Quality control method for manufacturing biopolymer arrays

• US 20040235022A1
• Filed: 03/17/2004
• Published: 11/25/2004
• Est. Priority Date: 03/19/2003
• Status: Abandoned Application

• Current Assignee: Roche Diagnostics Operations Incorporated (Roche Holding AG)
• Original Assignee: Roche Diagnostics Operations Incorporated (Roche Holding AG)
• Inventors: Heindl, Dieter, Mauritz, Ralf
• Application Number:
  US10/802,249
• Publication Number:
  US 20040235022A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 8/0221 in a cylindrical shaped bed B01J8/0214 takes precedence

Abstract

The invention relates to a quality control method for manufacturing biopolymer arrays comprising (a) synthesizing a plurality of different biopolymer species on an array from monomeric or oligomeric building blocks comprising detectable protecting groups; (b) optionally carrying out a determination of the detectable protecting groups on the array after synthesis; (c) cleaving off the detectable protecting groups; and (d) carrying out a determination of the detectable protecting groups on the array after cleavage in order to determine the efficacy of deprotection.

Claims

1. A quality control method for manufacturing a biopolymer array comprising

(a) synthesizing a plurality of different biopolymer species on an array from monomeric or oligomeric building blocks comprising detectable protecting groups,

(b) cleaving off the detectable protecting groups, and

(c) carrying out a determination of the detectable protecting groups on the array after cleavage in order to determine the efficacy of deprotection.

2. The method of claim 1, wherein the detectable protecting groups are fluorescent groups.

3. The method of claim 2, wherein the fluorescent groups are selected from the group consisting of compounds comprising pyrene, dansyl, stilbene, rhodamine, or coumarin.

4. The method of claim 1, wherein the detectable protecting groups are radioactively detectable groups.

5. The method of claim 4, wherein the radioactively detectable groups are selected from the group consisting of ¹⁴C, ³²P, and ³H doped moieties.

6. The method of claim 1, wherein the detectable protecting groups are electrochemically detectable groups.

7. The method of claim 6, wherein the electrochemically detectable groups are selected from the group consisting compounds comprising ferrocene or phenothiazine moieties.

8. The method of claim 1, wherein the detectable protecting groups are UV- or IR-detectable groups.

9. The method of claim 8, wherein the UV- or IR-detectable groups are selected from the group consisting of compounds comprising aromatic nitro moieties, hydroxyl moieties, thiol, thioether, and thiophenol moieties, nitrile moieties, isocyanate, or halo moieties.

10. The method of claim 1, wherein the detectable protecting groups are bioaffinity groups.

11. The method of claim 10, wherein the bioaffinity groups are selected from the group consisting of compounds comprising biotin, digoxin, or digoxigenin moieties.

12. The method of claim 1, wherein the biopolymer species are selected from the group consisting of nucleic acids, nucleic acid analogs, peptides, and peptide analogs.

13. The method of claim 1, wherein the biopolymer species are selected from the group consisting of nucleic acids and nucleic acid analogs and wherein the detectable protecting groups are coupled to nucleobases.

14. The method of claim 13 wherein the detectable protecting groups are coupled to amino groups of nucleobases.

15. The method of claim 1, wherein the building blocks for the biopolymer synthesis are nucleotide building blocks having the general structural formulae (I) or (II):

16. The method of claim 15, wherein R¹ is selected from the group consisting of substituted triphenylmethyl groups, pixyl groups, photocleavable groups, and substituted silyl protecting groups.

17. The method of claim 15, wherein R¹ is selected from the group consisting of 4,4′

-dimethoxy triphenylmethyl compounds, 4-monomethoxy triphenyl compounds, p-nitrophenylpropoxy carbonyl (NPPOC), (α

-methyl)-6-nitropiperonyloxy carbonyl (MeNPOC), tert-butyldimethyl silyl (TBDMS), and tert-butyldiphenyl silyl (TBDPS).

18. The method of claim 15, wherein R³ is a phosphite amide group.

19. The method of claim 12 wherein R³ is —

P(R⁶)—

NR⁴R⁵ wherein R⁴ and R⁵ are independently selected from the group consisting of —

H, —

(C₁-C₁₀)-alkyl, —

(C₂-C₁₀)-alkenyl, and —

(C₆-C₂₂)-aryl, and R⁶ is selected from the group consisting of H, —

(C₂-C₆)-alkenyloxy, —

(C₂-C₆)-alkenyl, —

(C₁-C₆)-alkyl, and —

(C₁-C₆)-alkoxy, wherein each group contains a substituent selected from the group consisting of -halo, p-nitroaryloxy, and -cyano.

20. The method of claim 19, wherein R⁶ is a 2-cyanoethyloxy group.

21. The method of claim 15 wherein L has the structure —

C(O)—

R when n=1, or ═

CH—

NR⁸R when n=0, wherein R is a residue of the protecting group and R⁸ is selected from the group consisting of H and —

(C₁-C₃)-alkyl.

22. The method of claim 15, wherein B is selected from the group consisting of adenine, guanine, cytosine, aza and deaza analogs thereof, and analogs containing additional amino groups.

23. A nucleic acid synthesis building block having the general structural formulae (I) or (II):

24. A method for the production of a nucleic acid array comprising

(a) synthesizing a plurality of different biopolymer species on an array from monomeric or oligomeric building blocks comprising detectable protecting groups according to claim 23,

(b) cleaving off the detectable protecting groups, and

(c) carrying out a determination of the detectable protecting groups on the array after cleavage.

25. A reagent kit for the synthesis of a nucleic acid array comprising a nucleic acid synthesis building block according to claim 23.

26. A reagent kit for the synthesis of a nucleic acid array comprising at least 2 nucleic acid synthesis building blocks according to claim 23, each building block carrying a different detectable protecting group.