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  Sets of digital antibodies directed against short epitopes, and methods using sameUSPTO Application #: 20080090250Title: Sets of digital antibodies directed against short epitopes, and methods using same Abstract: The present invention relates generally to sets of digital antibodies directed against short epitopes, and use thereof in methods for protein analysis. (end of abstract)
Agent: Wilson Sonsini Goodrich & Rosati - Palo Alto, CA, US Inventors: Jianfu Jeffrey Wang, Weixing Helen Hu USPTO Applicaton #: 20080090250 - Class: 435007100 (USPTO) Related Patent Categories: Chemistry: Molecular Biology And Microbiology, Measuring Or Testing Process Involving Enzymes Or Micro-organisms; Composition Or Test Strip Therefore; Processes Of Forming Such Composition Or Test Strip, Involving Antigen-antibody Binding, Specific Binding Protein Assay Or Specific Ligand-receptor Binding Assay The Patent Description & Claims data below is from USPTO Patent Application 20080090250. Brief Patent Description - Full Patent Description - Patent Application Claims
CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the priority benefit of provisional application U.S. Ser. No. 60/418,277, filed Oct. 15, 2002, and Ser. No. ______, filed Aug. 18, 2003, the contents of both of which are incorporated by reference in their entirety. FIELD OF INVENTION [0002] The present invention relates generally to sets of digital antibodies directed against short epitopes, and use thereof in methods for protein analysis. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT [0003] Not applicable. BACKGROUND OF THE INVENTION [0004] Proteomics involves the measurement of gene activity at the protein level. Today, the most common tool for proteomics purposes is the combination of two-dimensional gel electrophoresis coupled with mass spectrometry (2D-MS). This system has several limitations. First, the detection sensitivity and resolution of 2D electrophoresis is low. Second, use of mass spectrometric analysis dramatically increases the cost. Finally, 2D electrophoresis is time-consuming. A very well-equipped laboratory can only perform about 200 to 400 2D gels each week. Accordingly, there is a need for improved protein-analysis methods. [0005] Detection and characterization of bacterial or viral infection is of crucial importance in the practice of clinical microbiology and in environmental testing, such as food safety and biohazard safety testing. Microorganisms are very diverse in terms of both phenotype and genotype, for instance, staphylococci consist of 32 species and 15 subspecies. Current diagnostic methods, however, are generally capable of detecting only a single microorganism or virus, necessitating the use of a number of specific tests in order to detect and characterize a microorganism or virus. Thus, there is a need for new methods for detection and characterization (including identification) of protein samples, including samples comprising or derived from bacteria and/or viruses. [0006] Cancer can be classified based on tissue type and site of cancer. Each type of cancer can be further classified to different stages based on mostly tumor size and whether it has invaded other organ. For example, a prostate cancer may be classified into stages from T0 to T4 using current methods. In another example, cancers can also be classified to different grades based on, e.g., structural organization of a tumor, and/or the level of cell differentiation. However these morphological and/or histological classifications often do not correlate well with clinical treatment, and frequently fail to identify early stage cancer or pre-cancerous cells. Thus there is a need for new methods for detection and characterization (including identification) of protein samples comprising or derived from cancerous cells and/or tissues. [0007] All references cited herein, including patent applications and publications, are incorporated by reference in their entirety. SUMMARY OF THE INVENTION [0008] The present invention provides sets of digital antibodies, and methods comprising use of digital antibodies. [0009] Accordingly, in one aspect, the invention provides sets of digital antibodies, wherein the set comprises at least about 15 digital antibodies, wherein each digital antibody binds a different epitope, and wherein each digital antibody binds an epitope consisting of 3 consecutive amino acids, or 4 consecutive amino acids. In some embodiments, the set comprises at least about any of 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 125, 150, 175, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more antibodies. In some embodiments, the set comprises 100 digital antibodies that bind epitopes consisting of 3 consecutive amino acids. In other embodiments, the set further comprises 100 digital antibodies that bind epitopes consisting of 4 consecutive amino acids. In still other embodiments, the set further comprises 100 digital antibodies that bind epitopes consisting of 5 consecutive amino acids. In other embodiments, the set of digital antibodies comprises at least about 100, 200, 300, 400, 500, 600, 700 800, 900, or 1000 digital antibodies, wherein each digital antibody binds a different epitope, and wherein each digital antibody binds an epitope consisting of 3 consecutive amino acids, 4 consecutive amino acids, or 5 consecutive amino acids. In still other embodiments, the set of digital antibodies comprises at least 1000 digital antibodies that bind epitopes consisting of 4 consecutive amino acids. In still other embodiments, the set further comprises at least 100 digital antibodies that bind epitopes consisting of 5 consecutive amino acids. In other embodiments, the set further comprises at least 100 digital antibodies that bind epitopes consisting of 3 consecutive amino acids. It is understood that "different epitopes" encompasses epitopes with overlapping amino acid sequences, as well as epitope with non-overlapping amino acid sequences. [0010] In another aspect, the invention provides an array comprising any of the digital antibody sets described herein. Methods for generating arrays are well known in the art, and further described herein. [0011] In another aspect, the invention provides methods for generating a protein binding profile said methods comprising (a) contacting a sample with any of the sets of digital antibodies described herein under conditions that permit binding; (b) optionally removing unbound protein (in some embodiments, removing protein that is not specifically bound); and (c) detecting binding of protein to antibodies, whereby a protein binding profile is generated. [0012] In another aspect, the invention provides methods for generating a protein binding profile, said methods comprising detecting protein bound to a set of digital antibodies, whereby a protein binding profile is generated, wherein the protein bound to the set of digital antibodies is generated by a methods comprising (a) contacting a sample with any of the sets of digital antibodies described herein; and (b) optionally removing unbound protein. [0013] In another aspect, the invention provides methods for generating a protein binding profile, said methods comprising (a) separating unbound protein from a set of digital antibodies contacted with a sample; and (b) detecting binding of protein to antibodies, whereby a protein binding profile is generated, wherein the unbound protein from a set of digital antibodies contacted with a sample is generated by a method comprising contacting a sample with any of the sets of digital antibodies described herein. [0014] As is evident, one or more steps may be combined and/or performed sequentially (often in any order, as long as the requisite product(s) are able to be formed), and, as is evident, the invention includes various combinations of the steps described herein. It is also evident, and is described herein, that the invention encompasses methods in which the initial, or first, step is any of the steps described herein. Methods of the invention encompass embodiments in which later, "downstream" steps are an initial step. [0015] In another aspect, the invention provides methods for generating a protein binding profile, said methods comprising (a) incubating a reaction mixture, said reaction mixture comprising: (i) any of the sets of digital antibodies described herein; and (ii) a sample; wherein the incubating is under condition permitting binding; (b) optionally separating unbound protein; and (c) detecting binding of protein to antibodies, whereby a protein binding profile is generated. [0016] In another aspect, the invention provides methods for generating a protein binding profile, said methods comprising detecting binding of protein to a set of digital antibodies, whereby a protein binding profile is generated, wherein the protein bound to the set of digital antibodies is generated by a methods comprising incubating a reaction mixture, said reaction mixture comprising: (i) any of the sets of digital antibodies described herein; and (ii) a sample; wherein the incubating is under condition permitting binding; (b) optionally separating unbound protein. [0017] As is evident to one skilled in the art, aspects that refer to combining and incubating the resultant mixture also encompasses method embodiments which comprise incubating the various mixtures (in various combinations and/or subcombinations) so that the desired products are formed. [0018] In some embodiments, the methods of generating a protein binding profile further comprise a step of treating the sample with a protein cleaving agent, whereby polypeptide fragments are generated. The sample can treated with a protein cleaving agent prior to step (a) of contacting the sample with the set of digital antibodies under conditions that permit binding. The protein cleaving agent may be an enzyme (such as chymotrypsin or trypsin) or a chemical agent (such as cyanogen bromide). [0019] It is understood that a protein binding profile includes information regarding absence of binding between a digital antibody and protein. It is further understood that a protein binding profile may be generated without the need to have prior knowledge of the identity of the protein being analyzed, and both known and unknown proteins may be detected. Thus, in some embodiments, the protein binding profile may be used to identify and/or detect a previously unknown agent, such as a novel pathogen. Continue reading... Full patent description for Sets of digital antibodies directed against short epitopes, and methods using same Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Sets of digital antibodies directed against short epitopes, and methods using same patent application. ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. 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