Nucleic acid affinity columns

• US 20060204991A1
• Filed: 02/22/2006
• Published: 09/14/2006
• Est. Priority Date: 03/11/1996
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Chee, Mark S., Gingeras, Thomas R., Morris, MacDonald S.
• Application Number:
  US11/360,146
• Publication Number:
  US 20060204991A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 of making a nucleic acid pool comprising a plurality of different nucleic acids, said method comprising the steps of:

a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 20 oligonucleotides having different predetermined nucleic acid sequences, and wherein;

i) each different oligonucleotide is localized in a predetermined region of said surface;

ii) the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2; and

iii) said different oligonucleotides have an identical terminal 5′

nucleic acid sequence;

b) amplifying said multiplicity of oligonucleotides at least about 10 fold to provide said nucleic acid pool.

2-40. -40. (canceled)