Molecular recognition of materials

Abstract

The present invention includes methods for selective binding of inorganic materials and the compositions that made up of the selecting agent and the target materials. One form of the present invention is a method for selecting crystal-binding peptides with binding specificity including the steps of contacting one or more amino acid oligomers with one or more single-crystals of a semiconductor material so that the oligomers may bind to the crystal and eluting the bound amino acid oligomers from the single-crystals.

What is claimed is:  
     
         1 . A method for selecting crystal-binding peptides with binding specificity comprising the steps of: 
 contacting one or more amino acid oligomers with one or more single-crystals of a semiconductor material so that the oligomers may bind to the crystal; and    eluting the bound amino acid oligomers from the single-crystals.    
     
     
         2 . The method recited in  claim 1 , further comprising the step of contacting the eluted amino acid oligomers with one or more semiconductor crystals, and repeating the eluting step.  
     
     
         3 . The method recited in  claim 1 , wherein the nucleic acid sequence underlying eluted oligomers is amplified.  
     
     
         4 . The method recited in  claim 3 , wherein the amplification is accomplished using a polymerase chain reaction.  
     
     
         5 . The method recited in  claim 1 , further comprising the step of determining the sequence of the eluted amino acid oligomers.  
     
     
         6 . The method recited in  claim 1 , wherein the semiconductor material is chosen from the group consisting of gallium arsenide, indium phosphide, gallium nitride, zinc sulfide, cadmium sulfide, aluminum arsenide, gallium stibinide, aluminum gallium arsenide, aluminum stibinide, cadmium selenide, zinc selenide, cadmium telluride, zinc selenide, indium arsenide, aluminum arsenide and silicon.  
     
     
         7 . The method recited in  claim 1 , wherein the semiconductor material is chosen from the group consisting of a Group II-Group V semiconductor and a Group III-Group VI semiconductor.  
     
     
         8 . The method recited in  claim 1 , wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a phage-display library.  
     
     
         9 . The method recited in  claim 1 , wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise an antibody expression library.  
     
     
         10 . The method recited in  claim 1 , wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a bacterial expression library.  
     
     
         11 . The method recited in  claim 1 , where the amino acid oligomers are about 12 amino acids in length.  
     
     
         12 . The method recited in  claim 1 , wherein the one or more amino acid oligomers that are contacted with the single crystal further comprise a library of random amino acid sequences.  
     
     
         13 . The method recited in  claim 12 , where the amino acid oligomers are about 12 amino acids in length.  
     
     
         14 . The method recited in  claim 12 , wherein the amino acid oligomers are about 7 amino acids in length.  
     
     
         15 . The method recited in  claim 12 , wherein the amino acid oligomers are between about 7 to 15 amino acids in length, and disulfide constrained.  
     
     
         16 . The method recited in  claim 1 , wherein the eluting is done at high stringency.  
     
     
         17 . The method recited in  claim 1 , wherein the eluting is done at moderate stringency.  
     
     
         18 . The method recited in  claim 1 , wherein the eluting is done at low stringency.  
     
     
         19 . An amino acid sequence for the binding GaAs (100) chosen from the group consisting of Seq. ID Nos. 1 through 11, inclusive.  
     
     
         20 . A method for selecting amino acid sequences with binding specificity comprising the steps of: 
 contacting one or more amino acid oligomers with one or more single-crystals of a magnetic, mineral or optical material so that the oligomers may bind to the crystal; and    eluting the bound amino acid oligomers from the single-crystals.    
     
     
         21 . The method recited in  claim 20 , further comprising the step of contacting the eluted amino acid oligomers with one or more single-crystals of a magnetic material, and repeating the eluting step.  
     
     
         22 . The method recited in  claim 20 , wherein nucleic acid sequence underlying the eluted oligomers is amplified.  
     
     
         23 . The method recited in  claim 22 , wherein the amplification is accomplished using a polymerase chain reaction.  
     
     
         24 . The method recited in  claim 20 , further comprising the step of determining the sequence of the eluted amino acid oligomers.  
     
     
         25 . The method recited in  claim 20 , wherein the magnetic, mineral or optical material is chosen from the group consisting of FePd, cobalt, manganese, lithium niobate, iron oxides and calcium carbonate.  
     
     
         26 . The method recited in  claim 20 , wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a phage-display library.  
     
     
         27 . The method recited in  claim 26 , where the amino acid oligomers are about 12 amino acids in length.  
     
     
         28 . The method recited in  claim 20 , wherein the one or more amino acid oligomers that are contacted with the single crystal further comprise a library of random amino acid sequences.  
     
     
         29 . The method recited in  claim 28 , where the amino acid oligomers are about 12 amino acids in length.  
     
     
         30 . The method recited in  claim 28 , wherein the amino acid oligomers are between about 7 and 15 amino acids in length.  
     
     
         31 . The method recited in  claim 28 , wherein the amino acid oligomers are 7 amino acids in length, and disulfide constrained.  
     
     
         32 . The method recited in  claim 20 , wherein the eluting is done at moderate stringency.  
     
     
         33 . The method recited in  claim 20 , wherein the eluting is done at low stringency.  
     
     
         34 . A method for selecting crystal-bonding amino acids comprising the steps of: 
 contacting one or more amino acid oligomers with one or more crystals of a target material so that the oligomers may bind to the crystal; and    eluting the bound amino acid oligomers from the crystals.    
     
     
         35 . The method recited in  claim 34 , further comprising the step of contacting the eluted amino acid oligomers with one or more semiconductor crystals, and repeating the eluting step.  
     
     
         36 . The method recited in  claim 34 , wherein nucleic acid sequence underlying the eluted oligomers is amplified.  
     
     
         37 . The method recited in  claim 36 , wherein the amplification is accomplished using a polymerase chain reaction.  
     
     
         38 . The method recited in  claim 34 , further comprising the step of determining the sequence of the eluted amino acid oligomers.  
     
     
         39 . The method recited in  claim 34 , wherein the semiconductor material is chosen from the group consisting of gallium arsenide, indium phosphide, gallium nitride, zinc sulfide, cadmium sulfide, aluminum arsenide, gallium stibinide, aluminum gallium arsenide, aluminum stibinide, aluminum arsenide, cadmium selenide, zinc selenide, cadmium telluride, zinc selenide, indium arsenide and silicon.  
     
     
         40 . The method recited in  claim 34 , wherein the semiconductor material is chosen from the group consisting of a Group III-Group V semiconductor and a Group II-Group VI semiconductor.  
     
     
         41 . The method recited in  claim 34 , wherein the one or more amino acid oligomers that are contacted with the single-crystal further comprise a phage-display library.  
     
     
         42 . The method recited in  claim 41 , where the amino acid oligomers are about 12 amino acids in length.  
     
     
         43 . The method recited in  claim 20 , wherein the one or more amino acid oligomers that are contacted with the single crystal further comprise a library of random amino acid sequences.  
     
     
         44 . The method recited in  claim 43 , where the amino acid oligomers are about 12 amino acids in length.  
     
     
         45 . The method recited in  claim 43 , wherein the amino acid oligomers are about 7 to 15 amino acids in length.  
     
     
         46 . The method recited in  claim 43 , wherein the amino acid oligomers are 7 amino acids in length, and disulfide constrained.  
     
     
         47 . An amino acid sequence for the binding GaAs (100) chosen from the group consisting of Seq. ID Nos. 1 to 11.  
     
     
         48 . A specificity structure comprising: 
 one or more single crystals of gallium arsenide; and    a selective binding amino acid sequence.    
     
     
         49 . The specificity structure recited in  claim 48 , wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 1,2,3,4,5,6,7,8,9,10, 11 and 117.  
     
     
         50 . A specificity structure comprising: 
 one or more single crystals of cadmium sulfide; and    a selective binding amino acid sequence.    
     
     
         51 . The specificity structure recited in  claim 50 , wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 12 through 82.  
     
     
         52 . A specificity structure comprising: 
 one or more single crystals of zinc sulfide; and    a selective binding amino acid sequence.    
     
     
         53 . The specificity structure recited in  claim 52 , wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 83 through 116.  
     
     
         54 . A specificity structure comprising: 
 one or more single crystals of lead sulfide; and    a selective binding amino acid sequence.    
     
     
         55 . The specificity structure recited in  claim 54 , wherein the selective binding amino acid sequence is chosen from the group consisting of Seq. ID Nos. 118 through 158.  
     
     
         56 . A crystal binding amino acid oligomers comprising the sequence motif (ser/tyr/thr)-(arg/asp/ser)-Xaa-(ser/asn/glu/arg/thr)-Xaa-Xaa-(ser/thr/glu/asp)-(ser/thr/tyr).  
     
     
         57 . A crystal binding amino acid oligomers comprising the sequence motif Xaa-Xaa-(ser/tyr/thr)-(arg/asp/ser)-Xaa -(ser/asn/glu/arg/thr)-Xaa-Xaa-(ser/thr/glu/asp)-(ser/thr/tyr) -(ser/thr/his)-Xaa-Xaa.  
     
     
         58 . A method of determining a binding motif comprising the steps: 
 contacting a binding library with one or more crystals of a target material to allow components of the library to bind via a binding region to the crystals;    eluting off bound components; and    sequencing the eluted components.    
     
     
         59 . The method recited in  claim 58 , wherein the library is comprised of peptides.  
     
     
         60 . The method recited in  claim 58 , wherein the library is a phage display library.  
     
     
         61 . The method recited in  claim 58 , wherein the library is an antibody display library.  
     
     
         62 . The method recited in  claim 58 , wherein the library is comprised of chimeric proteins with protein cleavage sites adjacent to the binding region.