Polymeric arrays and methods for their use in binding assays

Chemistry: molecular biology and microbiology – Apparatus – Including measuring or testing

Reexamination Certificate

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C435S005000, C435S006120, C435S007100, C435S091100, C435S091200, C536S022100, C536S023100, C536S024300, C536S024310, C536S024320, C536S024330, C530S334000, C530S350000

Reexamination Certificate

active

06489159

ABSTRACT:

INTRODUCTION
Technical Field
The field of this invention is biopolymeric micro arrays.
BACKGROUND OF THE INVENTION
“Biochips” or micro arrays of binding agents, such as oligonucleotides, have become an increasingly important tool in the biotechnology industry and related fields. These binding agent micro arrays, in which a plurality of binding agents are deposited onto a solid support surface in the form of an array or pattern, find use in a variety of applications, including drug screening, oligonucleotide sequencing, and the like. One important use of biochips is in the analysis of differential gene expression, where the expression of genes in different cells, normally a cell of interest and a control, is compared and any discrepancies in expression are identified. In such assays, the presence of discrepancies indicates a difference in the classes of genes expressed in the cells being compared. Differential gene expression assays allow one to generate expression profiling data for several hundred or even thousand of genes simultaneously for a limited number of biological samples.
However, in certain instances it is desirable to analyze the expression level of a limited number of genes in hundreds or thousands of biological samples simultaneously. For example, such a “reverse approach” would be critical not only for biological samples derived from healthy organisms but also for discovery of novel drug targets and diagnostic markers in large numbers of biological samples derived from different kinds of human pathological samples or model organisms like mouse, rat, etc. which imitate human diseases. The high throughput screening of disease-related biological samples requires the use of large numbers of samples in order to obtain statistically reliable data concerning specificity of gene expression changes in a particular disease state.
As such, there is continued interest in the development of array formats that can provide for high throughput expression analysis in a large number of different biological samples.
RELEVANT LITERATURE
Patents and patent applications describing arrays of biopolymeric compounds and methods for their fabrication include: U.S. Pat. Nos. 5,242,974; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,445,934; 5,472,672; 5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,556,752; 5,561,071; 5,599,895; 5,624,711; 5,639,603; 5,658,734; WO 93/17126; WO 95/11995; WO 95/35505; EP 742 287; and EP 799 897.
Patents and patent application describing methods of using arrays in various applications include: U.S. Pat. Nos. 5,143,854; 5,288,644; 5,324,633; 5,432,049; 5,470,710; 5,492,806; 5,503,980; 5,510,270; 5,525,464; 5,547,839; 5,580,732; 5,661,028; WO 95/21265; WO 96/31622; WO 97/10365; WO 97/27317; EP 373 203; and EP 785 280.
Other references providing a review of micro array technology, including formats for arrays and methods of their use include: Lockhart et al., Nature Biotechnology (December 1996) 14: 1675.
Clontech Catalogue, 97/98, (Clontech Laboratories, Inc. 1020 East Meadow Circle, Palo Alto Calif. 94303) p. 81 describes premade Northern blots.
SUMMARY OF THE INVENTION
Arrays of a plurality of different heterogeneous polymeric target compositions immobilized on the surface of a solid support are provided. In the subject arrays, the constituent polymeric targets of the heterogeneous target compositions are generally biopolymeric compounds, e.g., nucleic acids and peptides or proteins. The subject arrays find use in a variety of different applications, including high throughput gene expression analysis applications.
Definitions
The term “peptide” as used herein refers to any compound produced by amide formation between a carboxyl group of one amino acid and an amino group of another group.
The term “oligopeptide” as used herein refers to peptides with fewer than about 10 to 20 residues, i.e. amino acid monomeric units.
The term “polypeptide” as used herein refers to peptides with more than 10 to 20 residues.
The term “protein” as used herein refers to polypeptides of specific sequence of more than about 50 residues.
The term “nucleic acid” as used herein means a polymer composed of nucleotides, e.g. deoxyribonucleotides or ribonucleotides.
The terms “ribonucleic acid” and “RNA” as used herein means a polymer composed of ribonucleotides.
The term “mRNA” as used herein refers to only that fraction of the total ribonucleic acids found in a biological source which are capable of being translated into proteins, and therefore includes messenger RNA and polyA+ RNA, but does not include ribosomal RNAs or tRNAs.
The terms “deoxyribonucleic acid” and “DNA” as used herein means a polymer composed of deoxyribonucleotides.
The term “oligonucleotide” as used herein denotes single stranded nucleotide multimers of from about 10 to 100 nucleotides and up to 200 nucleotides in length.
The term “polynucleotide” as used herein refers to single or double stranded polymer composed of nucleotide monomers of generally greater than 100 nucleotides in length.
DESCRIPTION OF THE SPECIFIC EMBODIMENTS
Arrays of a plurality of different heterogeneous polymeric target compositions immobilized on the surface of a solid support are provided. In the subject arrays, the constituent polymeric targets of the heterogeneous target compositions are generally biopolymeric compounds, e.g., nucleic acids and peptides or proteins. The subject arrays find use in a variety of different applications, including high throughput gene expression analysis applications. In further describing the subject invention, the subject arrays will be described first, followed by a review of representative methods of using the arrays and kits for use in practicing such methods.
Before the subject invention is further described, it is to be understood that the invention is not limited to the particular embodiments of the invention described below, as variations of the particular embodiments may be made and still fall within the scope of the appended claims. It is also to be understood that the terminology employed is for the purpose of describing particular embodiments, and is not intended to be limiting. Instead, the scope of the present invention will be established by the appended claims.
In this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention belongs.
Arrays
As summarized above, the subject arrays are arrays of polymeric target compositions that are immobilized on a solid support. The polymeric target constituents of the different polymeric target compositions of the subject arrays, i.e., the individual molecules that make up each target composition on the array, are typically biopolymeric, by which is meant that they are naturally occurring polymeric compounds or at least mimetics or analogues of naturally occurring polymeric compounds. Biopolymeric compounds of particular interest are nucleic acids, including ribonucleic acids, as well as ribonucleic and deoxyribonucleic acid derivatives thereof generated through a variety of processes (usually enzymatic processes) such as reverse transcription, amplification, transcription, etc., e.g. cDNA amplified from RNA (both single and double stranded), cDNA inserts from cDNA libraries, and the like, where in certain embodiments the targets are cDNA molecules generated using the target generation protocols described in U.S. Pat. No. 5,962,272 (e.g., the SMART™ technology) which disclosure is incorporated herein by reference; and peptides, such as oligopeptides, polypeptides and proteins.
In certain preferred embodiments, the polymeric targets are ribonucleic acids. Ribonucleic acids of interest as polymeric targets include total RNA, polyA
+
RNA, polyA

RNA, snRNA (small nuclear), hnRNA (heterogeneous nuclear), cytoplasmic RNA, pre mRNA, mRNA, cRNA (complementary),

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