Universal microarray system
First Claim
1. A universal microarray comprising a solid substrate and a plurality of oligonucleotide probes wherein the plurality of oligonucleotide probes are bound on said substrate in a plurality of spots, wherein a pool of oligonucleotide probes of said plurality of oligonucleotide probes is bound to each spot of the microarray, each oligonucleotide of said plurality of oligonucleotide probes has the form:
-
B-C-Dwhereina) portion B is a unique z-mer comprising from 5 to 8 nucleotide bases such that all 4Z permutations of A, G, C, and T are represented in said plurality of oligonucleotide probes;
b) portion C is a variable x-mer comprising from 1 to 5 nucleotide bases such that all 4X permutations of A, G, C, and T are represented in said plurality of oligonucleotide probes;
c) portion D is a universal n-mer comprising from 5 to 8 nucleotide bases that is the same for every probe; and
wherein a pool of oligonucleotide probes contains oligonucleotide probes wherein only one of said 4Z permutation of B is present and all 4X permutations of C are present in about equal concentrations.
7 Assignments
0 Petitions
Accused Products
Abstract
The present invention provides a simple, cost-effective, universal method for determining and/or quantifying differences in nucleic acid levels between two or more test mixtures without prior knowledge of the sequence of the nucleic acids of interest. The method involves providing a universal microarray containing a plurality of spots, where each spot contains a plurality, or pool, of different oligonucleotide probes having at least three distinct portions: a universal sequence portion, a short central variable “wobble” sequence portion, and a unique sequence portion. A set of probes is synthesized such that the universal sequence portion is the same for every probe, and all possible permutations of the wobble sequence and unique sequence portions are represented in approximately equal concentrations in the set. The probes are pooled on the universal microarray such that probes in a given spot have the same unique portion and every permutation of the short wobble, while probes on different spots have different unique portions. Primers complementary to the universal and wobble portions of the probes are used to synthesize, for example, cDNA from an mRNA preparation. The cDNA is hybridized to the universal microarray, and through the use of differential labeling, is identified and/or quantified.
-
Citations
52 Claims
-
1. A universal microarray comprising a solid substrate and a plurality of oligonucleotide probes wherein the plurality of oligonucleotide probes are bound on said substrate in a plurality of spots, wherein a pool of oligonucleotide probes of said plurality of oligonucleotide probes is bound to each spot of the microarray, each oligonucleotide of said plurality of oligonucleotide probes has the form:
-
B-C-Dwherein a) portion B is a unique z-mer comprising from 5 to 8 nucleotide bases such that all 4Z permutations of A, G, C, and T are represented in said plurality of oligonucleotide probes; b) portion C is a variable x-mer comprising from 1 to 5 nucleotide bases such that all 4X permutations of A, G, C, and T are represented in said plurality of oligonucleotide probes; c) portion D is a universal n-mer comprising from 5 to 8 nucleotide bases that is the same for every probe; and wherein a pool of oligonucleotide probes contains oligonucleotide probes wherein only one of said 4Z permutation of B is present and all 4X permutations of C are present in about equal concentrations. - 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, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48)
-
-
26. A universal microarray comprising a solid substrate and a plurality of oligonucleotide probes wherein the plurality of oligonucleotide probes are bound on said substrate in a plurality of spots, wherein a pool of oligonucleotide probes of said plurality of oligonucleotide probes is bound to each spot of the microarray, each oligonucleotide of said plurality of oligonucleotide probes has the form:
-
B-C-Dwherein a) portion B is a unique hexamer such that all 46 permutations of A, G, C, and T are represented in said plurality of oligonucleotide probes; b) portion C is a variable dimer such that all 42 permutations of A, G, C, and T are represented in said plurality of oligonucleotide probes; c) portion D is a universal hexamer that is the same for every probe; and wherein a pool of oligonucleotide probes contains oligonucleotide probes wherein only one of said 46 permutation of B is present and all 42 permutations of C are present in about equal concentrations.
-
-
49. A set of oligonucleotide probes separated into a plurality of pools, each of said pools comprising a plurality of oligonucleotide probes, said oligonucleotide probes having the form:
-
B-C-Dwherein a) portion B is a unique z-mer comprising from 5 to 8 nucleotide bases such that all 4Z permutations of A, G, C, and T are represented in said set of oligonucleotide probes and only one of said 4Z permutations is present in each pool; b) portion C is a variable x-mer comprising from 1 to 5 nucleotide bases such that all 4X permutations of A, G, C, and T are represented in said set of oligonucleotide probes and all 4Z permutations are present in every pool in about equal concentrations; and c) portion D is a universal n-mer comprising from 5 to 8 nucleotide bases that is the same for every oligonucleotide probe. - View Dependent Claims (50, 51)
-
-
52. A set of oligonucleotide probes separated into a plurality of pools, each of said pools comprising a plurality of oligonucleotide probes, said oligonucleotide probes having the form:
-
B-C-Dwherein a) portion B is a unique hexamer such that all 46 permutations of A, G, C, and T are represented in said set of oligonucleotide probes and only one of said 46 permutations is present in each pool; b) portion C is a variable dimer such that all 42 permutations of A, G, C, and T are represented in said set of oligonucleotide probes and all 42 permutations are present in every pool in about equal concentrations; and c) portion D is a universal hexamer that is the same for every oligonucleotide probe.
-
Specification