Primer array synthesis and validation

• US 8,338,093 B2
• Filed: 12/30/2005
• Issued: 12/25/2012
• Est. Priority Date: 12/31/2004
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Kuimelis, Robert G., McGall, Glenn H.
• Primary Examiner(s): Babic, Christopher M.
• Application Number:
  US11/323,067
• Publication Number:
  US 20060147969A1
• Time in Patent Office: 2,552 Days
• Field of Search: None
• US Class Current: 435/6.1
• 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 2219/00452 Means for the recovery of reactants or products
• CPC Class Codes: B01J 2219/00454 by chemical cleavage from the solid support
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00574 radioactive
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00578 electrophoric
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00729 Peptide nucleic acids [PNA]
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 80/00 Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers

Abstract

Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array.

Claims

1. A method for synthesizing primers from an array of polymers on a solid substrate, said method comprising the steps of:

providing a solid substrate, wherein said substrate has a density, wherein a plurality of different known oligonucleotides sequences are located in a plurality of different, known locations on a surface of said substrate;

attaching a plurality of linkers to the substrate, wherein the plurality of linkers comprises a photogroup, wherein the photo group is a compound selected from the group consisting of compounds represented by the following structural formula;

2. The method according to claim 1 wherein said primers comprising said first group of linkers that are released comprise from 10¹ to 10⁵ different nucleotide sequences.

3. The method according to claim 2 wherein said primers comprising said first group of linkers and second group of linkers are less than 60 bases in length.

4. The method according to claim 1 wherein said polymer is a DNA oligonucleotide.

5. The method according to claim 1 wherein said primers comprising said first group of linkers and said second group of linkers are labeled with a detectable moiety.

6. The method according to claim 1 wherein said primers comprising said first group of linkers and second group of linkers comprise between 10¹ to 10⁵ features, each feature comprising a unique nucleotide sequence.

7. The method according to claim 1 wherein said primers comprising said first group of linkers and second group of linkers range between about 80 to about 160 nucleotides.

8. The method according to claim 1 wherein said primers comprising said first group of linkers and second group of linkers are present on the array at a density between 200-2000 pmol/cm².

9. The method according to claim 1 further comprising performing an ionization step.

10. The method according to claim 1 wherein said performing said MALDI-TOF mass spectrometry is part of an automated analysis.

11. A method for synthesizing primers from an array of polymers on solid substrate, said method comprising the steps of:

providing a solid substrate,

attaching a plurality of linkers to the substrate, attaching a plurality of linkers to the substrate, wherein the plurality of linkers comprises a photogroup, wherein the photo group is selected from the group consisting of a compound represented by the following structural formula;

12. The method according to claim 11 wherein the compound is represented by the following structural formula:

13. The method according to claim 11 wherein the compound is represented by the following structural formula:

14. The method according to claim 11 wherein the compound is represented by the following structural formula:

15. The method according to claim 11 wherein the compound is represented by the following structural formula: