Methods for multiplexed selection of functional ligands

Abstract

The present invention relates to methods for generating functional biomolecules. In one exemplary aspect of the invention, generation of functional biomolecules may be performed against multiple targets simultaneously within a single system. In general, a plurality of targets may be disposed within in a single reaction volume and a library of biomolecules, such as a nucleic acid library, may be applied to the reaction volume. The members of the library that do not bind to any of the plurality of targets under given conditions may then be partitioned. The remaining members of the library may then be marked and/or tagged, such as to identify the particular target or targets to which the member of the library binds. The binding members of the library may then be isolated and, by virtue of the marking or tagging, be matched to a particular target or targets.

1 . A method of selecting aptamers comprising:
 contacting a plurality of identifiers each of which comprising an oligonucleotide comprising a unique identity sequence denoting a predetermined position on a substrate with a corresponding plurality of target spots disposed at predetermined positions on said substrate, wherein each of said target spots comprising at least one potential aptamer bound to at least one target molecule; and   attaching any of said plurality of identifiers to any of said at least one aptamers bound at one of said target spots by hybridizing, each of said oligonucleotides comprising a first constant region which hybridizes to a second constant region on each of said aptamers;   
       wherein each of said unique identity sequences of said plurality of identifiers correlate to one of said predetermined positions on said substrate. 
     
     
         2 . The method of  claim 1 , wherein said aptamers and said identifiers further comprise constant priming regions. 
     
     
         3 . The method of  claim 2 , wherein said attaching comprises hybridizing said constant region of said identifiers to said constant region of said aptamers. 
     
     
         4 . The method of  claim 2 , further comprising performing a nucleic acid extension reaction on any of said hybridized oligonucleotide and aptamer to produce an extension product comprising said identity sequence and a complementary sequence to said aptamer, or their complements. 
     
     
         5 . The method of  claim 4 , further comprising sequencing said extension product to determine the original sequence of said aptamer and the predetermined position to which said aptamer was bound. 
     
     
         6 . The method of  claim 4 , further comprising adding primers substantially complementary to said constant priming regions. 
     
     
         7 . The method of  claim 1 , wherein each of said target spots comprises a different target molecule. 
     
     
         8 . The method of  claim 1 , wherein said target spots are obtained by contacting a library of oligonucleotides with a plurality of target molecules disposed on a substrate to obtain a group of oligonucleotides bound to said plurality of target molecules. 
     
     
         9 . The method of  claim 8 , wherein said group of oligonucleotides are washed to remove non-bound oligonucleotides. 
     
     
         10 . A method of selecting aptamers from a library of oligonucleotides comprising:
 contacting a plurality of identifiers each of which comprising an oligonucleotide comprising a unique identity sequence denoting a predetermined position on a substrate with a corresponding plurality of target spots disposed at predetermined positions on said substrate, each of said target spots comprising least one target molecule contacted with members of a library of oligonucleotides and washed to remove non-binders; and   attaching any of said plurality of identifiers to any of said members of said library of oligonucleotides bound at one of said target spots by hybridizing, each of said identifiers comprising a first constant region which hybridizes to a second constant region on each of said members of said library of oligonucleotides;   
       wherein each of said unique identity sequences of said plurality of identifiers correlate to one of said predetermined positions on said substrate. 
     
     
         11 . The method of  claim 10 , wherein said contacting comprises applying identifiers using manual pipetting, automatic pipetting, inkjet printing, applying micro-contact pins or applying a membrane with identifiers disposed thereon. 
     
     
         12 . The method of  claim 11 , wherein said contacting further comprises applying primers. 
     
     
         13 . The method of  claim 12 , further comprising performing a nucleic acid extension reaction on any of said hybridized identifier and member of said library of oligonucleotides to produce an extension product comprising said identity sequence and a complementary sequence to said member of said library of oligonucleotides, or their complements. 
     
     
         14 . The method of  claim 13 , further comprising sequencing said extension product to determine the original sequence of said member of said library of oligonucleotides and the predetermined position to which said member of said library of oligonucleotides was bound. 
     
     
         15 . The method of  claim 13 , further comprising performing a nucleic acid amplification reaction to generate additional copies of said extension product. 
     
     
         16 . The method of  claim 10 , wherein said substrate comprises a high content protein array. 
     
     
         17 . A method of selecting aptamers comprising:
 contacting an identifier comprising an oligonucleotide comprising a unique identity sequence denoting a predetermined position on a substrate with a corresponding target spot disposed at said predetermined position on said substrate, said target spot comprising an aptamer bound to a target molecule;   attaching said identifier to said aptamer bound at said target spot by hybridizing, said oligonucleotide comprising a first constant region which hybridizes to a second constant region on said aptamer; and   performing a nucleic acid extension reaction on said hybridized identifier and said aptamer to produce an extension product comprising said identity sequence and a complementary sequence to said aptamer, or their complements;   
       wherein each of said unique identity sequence correlates to said predetermined position on said substrate. 
     
     
         18 . The method of  claim 17 , further comprising sequencing said extension product to determine the original sequence of said aptamer and the predetermined position to which said aptamer was bound. 
     
     
         19 . The method of  claim 17 , wherein identifier comprises a constant region which hybridizes to any aptamer in a selection. 
     
     
         20 . The method of  claim 17 , wherein said target spot is physically isolated within a discrete fluid droplet from other target spots on said substrate during said contacting.