Methods for array preparation using substrate rotation

• US 20060147981A1
• Filed: 02/28/2006
• Published: 07/06/2006
• Est. Priority Date: 06/01/2000
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Kreger, Bradley A., McGall, Glenn, Kajisa, Lisa
• Application Number:
  US11/365,770
• Publication Number:
  US 20060147981A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical

Abstract

Methods are provided for the preparation of polymer arrays on wafers wherein the wafers are rotated between synthesis steps to provide more uniform results across the entire wafer.

Claims

1. A method of preparing a nucleic acid array on a support, wherein each nucleic acid occupies a separate known region of the support, said synthesizing comprising:

(a) activating a region of the support;

(b) attaching a nucleotide to a first region, said nucleotide having a masked reactive site linked to a protecting group;

(c) repeating steps (a) and (b) on other regions of said support whereby each of said other regions has bound thereto another nucleotide comprising a masked reactive site link to a protecting group, wherein said another nucleotide may be the same or different from that used in step (b);

(d) removing the protecting group from one of the nucleotides bound to one of the regions of the support to provide a region bearing a nucleotide having an unmasked reactive site;

(e) binding an additional nucleotide to the nucleotide with an unmasked reactive site;

(f) repeating steps (d) and (e) on regions of the support until a desired plurality of nucleic acids is synthesized, each nucleic acid occupying separate known regions of the support;

wherein the surface of said substrate is maintained in a position which is vertical or within about 30 degrees of vertical, and

wherein the substrate is rotated around an axis perpendicular to said surface by an amount of from about 20 degrees to about 180 degrees, said rotating being done prior to, coincident with or subsequent to at least one of said attaching or binding steps.

2. A method in accordance with claim 1, wherein said rotating is conducted prior to, coincident with or subsequent to at least 50% of said attaching or binding steps.

3. A method in accordance with claim 1, wherein said rotating is conducted prior to, coincident with or subsequent to at least 80% of said attaching or binding steps.

4. A method in accordance with claim 1, wherein said rotating is in an amount of from about 75 to about 105 degrees.

5. A method in accordance with claim 1, wherein said rotating is in an amount of about 90 degrees.

6. A method in accordance with claim 1, wherein said interface is vertical or within about 10 degrees of vertical and said rotating is in an amount of about 90 degrees.

7. A method in accordance with claim 1, wherein said substrate is a substantially square planar silica chip, said interface is vertical or within about 10 degrees of vertical and said rotating is in an amount of about 90 degrees.

8. A method in accordance with claim 7, wherein said substantially square planar silica chip is held in a vertical position with one of the four square verticies pointing downward.

9. A method in accordance with claim 1, wherein at least 10 different nucleic acids are formed on said surface.

10. A method in accordance with claim 1, wherein at least 100 different nucleic acids are formed on said surface.

11. A method in accordance with claim 1, wherein at least 1000 different nucleic acids are formed on said surface.

12. A method in accordance with claim 1, wherein at least 10,000 different nucleic acids are formed on said surface.

13. A method in accordance with claim 1, wherein at least 100,000 different nucleic acids are formed on said surface.

14. A method in accordance with claim 1, wherein each different nucleic acid is in a region having an area of less than about 1 cm².

15. A method in accordance with claim 1, wherein each different nucleic acid is in a region having an area of less than about 1 mm².