Self-assembling arrays and uses thereof
First Claim
1. A combination, comprising:
- (a) an addressable collection of capture agents;
(b) a plurality of sets of binding partners, wherein each set of binding partners specifically binds to a unique capture agent; and
(c) either or both of;
one or more conjugation reagents for effecting covalent linkage of a binding partner to a displayed molecule and/or displayed biological particle; and
/or instructions for use of the addressable collection of capture agents and binding partners to prepare self-assembled arrays.
2 Assignments
0 Petitions
Accused Products
Abstract
Provided herein are methods, combinations, kits and systems for self-assembly of a self-assembling array to produce self-assembled arrays. The self-assembling arrays contain addressed collections of capture agents and are used with binding partners and reagents for conjugation of binding partners to molecules and/or biological particles for display in self-assembled arrays. The capture agents at each locus in a self-assembling array are specific to one of a set of binding partner molecules. The binding partners are conjugated to molecules and/or biological particles for display. Following conjugation, the resulting conjugates are sorted on the array based on the specific interaction of the binding partner and the capture agent to produce a self-assembled array.
128 Citations
247 Claims
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1. A combination, comprising:
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(a) an addressable collection of capture agents;
(b) a plurality of sets of binding partners, wherein each set of binding partners specifically binds to a unique capture agent; and
(c) either or both of;
one or more conjugation reagents for effecting covalent linkage of a binding partner to a displayed molecule and/or displayed biological particle; and
/orinstructions for use of the addressable collection of capture agents and binding partners to prepare self-assembled arrays. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
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35. A combination, comprising:
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an addressable collection of capture agents; and
a list setting forth the amino acid sequences that comprise the binding portion of polypeptide binding partners for each member of the collection of capture agents or setting forth sequences of nucleotides that encode the sequences of amino acids of binding partners that specifically bind to each member of the collection of capture agents. - View Dependent Claims (36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62)
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63. A combination, comprising:
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an addressable collection of capture agents;
a collection of sets of nucleic acid molecules, wherein;
the nucleic acid molecules of each set encode all or a portion of a polypeptide binding partner;
the encoded polypeptide binding partner or portion binds to a capture agent; and
one or more conjugation reagent(s) for linking the encoded polypeptides to molecules and/or biological particles. - View Dependent Claims (64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90)
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91. A method for preparing a self-assembled array, comprising:
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a) providing an addressable array of capture agents that have predetermined binding partners;
b) preparing a plurality of sets of conjugates, wherein;
each set of conjugates comprises a biological particle and/or molecule linked to a binding partner or plurality thereof, wherein the binding partner binds to one of the capture agents in the array; and
c) contacting the addressable array of capture agents with the sets of conjugates to produce the self-assembled array. - View Dependent Claims (93, 94, 95, 96, 97, 98, 99, 100, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154)
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92. A method for preparing a self-assembled array, comprising:
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a) providing an addressable array of capture agents that have predetermined binding partners;
b) preparing sets of binding partners, wherein a binding partner is a polypeptide encoded by a nucleic acid;
c) preparing a plurality of sets of conjugates, wherein;
each set of conjugates comprises a biological particle and/or molecule linked to a binding partner or plurality thereof from one set of binding partners, wherein the binding partner binds to one of the capture agents in the array; and
d) contacting the addressable array of capture agents with the sets of conjugates to produce the self-assembled array. - View Dependent Claims (101)
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102. A method for preparing a self-assembled array, comprising:
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a) providing an addressable array of capture agents that have predetermined binding partners;
b) providing a plurality of sets binding partners, wherein each set of binding partners specifically binds to a unique capture agent, and each set of binding partners is separate from each other set; and
c) crosslinking each set of binding partners to molecules and/or biological particles to produce sets of conjugates. - View Dependent Claims (106)
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103. A method for preparing a self-assembled array, comprising:
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a) providing an addressable array of capture agents that have predetermined binding partners;
b) providing a plurality of sets binding partners, wherein each set of binding partners specifically binds to a unique capture agent, and each set of binding partners is separate from each other set; and
c) linking each set of binding partners to beads to produce sets of binding partner beads. - View Dependent Claims (104, 105)
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155. A self-assembled array, comprising:
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a) an addressable array of capture agents that have predetermined binding partners; and
b) a plurality of sets of conjugates, wherein;
each set of conjugates comprises a biological particle and/or molecule linked to a binding partner or plurality thereof, wherein the binding partners are specifically bound to their capture agents. - View Dependent Claims (156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 211, 212)
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179. A combination, comprising:
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an addressable collection of capture agents;
a plurality of sets of binding partners, wherein each set of binding partners specifically binds to a unique capture agent; and
wherein the binding partner is linked to a linker or intermediate molecule; and
wherein a displayed molecule and/or a displayed particle is attached to the linker or intermediate molecule. - View Dependent Claims (180, 181, 182, 183, 184, 185, 186)
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187. A method of analyzing and/or processing a signal or plurality thereof at loci on an exposed positionally addressable array, comprising:
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a) receiving image data corresponding to pixel luminosity information at the exposed locus within the positionally addressable array, wherein the locus comprises capture agents;
b) specifying pre-determined input parameters for processing the received image data that include parameters that specify a predetermined array locus or plurality thereof on a surface of the array;
c) determining an actual location of a locus or plurality thereof on the array; and
d) processing the image data for each exposed locus in accord with the determined actual locus and the input parameters. - View Dependent Claims (188, 189, 190, 191, 194)
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192. A method for processing a signal or plurality thereof at loci that display a detectable signal in or on an array, comprising:
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a) receiving image data corresponding to pixel luminosity information for locations for a plurality of the loci of the array;
b) for a particular locus of the array, determining neighbor luminosity effects on the image data for the particular locus that are produced from adjacent neighbor loci; and
c) compensating for the neighbor luminosity effects of the adjacent neighbor loci from the image data for the particular locus. - View Dependent Claims (193)
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195. A method of processing a signal or plurality thereof at loci on a positionally addressable array, comprising:
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a) receiving image data corresponding to pixel luminosity information of the locations for a plurality of the loci of the array;
b) for a particular locus of the array, determining neighbor luminosity effects on the image data for the particular locus that are produced from adjacent neighbor loci; and
c) compensating for the neighbor luminosity effects of the adjacent neighbor loci from the image data for the particular locus. - View Dependent Claims (196, 197, 198, 199, 200)
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201. A program product for use in a computer device that executes program instructions recorded in a computer-readable medium to perform a method for analyzing arrays that have loci that display a detectable signal in or on the array, the program product comprising:
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a recordable medium; and
a plurality of computer-readable instructions executable by the computer device to perform a method comprising;
receiving image data corresponding to pixel luminosity information of the loci;
specifying input parameters for processing the received image data that include parameters that specify a predicted array location for each locus of the array, determining an actual location for each locus; and
processing the image data for each location in accord with the determined actual location and the input parameters. - View Dependent Claims (202, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247)
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203. A program product for use in a computer device that executes program instructions recorded in a computer-readable medium to perform a method for processing an array with loci that display a detectable signal in or on the array, comprising:
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a recordable medium; and
a plurality of computer-readable instructions executable by the computer device to perform the method comprising receiving image data corresponding to pixel luminosity information of the loci for a plurality of the locations of the array, for a particular locus in the array, determining neighbor luminosity effects on the image data for the particular location that are produced from adjacent neighbor locations, and compensating for the neighbor luminosity effects of the adjacent neighbor locations from the image data for the particular location. - View Dependent Claims (204, 205, 206)
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207. An apparatus that processes data produced from imaging detectable loci on an array, comprising:
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a computer processor that executes program instructions;
an input processor that receives input parameters for processing received image data, including input parameters that specify a predicted array location for each locus on the array, wherein the image data corresponds to pixel luminosity information for loci in the array; and
an image analysis processor that determines an actual location on the array for each locus, and processes the image data for each location in accord with the determined actual location and the input parameters. - View Dependent Claims (208)
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209. An apparatus that processes data produced from imaging detectable loci in an array, the apparatus comprising:
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a computer processor that executes program instructions;
an input processor that receives image data comprising pixel luminosity information for loci in the array; and
an image analysis processor that determines neighbor luminosity effects on image data for a particular locus produced from adjacent neighbor locations, and that compensates for the neighbor luminosity effects of the adjacent neighbor locations from the image data for the particular location. - View Dependent Claims (210)
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213. A system for analysis of a collection of self-assembled arrays, comprising:
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an addressable collection of capture agents and binding partners, comprising sets of capture agents and binding partners, wherein a set of capture agents is selected to specifically bind to a set of binding partners with sufficiently high affinity to produce collections of self-assembled arrays;
a conjugation reagent, comprising a compound or molecule sufficient for the conjugation of the sets of binding partners to sets of molecules or biological particles;
a computer programmed with instructions for controlling and directing production of an image of the conjugated sets of molecules or biological particles displayed on the collections of self-assembled arrays; and
software for processing of image data produced by the collections of self-assembled arrays. - View Dependent Claims (214, 215, 216)
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Specification