Methods for production of arrays with modified oligonucleotide and polynucleotide compositions

Abstract

The present invention provides methods for producing arrays having associated modified nucleic acid structures, e.g. acid stable and/or end-blocked nucleic acids such as 2′-O—R oligonucleotides. In one embodiment, arrays produced using the methods 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 produced using the methods 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 produced using the methods of the invention exhibit substantial resistance to nuclease degradation.

1 . An array comprising a plurality of modified oligonucleotide compositions stably associated with the surface of a support, wherein each oligonucleotide composition is characterized by: 
 an oligonucleotide backbone structure modified from that of a naturally occurring nucleotide polymer;    wherein the oligonucleotides of the composition are characterized by a binding affinity greater than that of a corresponding, non-modified oligonucleotide.    
     
     
         2 . The array of  claim 1 , wherein the oligonucleotides are comprised of a modification at the 2′ site of the sugar group of at least one nucleotide.  
     
     
         3 . The array of  claim 1 , wherein the oligonucleotides are comprised of at least one modified internucleoside linkage.  
     
     
         4 . The array of  claim 1 , wherein said modified oligonucleotides have an average length of from about 80 to about 300 nucleotides.  
     
     
         5 . The array of  claim 1 , wherein said modified oligonucleotides have an average length of from about 100 to about 200 nucleotides.  
     
     
         6 . The array of  claim 1 , wherein oligonucleotides of each of said oligonucleotide compositions has a different sequence from oligonucleotides of any other oligonucleotide composition on the array.  
     
     
         7 . The array of  claim 1 , wherein each oligonucleotide composition comprises a population of identical oligonucleotides.  
     
     
         8 . The array of  claim 1 , wherein each oligonucleotide composition comprises a plurality of oligonucleotides that bind to a particular nucleic acid.  
     
     
         9 . The array of  claim 1 , wherein the number of oligonucleotide compositions on said array ranges from about 2 to about 10 9 .  
     
     
         10 . An array comprising a plurality of modified oligonucleotide compositions stably associated with the surface of a support, wherein each oligonucleotide composition is characterized by: 
 an oligonucleotide backbone structure modified from that of a naturally occurring nucleotide polymer;    wherein the oligonucleotides of the composition is characterized by a pH stability of at least one hour at 37° C. at a pH in a range of about 0.5 to about 10.    
     
     
         11 . The array of  claim 10 , further comprising a blocking chemical modification at or near at least one end of said oligonucleotide, wherein the oligonucleotide is further characterized by having 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 10 , wherein the oligonucleotide is stable at a pH of from 0.5 to 6.0.  
     
     
         13 . The array of  claim 10 , wherein the modified oligonucleotide is further characterized by modification of at least 25% of the intemucleoside linkages of the oligonucleotide.  
     
     
         14 . An array comprising a plurality of oligonucleotide compositions stably associated with the surface of a support, wherein each oligonucleotide composition is characterized by: 
 an oligonucleotide backbone structure modified from that of a naturally occurring nucleotide polymer; and    a blocking chemical modification at or near at least one end of the oligonucleotide;    wherein the oligonucleotide is characterized by a nuclease resistance of at least twice that of a naturally occurring polymer having the same number of nucleotides.    
     
     
         15 . An array of modified oligonucleotides, the array comprising: 
 a planar, non-porous solid support having a surface;    a plurality of different modified oligonucleotides attached to the surface of the solid support at a density exceeding 400 different modified oligonucleotides/cm 2 ,    wherein each of the different modified oligonucleotides is attached to the surface of the solid support in a different predefined region, has a different determinable sequence, and is at least 80 nucleotides in length; and    further wherein the modified oligonucleotides are characterized by a characteristic selected from the group consisting of (a) a binding affinity of at least about 1.25 times that of a corresponding, non-modified oligonucleotide, (b) a pH stability of at least one hour at 37° C. at a pH in a range of about 0.5 to 10; and (c) a nuclease resistance of at least twice that of a naturally occurring oligonucleotide having the same sequence and number of bases.    
     
     
         16 - 21 . (canceled)