Method for deriving epitopes

Abstract

A method of generating a nucleic acid species which are immunologically cross-reactive with non-nucleic acid immunogens is disclosed. The method comprises combining an antigen binding protein which binds said immunogen with a degenerate pool of nucleic acid species, and then recovering a nucleic acid species bound by said antigen binding protein from said degenerate pool. Also disclosed are the nucleic acid species so made, along with the use thereof for tagging molecules for immunological detection, for detecting antibodies to predetermined non-nucleic acid immunogens, for blocking complex formation between an antigen binding protein and a non-nucleic acid immunogen, and for inducing an immune response to the immunogen in a human or animal subject. Preferred immunogens are peptides and preferred antigen binding proteins are antibodies.

That which is claimed is:  
     
         1 . A method of generating a nucleic acid species which is immunologically cross-reactive with an immunogen, which immunogen is not a nucleic acid, said method comprising: 
 combining an antigen binding protein which binds said immunogen with a degenerate pool of nucleic acid species; and then    recovering a nucleic acid species bound by said antigen binding protein from said degenerate pool.    
     
     
         2 . A method according to  claim 1 , wherein said antigen binding protein is selected from the group consisting of antibodies and T cell receptors.  
     
     
         3 . A method according to  claim 1 , wherein said antigen binding protein is a monoclonal antibody.  
     
     
         4 . A method according to  claim 1 , wherein said antigen binding protein is a polyclonal antibody.  
     
     
         5 . A method according to  claim 1 , wherein said antigen binding protein is an anti-g10 antibody.  
     
     
         6 . A method according to  claim 1 , wherein said immunogen is selected from the group consisting of peptides, glycoproteins, fats, lipids, polysaccharides, carbohydrates, viruses and allergens.  
     
     
         7 . A method according to  claim 1 , wherein said immunogen is an allergen.  
     
     
         8 . A method according to  claim 1 , wherein said degenerate pool of nucleic acid species is a degenerate pool of RNA species.  
     
     
         9 . A method according to  claim 1 , wherein said degenerate pool of nucleic acid species comprises a plurality of nucleic acids having from 2 to 200 nucleotides.  
     
     
         10 . A method according to  claim 1 , wherein said degenerate pool of nucleic acid species comprises a plurality of nucleic acids having from 4 to 100 nucleotides.  
     
     
         11 . A method according to  claim 1 , wherein said degenerate pool of nucleic acid species comprises a plurality of nucleic acids having a degenerate segment of from 2 to 25 nucleotides.  
     
     
         12 . A method according to  claim 1 , wherein said degenerate pool of nucleic acid species comprises a plurality of nucleic acids in an aqueous solution.  
     
     
         13 . A method according to  claim 1 , wherein said degenerate pool of nucleic acid species comprises a plurality of linear nucleic acids.  
     
     
         14 . A method according to  claim 1 , wherein said degenerate pool of nucleic acid species comprises a plurality of nucleic acids having a stem and loop configuration.  
     
     
         15 . A method according to  claim 1 , wherein said nucleic acid species is an RNA species, said method further comprising the step of synthesizing a DNA encoding said RNA species from said RNA species.  
     
     
         16 . A method according to  claim 1 , further comprising the step of assaying the immunological cross-reactivity of said immunogen and said nucleic acid species.  
     
     
         17 . A method according to  claim 1 , further comprising the step of collecting said antibodies from a human or animal subject prior to said combining step.  
     
     
         18 . A method according to  claim 1 , further comprising the step of producing said antigen binding protein by immunizing an animal with said immunogen.  
     
     
         19 . A method according to  claim 1 , further comprising the step of collecting said antibodies from a human or animal subject afflicted with an autoimmune disease.  
     
     
         20 . A method according to  claim 1 , further comprising the step of collecting said antibodies from a human subject, which human subject is afflicted with a condition selected from the group consisting of systemic lupus erythematosus, myasthenia gravis, and rheumatoid arthritis.  
     
     
         21 . A method according to  claim 1 , wherein said antigen binding protein is immobilized on a solid support, and said recovering step is carried out by contacting said degenerate pool of nucleic acid species to said solid support.  
     
     
         22 . A method according to  claim 21 , wherein said contacting step is followed by the steps of: 
 separating nucleic acid species bound to said solid support; then    producing a pool of complementary nucleic acids from said nucleic acid species separated from said solid support; then    amplifying said pool of complementary nucleic acids to produce a subset degenerate pool of nucleic acid species; and then    repeating said step of contacting a degenerate pool of nucleic acid species to said solid support with said subset degenerate pool of nucleic acid species.    
     
     
         23 . A method according to  claim 22 , wherein said subset degenerate pool of nucleic acids species bind to said antigen binding protein under conditions represented by a wash stringency of 0.15M NaCl.  
     
     
         24 . A method according to  claim 22 , wherein said amplifying step is carried out in vivo.  
     
     
         25 . A method according to  claim 22 , wherein said amplifying step is carried ou in vitro.  
     
     
         26 . An isolated nucleic acid which inhibits complex formation between an antigen binding protein and an immunogen, which immunogen is not a nucleic acid.  
     
     
         27 . An isolated nucleic acid according to  claim 26 , which immunogen is a peptide.  
     
     
         28 . An isolated nucleic acid according to  claim 26  which inhibits complex formation between a self peptide autoantigen and an antigen binding protein, wherein said antigen binding protein is from a human or animal subject which expresses said self peptide.  
     
     
         29 . An isolated nucleic acid according to  claim 26 , which antigen binding protein is selected from the group consisting of antibodies and T cell receptors.  
     
     
         30 . An isolated nucleic acid according to  claim 26  which binds to said antigen binding protein at a K d  of from 10 −5  to 10 −14  moles per liter.  
     
     
         31 . An isolated nucleic acid according to  claim 26  consisting of from 2 to 50 nucleotides.  
     
     
         32 . An isolated nucleic acid according to  claim 26  which is linear.  
     
     
         33 . An isolated nucleic acid according to  claim 26  which has a stem and loop configuration.  
     
     
         34 . An isolated nucleic acid according to  claim 26  which binds to an antibody which binds to the g10 protein.  
     
     
         35 . An isolated nucleic acid according to  claim 26  conjugated to a tagged molecule, said tagged molecule selected from the group consisting of proteins and heterologous nucleic acids.  
     
     
         36 . A method of detecting an antigen binding protein which binds a predetermined immunogen, which predetermined immunogen is not a nucleic acid, said method comprising: 
 contacting a biological sample suspected of containing said antigen binding protein to a nucleic acid, which nucleic acid is capable of inhibiting complex formation between said antigen binding protein and said immunogen, under conditions which permit the formation of a reaction product; and then    detecting the presence or absence of a reaction product.    
     
     
         37 . A method according to  claim 36 , which antigen binding protein is an antibody.  
     
     
         38 . A method according to  claim 36 , which immunogen is a peptide.  
     
     
         39 . A method according to  claim 36 , which nucleic acid consists of from 2 to 50 nucleotides.  
     
     
         40 . A method of blocking complex formation between an immunogen and an antigen binding protein which binds said immunogen, wherein said immunogen is not a nucleic acid, said method comprising: 
 contacting said antigen binding protein to a nucleic acid, which nucleic acid inhibits complex formation between said antigen binding protein and said immunogen.    
     
     
         41 . A method according to  claim 40 , which antigen binding protein is selected from the group consisting of antibodies and T cell receptors.  
     
     
         42 . A method according to  claim 40 , which immunogen is a peptide.  
     
     
         43 . A method according to  claim 40 , which nucleic acid consists of from 2 to 50 nucleotides.  
     
     
         44 . A method of producing an immune response to an immunogen in a human or animal subject, which immunogen is not a nucleic acid, said method comprising: 
 administering a nucleic acid to said subject, which nucleic acid is capable of inhibiting complex formation between an antigen binding protein and said immunogen;    said nucleic acid being administered in an amount effective to induce an immune respone in said animal to said immunogen.    
     
     
         45 . A method according to  claim 44 , which antigen binding protein is selected from the group consisting of antibodies and T cell receptors.  
     
     
         46 . A method according to  claim 44 , which immunogen is a peptide.  
     
     
         47 . A method according to  claim 44 , which nucleic acid consists of from 2 to 50 nucleotides.  
     
     
         48 . A method according to  claim 44 , which nucleic acid is administered in an amount ranging from 50 micrograms to 5 milligrams per kilogram subject body weight.  
     
     
         49 . A method of generating a set of nucleic acid species useful as immunogens, and wherein at least two members of said set are not immunologically cross-reactive with one another, said method comprising: 
 collecting a plurality of antigen binding proteins from a human or animal subject, which antigen binding proteins are selected from the group consisting of antibodies and T cell receptors;    combining said antigen binding proteins with a degenerate pool of nucleic acid species; and then recovering a plurality of nucleic acid species bound by said antigen binding proteins from said degenerate pool to produce said set.    
     
     
         50 . A method according to  claim 49 , wherein a plurality of said nucleic acid species are immunologically cross-reactive with compounds which are not nucleic acids.  
     
     
         51 . A method-according to  claim 49 , wherein at least two members of said set are immunologically cross-reactive with different immunogens.  
     
     
         52 . A method according to  claim 49 , wherein at least two members of said set are immunologically cross-reactive with a different immunogen, each of which different immunogen is not a nucleic acid.  
     
     
         53 . A method according to  claim 49 , wherein said collecting step is carried out by harvesting T cell lymphocytes from said subject.  
     
     
         54 . A method according to  claim 49 , wherein said collecting step is carried out by collecting immune serum from said subject.  
     
     
         55 . A method according to  claim 49 , further comprising the step of producing said antigen binding proteins by immunizing said subject with an immunogen prior to said collecting step.  
     
     
         56 . A method according to  claim 49 , wherein said subject has been afflicted with a microbial disease.  
     
     
         57 . A method according to  claim 49 , wherein said subject has been afflicted with a viral disease.  
     
     
         58 . A method according to  claim 49 , wherein said antigen binding proteins are immobilized on a solid support, and said recovering step is carried out by contacting said degenerate pool of nucleic acid species to said solid support.  
     
     
         59 . A method according to  claim 58 , wherein said contacting step is followed by the steps of: 
 separating nucleic acid species bound to said solid support; then    producing a pool of complementary nucleic acids from said nucleic acid species separated from said solid support; then    amplifying said pool of complementary nucleic acids to produce a subset degenerate pool of nucleic acid species which subset degenerate pool comprises said plurality of nucleic acid species; and then    repeating said step of contacting a degenerate pool of nucleic acid species to said solid support with said subset degenerate pool of nucleic acid species.    
     
     
         60 . A method according to  claim 59 , wherein said subset degenerate pool of nucleic acid species bind to said antigen binding proteins under conditions represented by a wash stringency of 0.15M NaCl.  
     
     
         61 . A set consisting essentially of isolated nucleic acids, each of which nucleic acids inhibits complex formation between an antigen binding protein and an immunogen, wherein said antigen binding proteins are selected from the group consisting of antibodies and T cell receptors, and wherein at least two members of said set do not bind to the same antigen binding protein.  
     
     
         62 . A set according to  claim 61 , wherein at least two members of said set inhibit complex formation between an antigen binding protein and an immunogen, which immunogen is not a nucleic acid.  
     
     
         63 . A set according to  claim 61 , wherein at least two members of said set inhibit complex formation between an antigen binding protein and an immunogen, which immunogen is not a nucleic acid, and wherein said at least two members bind to antigen binding proteins which do not bind to the same immunogen.  
     
     
         64 . A set according to  claim 61 , wherein; at least two members of said set are immunologically cross-reactive with a different immunogen, each of which immunogens is not a nucleic acid.  
     
     
         65 . A set of isolated nucleic acid species according to  claim 61 , wherein said each of said nucleic acid species bind to said antigen binding protein at a K d  of from 10 −5  to 10 −14  moles per liter.  
     
     
         66 . A set of isolated nucleic acid species according to  claim 61  in an aqueous carrier solution.  
     
     
         67 . A cDNA library encoding a set of isolated nucleic acid species according to  claim 61 .  
     
     
         68 . A method of generating a plurality of nucleic acid species which are immunologically cross-reactive with a drug compound and are useful for rational drug design, which compound is not a nucleic acid, said method comprising: 
 combining an antigen binding protein which binds said compound with a degenerate pool of nucleic acid species; and then    recovering a plurality of nucleic acid molecules bound by said antigen binding protein from said degenerate pool    and wherein at least two of said nucleic acid species do not bind to the same antigen binding protein.    
     
     
         69 . A method according to  claim 68 , wherein said antigen binding protein is selected from the group consisting of antibodies and T cell receptors.  
     
     
         70 . A method according to  claim 68 , wherein said compound is selected from the group consisting of peptides, glycoproteins, fats, lipids, polysaccharides, and carbohydrates.  
     
     
         71 . A method according to  claim 68 , wherein said antigen binding protein is immobilized on a solid support, and said recovering step is carried out by contacting said degenerate pool of nucleic acid species to said solid support.  
     
     
         72 . A method according to  claim 68 , wherein said contacting step is followed by the steps of: 
 separating nucleic acid species bound to said solid support; then    producing a pool of complementary nucleic acids from said nucleic acid species separated from said solid support; then    amplifying said pool of complementary nucleic acids to produce a subset degenerate pool of nucleic acid species, which subset degenerate pool comprises said plurality of nucleic acid species; and then    repeating said step of contacting a degenerate pool of nucleic acid species to said solid support with said subset degenerate pool of nucleic acid species.    
     
     
         73 . A set consisting essentially of isolated nucleic acid species which inhibit complex formation between an antigen binding protein and a drug compound, which compound is not a nucleic acid, and wherein at least two of said nucleic acid species do not bind to the same antigen binding protein.  
     
     
         74 . A set of isolated nucleic acid species according to  claim 73 , which compound is selected from the group consisting of peptides, glycoproteins, fats, lipids, polysaccharides, and carbohydrates.  
     
     
         75 . A set of isolated nucleic acid species according to  claim 73  which isolated nucleic acid species bind to said antigen binding protein at a K d  of from 10 −5  to 10 −14  moles per liter.  
     
     
         76 . A set of isolated nucleic acid species according to  claim 73  in an aqueous carrier solution.  
     
     
         77 . A cDNA library encoding a set of isolated nucleic acid species according to  claim 73.