Arrays with modified oligonucleotide and polynucleotide compositions

• US 6,562,569 B1
• Filed: 03/13/2000
• Issued: 05/13/2003
• Est. Priority Date: 12/30/1998
• Status: Expired due to Term

• Current Assignee: Lakewood Amedex Inc.
• Original Assignee: Oligos Etc., Inc.
• Inventors: Dale, Roderic M. K.
• Primary Examiner(s): Wang, Andrew
• Assistant Examiner(s): SCHULTZ, JAMES
• Application Number:
  US09/524,092
• Time in Patent Office: 1,156 Days
• Field of Search: 435/6, 536/23.1, 536/24.3, 935/77, 935/78
• US Class Current: 435/6.12
• CPC Class Codes: C07B 61/00 Other general methods
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

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.

Claims

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, comprising at least one p-ethoxy internucleoside linkage, wherein the oligonucleotides of the composition are characterized by a binding affinity greater than that of a corresponding, non-modified oligonucleotide, wherein the oligonucleotides 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; and

wherein the oligonucleotides of the composition selectively hybridize to DNA.

3. The array of claim 1 or 2, wherein the oligonucleotides are comprised of a modification at a 2′

site of the sugar group of at least one nucleotide.

4. The array of claim 1 or 2, wherein the oligonucleotides further comprise a blocking chemical modification at or near at least one end of said oligonucleotides, and wherein the oligonucleotides are further characterized by a nuclease resistance of at least twice that of a naturally occurring oligonucleotide having the same sequence and number of bases.

5. The array of claim 1 or 2, wherein said modified oligonucleotides have an average length of from about 80 to about 300 nucleotides.

6. The array of claim 1 or 2, wherein said modified oligonucleotides have an average length of from about 100 to about 200 nucleotides.

7. The array of claim 1 or 2, wherein oligonucleotides of each of said oligonucleotide compositions have a different sequence from oligonucleotides of any other oligonucleotide composition on the array.

8. The array of claim 1 or 2, wherein each oligonucleotide composition comprises a population of identical oligonucleotides.

9. The array of claim 1 or 2, wherein each oligonucleotide composition comprises a plurality of oligonucleotides that bind to a particular nucleic acid.

10. The array of claim 1 or 2, wherein the number of oligonucleotide compositions on said array ranges from about 10 to about 10⁸.

11. The array of claim 1 wherein each modified oligonucleotide comprises at least 25% p-ethoxy internucleoside linkages.

12. The array of claim 1 wherein each modified oligonucleotide comprises at least 50% p-ethoxy internucleoside linkages.

13. The array of claim 1 or 2 wherein the modified oligonucleotides are modified at each monomer unit.

16. A method for selectively identifying DNA in a biological sample which contains DNA, comprising:

a) contacting said sample with the array of claim 1;

b) allowing the DNA in the biological sample to hybridize to a modified sequence of the array; and

c) analyzing the results of the hybridizing.

18. The method of claim 16 or 17 further comprising:

d) removing sequences hybridized to sequences of the array using a removing agent selected from the group consisting of a solution having a pH of less than 6.0 and a nuclease which enzymatically destroys natural nucleic acid sequences; and

e) repeating (a), (b), (c) and (d) with a second biological sample.

2. 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, comprising at least one 2′

-5′

-internucleoside linkage and one 3′

-O-methyl substituent,

wherein the oligonucleotides of the composition are characterized by a binding affinity greater than that of a corresponding, non-modified oligonucleotide, wherein the oligonucleotides 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; and

wherein the oligonucleotides of the composition selectively hybridize to RNA.

14. The array of claim 2, wherein each modified oligonucleotide comprises at least 25% 2′

-5′

internucleoside linkages.

15. The array of claim 2, wherein each modified oligonucleotide comprises at least 50% 2′

-5′

internucleoside linkages.

17. A method for selectively identifying RNA in a biological sample which contains RNA, comprising:

a) contacting said sample with the array of claim 2;

b) allowing the DNA in the biological sample to hybridize to a modified sequence of the array; and

c) analyzing the results of the hybridizing.