Selective Processing of Biological Material on a Microarray Substrate

• US 20100076185A1
• Filed: 09/18/2009
• Published: 03/25/2010
• Est. Priority Date: 09/22/2008
• Status: Abandoned Application

• Current Assignee: Ventana Medical Systems Incorporated (Roche Holding AG)
• Original Assignee: Ventana Medical Systems Incorporated (Roche Holding AG)
• Inventors: Oliphant, Arnold, Adey, Nils, Ao, Wanyuan
• Application Number:
  US12/562,543
• Publication Number:
  US 20100076185A1
• Time in Patent Office: Days
• US Class Current: 536/24.300
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence

Abstract

The present invention provides methods and systems for selectively eluting biological material from a distinct spatial location on a microarray slide. In one aspect, for example, a method for recovering biological material coupled to a microarray slide can include selecting a biological material to be recovered from the microarray slide, finding the biological material within a distinct spatial region on the microarray slide surface, and eluting at least a portion of the selected biological material from the distinct spatial region without eluting substantial amounts of non-selected biological material from regions of the microarray slide that are not within the distinct spatial region.

Claims

1. A method for recovering biological material coupled to a microarray slide, comprising:

selecting a biological material to be recovered from the microarray slide;

finding the biological material within a distinct spatial region on the microarray slide surface; and

eluting at least a portion of the selected biological material from the distinct spatial region without eluting substantial amounts of non-selected biological material from regions of the microarray slide that are not within the distinct spatial region.

2. The method of claim 1, wherein eluting further includes applying an elution buffer to the distinct spatial region.

3. The method of claim 2, wherein the elution buffer is a denaturing buffer that functions to release the portion of biological material from the microarray slide surface.

4. The method of claim 2, wherein at least a portion of the distinct spatial region is heated to facilitate release of at least a portion of the selected biological material from the microarray surface.

5. The method of claim 1, wherein the selected biological material is a member selected from the group consisting of DNA, cDNA, RNA, peptides, and combinations thereof.

13. A method of using biological material as an in situ hybridization probe, comprising:

recovering the biological material as in claim 1;

utilizing the biological material as a probe for in situ hybridization.

14. The method of claim 13, wherein the biological material utilized as a probe without significant amplification.

15. The method of claim 13, wherein the biological material is amplified prior to being utilized as a probe.

16. The method of claim 13, wherein the in situ hybridization is fluorescent in situ hybridization.

6. A method for recovering nucleic acid material from a microarray, comprising:

selecting a nucleic acid material that has been hybridized onto a microarray slide surface in a distinct spatial region;

applying a denaturing buffer to the distinct spatial region to at least partially denature the selected nucleic acid material; and

flushing the microarray surface with an inert recovery buffer to recover the denatured portion of the selected nucleic acid material.

7. The method of claim 6, further comprising collecting the denatured portion of the selected nucleic acid material from the inert recovery buffer.

8. The method of claim 6, further including applying heat to the distinct spatial region to facilitate the denaturing of at least a portion of the selected nucleic acid material.

9. A system for recovering nucleic acid material from a microarray, comprising:

a microarray scanner configured to scan a microarray surface and identify a location of a nucleic acid material to be recovered;

a dispensing instrument configured to receive input from the microarray scanner and dispense an elution buffer on a discrete dispensing area of the microarray surface at the location indicated by the microarray scanner; and

a recovery instrument configured to recover the elution buffer from the microarray surface.

10. The system of claim 9, further comprising a heating device configured to heat the discrete dispensing area.

11. The system of claim 10, wherein the heating device is a laser.

12. The system of claim 10, wherein the recovery instrument is an electrically charged surface.

17. A method for selectively labeling biological material coupled to a microarray slide, comprising:

selecting a biological material to be labeled;

locating the biological material within a distinct spatial region on a surface of the microarray slide; and

labeling at least a portion of the selected biological material from the distinct spatial region without labeling substantial amounts of non-selected biological material from regions of the microarray slide that are not within the distinct spatial region.

18. The method of claim 17, wherein labeling further comprises:

selectively modifying the biological materials at the distinct spatial locations; and

treating either a portion of the microarray slide, or the entire microarray slide, using an agent with which only those biological materials that were previously modified can react.

19. The method of claim 18, wherein the biological materials are selectively modified using directed light.

20. The method of claim 18, wherein the biological materials are selectively modified using a dispensed reagent.

21. The method of claim 17, wherein labeling further includes:

applying a buffer to the distinct spatial region exclusive of regions of the microarray slide substantially outside of the distinct spatial region; and

adding a label to the buffer at the distinct spatial region, such that at least a portion of the biological material within the buffer incorporates the label.

22. The method of claim 17, wherein the selected biological material is a member selected from the group consisting of DNA, cDNA, RNA, peptides, and combinations thereof.

23. A method for selectively amplifying biological material coupled to a microarray slide, comprising:

selecting a biological material to be amplified;

locating the biological material within a distinct spatial region on the microarray slide surface; and

amplifying at least a portion of the selected biological material from the distinct spatial region without amplifying substantial amounts of non-selected biological material from regions of the microarray slide that are not within the distinct spatial region.

24. The method of claim 23, wherein labeling further comprises:

selectively modifying the biological materials at the distinct spatial locations; and

treating either a portion of the microarray slide, or the entire microarray slide, using an agent with which only those biological materials that were previously modified can react.

25. The method of claim 24, wherein the biological materials are selectively modified using directed light.

26. The method of claim 24, wherein the biological materials are selectively modified using a dispensed reagent.

27. The method of claim 23, wherein amplifying further includes:

applying an amplification buffer to the distinct spatial region exclusive of regions of the microarray slide substantially outside of the distinct spatial region; and

amplifying at least a portion of the selected biological material within the amplification buffer.

28. The method of claim 23, wherein the portion of the selected biological material is amplified by isothermal cycling.

29. The method of claim 23, wherein the portion of the selected biological material is amplified by thermal cycling.