Methods for production of arrays with modified oligonucleotide and polynucleotide compositions
First Claim
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.
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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.
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Citations
16 Claims
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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:
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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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9)
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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:
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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. - View Dependent Claims (11, 12, 13)
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14. An array comprising a plurality of oligonucleotide compositions stably associated with the surface of a support, wherein each oligonucleotide composition is characterized by:
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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.
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15. An array of modified oligonucleotides, the array comprising:
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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/cm2, 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.
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16-21. -21. (canceled)
Specification