Nucleic acid affinity columns

• US 6,828,104 B2
• Filed: 08/14/2002
• Issued: 12/07/2004
• Est. Priority Date: 03/11/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Chee, Mark S., Gingeras, Thomas R., Morris, MacDonald S., Lipshutz, Robert J.
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US10/219,006
• Publication Number:
  US 20030013114A1
• Time in Patent Office: 846 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 536/25.3, 536/25.4
• US Class Current: 435/5
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2565/107 Alteration in the property of hybridised versus free label oligonucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm², and all of said different oligonucleotides have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence. b) amplifying said multiplicity of oligonucleotides to provide a pool of amplified nucleic acids; and c) attaching the pool of nucleic acids to a solid support.

Claims

1. A method for eliminating a plurality of preselected gene products from a nucleic acid sample comprising:

providing an affinity matrix comprising at least one nucleic acid affinity ligand complementary to each of the plurality of preselected gene products;

hybridizing the nucleic acid sample to the affinity matrix; and

eluting the sample from the affinity matrix;

thereby substantially depleting the nucleic acid sample of the preselected gene products.

2. The method of claim 1 wherein the nucleic acid affinity ligand is an oligonucleotide probe.

3. The method of claim 2 wherein the nucleic acid affinity ligand is attached to a solid support.

4. The method of claim 3 wherein the solid support is selected from the group consisting of beads, porous beads, crushed particles, membranes, tubing and planar surfaces.

5. The method of claim 4 wherein the solid support is particulate.

6. The method of claim 1 wherein, at least, one of the preselected gene products is actin.

7. The method of claim 1 wherein, at least, one of the preselected gene products is GAPDH.