Arrays with modified oligonucleotide and polynucleotide compositions

• US 20030180789A1
• Filed: 05/12/2003
• Published: 09/25/2003
• Est. Priority Date: 12/30/1998
• Status: Abandoned Application

• Current Assignee: Lakewood Amedex Inc.
• Original Assignee: Lakewood Amedex Inc.
• Inventors: Dale, Roderic M.K.
• Application Number:
  US10/435,217
• Publication Number:
  US 20030180789A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/113 incorporating modified backbone
• CPC Class Codes: C12Q 2525/125 incorporating agents resulting in resistance to degradation

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 oligonucleotides associated with the array that selectively hybridize to RNA, wherein each modified oligonucleotide comprises at least one p-ethoxy internucleoside linkage and at least one 2′

-O-methyl substituent, wherein the oligonucleotides associated with the array are characterized by

(a) a binding affinity for target RNA greater than a corresponding, non-modified oligonucleotide, and

(b) a pH stability of at least one hour at 37°

C. at a pH range of about 0.5 to about 6.0.

4. The array of claim 1 or 2, wherein the modified oligonucleotides further comprise a blocking chemical modification at or near at least one 5′

or 3′

end, and wherein the oligonucleotides have a nuclease resistance greater than a corresponding, non-modified oligonucleotide.

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 RNA in a biological sample which contains both RNA and DNA comprising contacting the biological sample with the array of claim 1 or 2 under conditions that allow the RNA in the biological sample to selectively hybridize to a modified oligonucleotide of the array.

17. The method of claim 16 further comprising removing RNA hybridized to the array using a solution having a pH of less than 6.0 and a nuclease which enzymatically destroys the RNA and contacting the array with a second biological sample which contains both RNA and DNA.

2. An array comprising a plurality of modified oligonucleotides associated with the array that selectively hybridize to RNA, wherein each modified oligonucleotide comprises at least one 2′

-amino substituent, wherein the oligonucleotides associated with the array are characterized by

(a) a binding affinity for target RNA greater than a corresponding, non-modified oligonucleotide, and

(b) 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 2, wherein the modified oligonucleotides contain at least one modified internucleoside linkage.

14. The array of claim 3, wherein each modified oligonucleotide comprises at least 25% modified internucleoside linkages.

15. The array of claim 3, wherein each modified oligonucleotide comprises at least 50% modified internucleoside linkages.