Arrays with modified oligonucleotide and polynucleotide compositions

Abstract

The present invention provides arrays having associated modified oligonucleotides that selectively bind to DNA or RNA, methods of making such arrays, assays for using such arrays, and the like. In one embodiment, the arrays of the invention exhibit an increased binding affinity with complementary nucleic acids, and in particular with complementary RNA. In another embodiment, the associated nucleic acids of the array of the invention exhibit substantial acid resistance, allowing the arrays to be treated with low pH solutions. In another embodiment, the modified associated nucleic acids of the array of the invention exhibit substantial resistance to nuclease degradation.

That which is claimed is:  
     
         1 . An array, comprising: 
 a support comprised of a surface; and    a plurality of modified oligonucleotides associated with the surface;    wherein the modified oligonucleotides are characterized by selectively binding to a natural nucleotide target sequence based whether the target sequence is comprised an oxygen atom at the 2′ position of the ribose moiety of the sequence.    
     
     
         2 . The array of  claim 1 , wherein the modified oligonucleotides of each composition are further characterized by a pH stability of at least one hour at 37° C. at a pH range of about 0.5 to about 6.0.  
     
     
         3 . The array of  claim 1 , wherein the support comprises a plurality of distinct areas, and wherein a plurality of different modified oligonucleotides are associated with the distinct areas of the surface.  
     
     
         4 . The array of  claim 1 , wherein the array comprises a plurality of surfaces, each surface associated with a plurality of modified oligonucleotides having a same sequence.  
     
     
         5 . The array of  claim 1 , wherein the modified oligonucleotide compositions that selectively bind to DNA, and wherein each modified oligonucleotide in the composition further comprises an end-block, and further wherein the modified oligonucleotides are characterized by a nuclease resistance of at least twice that of a naturally occurring oligonucleotide having the same sequence and number of bases.  
     
     
         6 . The array of  claim 5 , wherein the modified oligonucleotide compositions are comprised of oligonucleotides having p-ethoxy internucleoside linkages, and wherein each modified oligonucleotide is comprised of between 6-200 nucleotides.  
     
     
         7 . The array of  claim 6 , wherein each modified oligonucleotide comprises at least 25% p-ethoxy intemucleoside linkages.  
     
     
         8 . The array of  claim 6 , wherein each modified oligonucleotide comprises at least 50% p-ethoxy intemucleoside linkages.  
     
     
         9 . The array of  claim 1 , wherein said modified oligonucleotides have an average length of from about 35 to about 100 monomer units.  
     
     
         10 . The array of  claim 1 , wherein the modified oligonucleotides are modified at each monomer unit.  
     
     
         11 . The array of  claim 1 , wherein the array is comprised of modified oligonucleotide compositions that selectively bind to RNA, and wherein each modified oligonucleotide in the composition further comprises an end-block, and further wherein the modified oligonucleotides are characterized by a nuclease resistance of at least twice that of a naturally occurring oligonucleotide having the same sequence and number of bases.  
     
     
         12 . The array of  claim 11 , wherein the modified oligonucleotide compositions are comprised of oligonucleotides having 2′-5′ internucleoside linkages, and wherein each modified oligonucleotide is comprised of between 6-200 monomer units.  
     
     
         13 . The array of  claim 12 , wherein each modified oligonucleotide comprises at least 25% 2′-5′ internucleoside linkages.  
     
     
         14 . The array of  claim 13 , wherein each modified oligonucleotide comprises at least 50% p-ethoxy internucleoside linkages.  
     
     
         15 . The array of  claim 1 , wherein said modified oligonucleotides have an average length of from about 35 to about 100 monomer units, and wherein the modified oligonucleotides are modified at each monomer unit.  
     
     
         16 . The array of  claim 15 , wherein the modified oligonucleotide compositions are comprised of oligonucleotides having at least one 3′-substitution.  
     
     
         17 . An array comprising a plurality of modified oligonucleotide compositions stably associated with the surface of a support, comprising: 
 a first set of compositions comprised of modified oligonucleotides that selectively bind to DNA, wherein the oligonucleotides of each composition have a specific determined sequence;    a second set of compositions comprised of modified oligonucleotide compositions that selectively bind to RNA, wherein the oligonucleotides of each composition have a specific determined sequence;    wherein each different modified oligonucleotide composition is stably associated with a different distinct area of the support, and further wherein each composition of the first set has a corresponding composition of the second set having a same nucleotide sequence.    
     
     
         18 . The array of  claim 17 , wherein the modified oligonucleotides of each composition are further characterized by a pH stability of at least one hour at 37° C. at a pH range of about 0.5 to about 6.0. wherein each composition of the first set has a corresponding composition of the second set with the same sequence.  
     
     
         19 . The array of  claim 18 , wherein each modified oligonucleotide in the composition further comprises an end-block, and further wherein the modified oligonucleotides are characterized by a nuclease resistance of at least twice that of a naturally occurring oligonucleotide having the same sequence and number of bases.  
     
     
         20 . A method for identifying a DNA or RNA molecule in a biological sample, comprising the steps of: 
 producing an array comprising a first set of compositions comprised of modified oligonucleotides that selectively bind to DNA, wherein the oligonucleotides of each composition have a specific determined sequence, and a second set of compositions comprised of modified oligonucleotide compositions that selectively bind to RNA, wherein each composition of the first set has a corresponding composition of the second set with the same sequence;    exposing said array to a biological sample;    hybridizing said sample to the array; and    detecting said hybridization;    wherein the nucleic acid is identified by comparison of hybridization to a composition in the first set of compositions to hybridization to the corresponding composition in the second set having the same sequence.