Microarray having a base cleavable linker

• US 10,261,075 B2
• Filed: 05/25/2018
• Issued: 04/16/2019
• Est. Priority Date: 09/19/2005
• Status: Active Grant

• Current Assignee: CustomArray, Inc. (Genscript Biotech Corp.)
• Original Assignee: CustomArray, Inc. (Genscript Biotech Corp.)
• Inventors: Maurer, Karl, Suciu, Dominic, Gao, Hetian
• Primary Examiner(s): Gross, Christopher M
• Application Number:
  US15/990,487
• Publication Number:
  US 20180267032A1
• Time in Patent Office: 326 Days
• Field of Search: None
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00454 by chemical cleavage from the solid support
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00713 Electrochemical synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C40B 50/18 using a particular method of attachment to the solid support
• CPC Class Codes: G01N 33/54353 with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393

Abstract

There is disclosed a microarray having base cleavable linkers and a process of making the microarray. The microarray has a solid surface with known locations, each having reactive hydroxyl groups. The density of the known locations is greater than approximately 100 locations per square centimeter. Optionally, oligomers are synthesized in situ onto the cleavable linkers and subsequently cleaved using a cleaving base. Optionally, the oligomers are cleaved and recovered as a pool of oligomers.

Claims

1. A compound of formula:

2. The compound of claim 1, where the nucleotide base group is selected from the group consisting of adenine, guanine, cytosine, uracil and thymine.

3. The compound of claim 1, where the acid labile protecting group is selected from the group consisting of dimethoxytrityl, t-butyloxycarbonyl and benzyloxycarbonyl.

4. The compound of claim 1, where the Spacer is selected from the group consisting of DNA, RNA, polyethylene glycol, and polypeptides, and combinations thereof.

5. The compound of claim 4, where the Spacer is between a one-mer and a thirty five-mer.

6. The compound of claim 1, where the Spacer is selected from the group consisting of 10-T (deoxythymidine₁₀) and 15-T (deoxythymidine₁₅).

7. The compound of claim 6, where deoxyadenosine, deoxyguanosine, deoxycytidine, deoxyuridine, adenosine, guanosine, cytidine, uridine and thymidine can be used instead of deoxythymidine.

8. The compound of claim 1, where the plurality of hydroxyl reactive groups are present on a porous reaction layer.

9. The compound of claim 8, where the porous reaction layer comprises sucrose.

10. The compound of claim 1, further comprising where at the first location the acid labile protecting group is removed and a protected monomer is bound to the 5′

hydroxyl to generate a first oligonucleotide strand.

11. The compound of claim 10, further comprising where the Spacer is attached through one or more of the plurality of hydroxyl reactive groups in a second known location, having a different nucleotide base group.

12. The compound of claim 11, further comprising where at the known second location the acid labile protecting group is removed and a protected monomer is bound to the 5′

hydroxyl to generate a second oligonucleotide strand.

13. A compound of formula:

14. The compound of claim 13, where the nucleotide base group is selected from the group consisting of adenine, guanine, cytosine, uracil and thymine.

15. The compound of claim 13, where the acid labile protecting group is selected from the group consisting of dimethoxytrityl, t-butyloxycarbonyl and benzyloxycarbonyl.

16. The compound of claim 13, where the Spacer is selected from the group consisting of DNA, RNA, polyethylene glycol, and polypeptides, and combinations thereof.

17. The compound of claim 13, where the plurality of hydroxyl reactive groups are present on a porous reaction layer.

18. The compound of claim 17, where the porous reaction layer comprises sucrose.