Surface-bound, unimolecular, double-stranded DNA

Abstract

Libraries of unimolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA. In a related aspect, the present invention provides libraries of conformationally restricted probes on a solid support. The probes are restricted in their movement and flexibility using double-stranded oligonucleotides as scaffolding. The probes are also useful in various screening procedures associated with drug discovery and diagnosis. The present invention further provides methods for the preparation and screening of the above libraries.

1 . A synthetic unimolecular, double-stranded oligonucleotide library comprising a plurality of different members, each member having the formula:  
         Y-L 1 -X 1 -L 2 -X 2    wherein, 
 Y is a solid support:  
 X 1  and X2 are a pair of complementary oligonucleotides:  
 L 1  is a spacer;  
 L 2  is a linking group having sufficient length such that X 1  and X 2  form a double-stranded oligonucleotide.  
   
     
     
         2 . A library in accordance with  claim 1 , wherein L 2  is a member selected from the group consisting of an alkylene group, a polyethyleneglycol group, a polyalcohol group, a polyamine group and a polyester group.  
     
     
         3 . A library in accordance with  claim 1 , wherein L 2  is a polyethylene glycol group.  
     
     
         4 . A library in accordance with  claim 1 , wherein X 1  and X 2  are complementary oligonucleotides each comprising of from 6 to 30 nucleic acid monomers.  
     
     
         5 . A library in accordance with  claim 1 , wherein said solid support is a silica support and L′ comprises an aminoalkylsilane and from 1 to 4 hexaethyleneglycols.  
     
     
         6 . A library in accordance with  claim 1 , wherein said solid support is a silica support, L 1  comprises an aminoalkylsilane and from 1 to 4 hexaethyleneglycols, L 2  is a polyethyleneglycol group and X 1  and X 2  are complementary oligonucleotides each comprising of from 6 to 30 nucleic acid monomers.  
     
     
         7 . A synthetic unimolecular, double-stranded oligonucleotide library of  claim 1 , wherein a portion of said double-stranded oligonucleotides formed by X 1  and X 2  further comprise a bulge.  
     
     
         8 . A synthetic unimolecular, double-stranded oligonucleotide library of  claim 1 , wherein a portion of said double-stranded oligonucleotides formed by X 1  and X 2  further comprise a loop.  
     
     
         9 . A synthetic unimolecular, double-stranded nucleic acid library of  claim 1 , wherein each member further comprises an identifier tag, said identifier tag identifying the sequence of said unimolecular, double-stranded nucleic acid.  
     
     
         10 . A synthetic unimolecular, double-stranded nucleic acid library of  claim 1 , wherein said solid support comprises a first bead linked to a second bead, wherein the double-stranded nucleic acid is attached to the first bead and an identifier tag is attached to the second bead.  
     
     
         11 . A method of forming a plurality of diverse unimolecular, double-stranded oligonucleotides on a solid support having optional spacers, said support comprising a surface with a plurality of preselected regions, said method comprising: 
 (a) forming on each of said preselected regions a different first oligonucleotide, each of said first oligonucleotides comprising of from 6 to 30 monomers;    (b) attaching to the distal end of each of said first oligonucleotides of step (a) a linking group; and    (c) forming on the distal end of each of said linking groups a second oligonucleotide, wherein each of said second oligonucleotides is complementary to said first oligonucleotide which is attached within the same preselected region, and wherein said linking groups have sufficient length such that said first and second oligonucleotides form a unimolecular, double-stranded oligonucleotide.    
     
     
         12 . A method in accordance with  claim 11 , wherein said method of construction of step (a) and step (b) is by light-directed synthesis.  
     
     
         13 .- 21 . (canceled)  
     
     
         22 . An adhesive for use in biological applications comprising a first surface having a plurality of attached oligonucleotides and a second surface having a plurality of attached oligonucleotides, wherein the oligonucleotides of said first surface are substantially complementary to the oligonucleotides of said second surface.