Methods for improved array preparation

• US 6,800,439 B1
• Filed: 02/07/2001
• Issued: 10/05/2004
• Est. Priority Date: 01/06/2000
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Kajisa, Lisa, McGall, Glenn, Trulson, Mark
• Primary Examiner(s): CELSA, BENNETT M
• Application Number:
  US09/779,389
• Time in Patent Office: 1,336 Days
• Field of Search: 435/6, 435/7.1, 436/518, 436/524, 436/527, 536/25.3
• US Class Current: 506/32
• CPC Class Codes: C07H 19/00 Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
• CPC Class Codes: C40B 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support

Abstract

Improved nucleic acid arrays are provided which have been prepared in a non-oxidizing atmosphere.

Claims

1. A method of reducing ozone related degradation of an oligonucleotide on an array during fabrication of said array, said fabrication comprising

generating a pattern of light and dark areas by selectively irradiating at least a first area of a surface of a substrate, said surface comprising immobilized nucleotides on said surface, said nucleotides capped with a photoremovable protective group, without irradiating at least a second area of said surface, to remove said protective group from said nucleotides in said first area;

contacting said first area and said second area of said surface with a first nucleotide to couple said first nucleotide to said immobilized nucleotides in said first area, and not in said second area, said first nucleotide capped with said photoremovable protecting group to provide a partially completed nucleotide array;

generating another pattern of light and dark areas by selectively irradiating with light at least a part of said first area of said surface and at least a part of said second area to remove said protective group in said at least a part of said first area and said at least a part of said second area;

contacting said first area and said second area of said surface with a second nucleotide to couple said second nucleotide to said immobilized nucleotides in at least a part of said first area and at least a part of said second area to provide to further complete said partially completed nucleotide array;

performing additional irradiating and nucleotide contacting and coupling steps so that a matrix array having at least 100 nucleic acids having different sequences is formed on said support; and

said method of reducing ozone related degradation comprising maintaining throughout the fabrication process said partially completed nucleotide arrays in an ozone depleted atmosphere.

2. A method according to claim 1 wherein said ozone depleted atmosphere comprises carbon-filtered air.

3. A method according to claim 2 wherein said ozone depleted atmosphere has an ozone concentration of less than 10 ppb.

4. A method according to claim 3 wherein said ozone depleted atomosphere has an ozone concentration of less than 5 ppb.

5. A method according to claim 4 wherein said ozone depleted atmosphere has an ozone concentration of 0 to 2 ppb.

6. A method for reducing ozone related degradation of an oligonucleotide array said method comprising maintaining said array in an ozone depleted atmosphere.

7. A method according to claim 6 wherein said ozone depleted atmosphere comprises carbon-filtered air.

8. A method according to claim 7 wherein said ozone depleted atmosphere has an ozone concentration of less than 10 ppb.

9. A method according to claim 8 wherein said ozone depleted atmosphere has an ozone concentration of less than 5 ppb.

10. A method according to claim 9 wherein said ozone depleted atmosphere has an ozone concentration of 0 to 2 ppb.