules on the addressable arrays based on the signals detected.

2. The method of claim 1 wherein a plurality of ligand groups in the first ligand sample comprise a plurality of different ligands and wherein a plurality of ligand groups in the second ligand sample comprise a plurality of different ligands.

3. The method of claim 1 wherein each ligand group in the first ligand sample comprise a plurality of different ligands and wherein each ligand group in the second ligand sample comprise a plurality of different ligands.

4. The method of any one of claims 1-3 wherein detectable labels are varied between a plurality of ligands in the second ligand sample relative to the first ligand sample.

5. The method of any one of claims 1-3 wherein detectable labels are varied between each ligand in the second ligand sample relative to the first ligand sample.

6. The method of any one of claims 1-5, wherein the ligands in the first and second ligand samples comprise ligands selected from the group consisting of polypeptides, lipids, carbohydrates, and nucleic acids.

7. The method of any one of claims 1-6, wherein the molecules to be assessed for binding to a ligand comprise polypeptides, lipids, carbohydrates, and nucleic acids.

8. The method of any one of claims 1-7 wherein the plurality of addressable arrays comprise identical species of molecules to be assessed for ligand binding.

9. The method of any one of claims 1 -8 wherein the plurality of addressable arrays comprise different molecules to be assessed for ligand binding that bind to the same ligand.

10. The method of any one of claims 1 -9 further comprising providing a third ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the third ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the third ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the third ligand sample, wherein signal generated from different ligand groups or secondary labels in the third ligand sample are distinguishable; wherein the ligands in the third ligand sample comprise a plurality of the same ligands as in the first ligand sample and the second ligand sample, and wherein detectable labels are varied between at least one ligand in the third ligand sample relative to the first ligand sample and the second ligand sample to provide mathematically independent group assignments in the third ligand sample relative to the first ligand sample and the second ligand sample;

(d) contacting at least a third addressable array with the third ligand sample under conditions to promote ligand binding to molecules on the addressable array; and

(e) detecting signal from ligand bound to molecules on the third addressable array.

11. The method of any one of claims 1-10 wherein the first ligand group and the second ligand group each comprise at least 3 different ligand samples.

12. The method of any one of claims 1-11 wherein the detectable labels comprise quantum dots.

13. The method of any one of claims 1-12, wherein the detecting and identifying steps comprise: (a) detecting the signal attributable to each label species with respect to each addressable array position for each addressable array;

(b) forming a set of equations selected from the group consisting of i) I = f{β, C); ii) I = f(δ,β,C) ; iii) / = /(«, δ, β,C); and

; and

14. A computer readable storage media comprising a set of instructions for causing a device to execute procedures for carrying out the method of any one of claims 1-13.

15. A computer readable storage medium comprising a set of instructions for causing a device to execute procedures comprising: (a) detecting signal from detectable labels associated with ligands bound to molecules on one or more addressable array, wherein the ligands comprise (i) a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signal generated from different ligand groups or secondary labels in the first ligand sample are distinguishable; and (ii) a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between at least one ligand in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample; and

(d) identifying ligand bound to molecules on the addressable arrays based on the signals detected.

16. The computer readable storage medium of claim 15 wherein a plurality of ligand groups in the first ligand sample comprise a plurality of different ligands and wherein a plurality of ligand groups in the second ligand sample comprise a plurality of different ligands.

17. The computer readable storage medium of claim 15 wherein each ligand group in the first ligand sample comprise a plurality of different ligands and wherein each ligand group in the second ligand sample comprise a plurality of different ligands.

18. The computer readable storage medium of any one of claims 15-17 wherein detectable labels are varied between a plurality of ligands in the second ligand sample relative to the first ligand sample.

19. The computer readable storage medium of any one of claims 15-17 wherein detectable labels are varied between each ligand in the second ligand sample relative to the first ligand sample.

20. A computer readable storage media comprising a set of instructions for causing a device to execute procedures comprising:

21. A device comprising the computer readable storage media of any one of claims 14-20.

22. A composition, comprising:

(a) a first ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the first ligand sample comprises a plurality of different ligands, and wherein each ligand in a given ligand group in the first ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the first ligand sample, and wherein signals generated from different ligand groups or secondary labels in the first ligand sample are distinguishable one from the other; and (b) a second ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable one from the other; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between at least one ligand in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample.

23. The composition of claim 22 wherein a plurality of ligand groups in the first ligand sample comprise a plurality of different ligands and wherein a plurality of ligand groups in the second ligand sample comprise a plurality of different ligands.

24. The composition of claim 22 wherein each ligand group in the first ligand sample comprise a plurality of different ligands and wherein each ligand group in the second ligand sample comprise a plurality of different ligands.

25. The composition of any one of claims 22-24 wherein detectable labels are varied between a plurality of ligands in the second ligand sample relative to the first ligand sample.

26. The composition of any one of claims 22-24 wherein detectable labels are varied between each ligand in the second ligand sample relative to the first ligand sample.

27. The composition of any one of claims 22-26, wherein the ligands in the first and second ligand samples comprise ligands selected from the group consisting of polypeptides, lipids, carbohydrates, and nucleic acids.

28. The composition of any one of claims 22-27 further comprising a third ligand sample comprising a plurality of ligand groups, wherein at least one ligand group in the third ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the third ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the third ligand sample, wherein signal generated from different ligand groups or secondary labels in the third ligand sample are distinguishable; wherein the ligands in the third ligand sample comprise a plurality of the same ligands as in the first ligand sample and the second ligand sample, and wherein detectable labels are varied between at least one ligand in the third ligand sample relative to the first ligand sample and the second ligand sample to provide mathematically independent group assignments in the third ligand sample relative to the first ligand sample and the second ligand sample.

29. A method for detection of ligand binding, comprising

(c) detecting signal from the detectable labels associated with ligands from the first ligand sample bound to molecules on the addressable array; (d) removing bound ligand from the addressable array;

(e) contacting the addressable array with a second ligand sample comprising a plurality of ligand groups under conditions to promote ligand binding to molecules on the addressable array, wherein at least one ligand group in the second ligand sample comprises a plurality of different ligands, wherein each ligand in a given ligand group in the second ligand sample is labeled with an indistinguishable detectable label or is capable of binding to an indistinguishable detectable secondary label that binds the ligands of said ligand group in preference to the ligands of any other ligand group present in the second ligand sample, wherein signal generated from different ligand groups or secondary labels in the second ligand sample are distinguishable; wherein the ligands in the second ligand sample comprise a plurality of the same ligands as in the first ligand sample, and wherein detectable labels are varied between at least one ligand in the second ligand sample relative to the first ligand sample to provide mathematically independent group assignments in the second ligand sample relative to the first ligand sample; (f) detecting signal from the detectable label associated with ligands from the second ligand sample bound to molecules on the addressable array; and