Methods and compositions for producing biopolymeric arrays

Details Methods and compositions for producing biopolymeric arrays Methods and compositions for producing biopolymeric arrays

1999-07-16

2002-02-12

Celsa, Bennett (Department: 1627)

Chemistry: analytical and immunological testing

Involving an insoluble carrier for immobilizing immunochemicals

C530S333000, C530S334000, C536S023100, C536S025300, C422S129000, C422S131000, C422S134000, C435S283100, C435S286500, C435S288400, C435S292100, C435S091500, C435S091500, C435S091500, C435S091500, C435S091500, C436S094000, C436S501000, C436S506000, C436S516000

Reexamination Certificate

active

06346423

ABSTRACT:

TECHNICAL FIELD
The field of this invention is polymeric arrays.
BACKGROUND OF THE INVENTION
“Biochips” or arrays of binding agents, such as oligonucleotides and peptides, have become an increasingly important tool in the biotechnology industry and related fields. These binding agent arrays, in which a plurality of binding agents are present on a solid support surface in the form of an array or pattern, find use in a variety of applications, including gene expression analysis, drug screening, nucleic acid sequencing, mutation analysis, and the like.
Such arrays may be prepared in a number of different ways. For example, DNA arrays may be prepared manually by spotting DNA onto the surface of a substrate with a micro pipette. See Khrapko et al., DNA Sequence (1991) 1:375-388. Alternatively, the dot-blot approach, as well as the derivative slot-blot approach, may be employed in which a vacuum manifold transfers aqueous DNA samples from a plurality of wells to a substrate surface. In yet another method of producing arrays of biopolymeric molecules, a pin is dipped into a fluid sample of the biopolymeric compound and then contacted with the substrate surface. By using a plurality or array of pins, one can transfer a plurality of samples to the substrate surface at the same time. Alternatively, an array of capillaries can be used to produce biopolymeric arrays. See WO95/35505. In another method of producing biopolymeric arrays, arrays of biopolymeric agents are “grown” on the surface of a substrate in discreet regions. See e.g. U.S. Pat. No. 5,143,854 and Fodor et al., Science (1991) 251:767-773.
Despite the variety of different methods available for the production of biopolymeric arrays, there are disadvantages associated with each method. For example, current methods of growing the polymeric agents on the surface of an array, such as the photoresist techniques described in Fodor supra, are expensive and require the use of specialized photosensitive protecting groups on the phosphoramidites. As such, there is continued interest in the development of new methods for producing polymeric arrays, particularly in the development of new methods for growing polymers on the surface of a substrate to produce an array.
Relevant Literature
Patents and patent applications describing arrays of biopolymeric compounds and methods for their fabrication and/or use include: U.S. Pat. Nos. 4,877,745; 5,143,854; 5,242,974; 5,338,688; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,445,934; 5,449,754; 5,472,672; 5,474,796; 5,510,270; 5,527,681; 5,529,756; 5,532,128; 5,545,531; 5,552,270; 5,554,501; 5,556,752; 5,658,802; 5,561,071; 5,599,695; 5,624,711; 5,639,603; 5,658,734; 5,670,322; 5,677,195; 5,698,089; 5,700,637; 5,723,320; 5,744,305; 5,759,779; 5,763,170; 5,846,708; WO90/10716; WO92/10588; WO93/17126; WO95/11995; WO95/35505; WO97/10365; WO97/27317; WO97/46313; EP0 373 203B1; EP742 287A2; and EP799 897A1.
SUMMARY OF THE INVENTION
Methods and compositions for making polymeric arrays are provided. In the subject methods, polymers are produced through the sequential covalent addition of polymeric subunits to a growing polymer chain on the surface of a substrate, where one or more locations of the substrate surface are selective protected (both spatially and temporally) by a protective bubble during the sequential synthesis protocol. The protective bubble may be produced on the surface in any convenient manner, including through activation of bubble producing means, e.g. resistors, stably associated with a surface of the substrate or part of a structure separate from the substrate. A variety of different types of polymeric arrays can be produced according to the subject methods, including polypeptide and nucleic acid arrays. The subject arrays find use in a variety of different analyte detection applications, including hybridization assays, where specific applications include gene discovery, differential expression and nucleic acid sequencing assays.
DEFINITIONS
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 mean a polymer composed of ribonucleotides.
The terms “deoxyribonucleic acid” and “DNA” as used herein mean a polymer composed of deoxyribonucleotides.
The term “oligonucleotide” as used herein denotes single stranded nucleotide multimers of from about 10 to up to about 100 nucleotides in length.
The term “polynucleotide” as used herein refers to a single or double stranded polymer composed of nucleotide monomers of generally greater than 100 nucleotides in length and up to about 8,000 or more nucleotides in length.
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 “array” as used herein means an substrate having a plurality of binding agents stably attached to its surface, where the binding agents may be spatially located across the surface of the substrate in any of a number of different patterns.
The term “binding agent” means any agent that is a member of a specific binding pair, where such agents include: peptides, e.g. proteins or fragments thereof; nucleic acids, e.g. oligonucleotides, polynucleotides; and the like; etc.
DESCRIPTION OF THE SPECIFIC EMBODIMENTS
Methods and compositions are provided for producing arrays of polymeric binding agents. In the subject methods, the individual polymers of the array are synthesized using solid phase synthesis techniques on the surface of a substrate. A critical feature of the invention is that one or more locations on the substrate surface are spatially and temporally protected by a protective bubble during the synthesis protocol, where the protective bubble may be produced using any convenient bubble producing means. The bubble producing means may be a component of either a substrate or a structure separate from the substrate. Also provided are the arrays produced by the subject methods, kits for use in practicing the subject methods, and methods of using the arrays in analyte detection assays, including hybridization assays, such as gene discovery, differential gene expression and gene sequencing assays.
Before the subject invention is described further, 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.
The subject invention provides methods for fabricating arrays of polymeric agents. The subject invention can be used to fabricate a number of different types of arrays in which a plurality of distinct polymeric binding agents are stably associated with at least one surface of a substrate. The polymeric binding agents may vary widely, where the only limitation is that the polymeric binding agents are capable of being fabricated in a step-wise fashion in which sub-units of the polymer, e.g. monomeric units, submonomers, macromonomers (i.e. compounds of two or more, usually no more than 10 and more us

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