Microarray for determining the relative abundances of polynuceotide sequences

• US 7,323,298 B1
• Filed: 07/30/1996
• Issued: 01/29/2008
• Est. Priority Date: 06/17/1994
• Status: Expired due to Fees

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Shalon, Tidhar Dari, Brown, Patrick O.
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US08/688,488
• Time in Patent Office: 4,200 Days
• Field of Search: 435/6, 435/172.3, 536/23.1, 536/201.31, 536/813, 935/3, 935/19, 935/78, 935/80, 523/168
• US Class Current: 435/6.16
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00367 capillary
• CPC Class Codes: B01J 2219/00475 Sheets
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential 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 2219/00612 the surface being inorganic
• 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 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 4/02 for feeding measured , i.e. prescribed quantities of reagents
• CPC Class Codes: B01L 3/0244 using pins
• CPC Class Codes: B01L 3/0248 Prongs, quill pen type dispenser
• CPC Class Codes: B01L 3/5088 : confining liquids at a location by surface tension, e.g. virtual wells on plates, wires B01L3/50857 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: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2001/282 : with mapping; Identification of areas; Spatial correlated pattern
• CPC Class Codes: G01N 2035/00237 : Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: G01N 2035/1037 : Using surface tension, e.g. pins or wires
• CPC Class Codes: G01N 33/54366 : Apparatus specially adapted for solid-phase testing

Abstract

A method of determining the relative amounts of individual polynucleotides in a complex mixture of different-sequence polynucleotides is disclosed. The polynucleotides, after fluorescent labeling, are contacted under hybridization conditions with an array of different DNA sequences disposed at discrete locations on a non-porous surface, at an array density of at least about 100 sequences/cm², where the different DNA sequences in the array are effective to hybridize to individual polynucleotides in the mixture. The level of fluorescence associated with each array sequence provides a measure of its relative amount in the mixture.

Claims

1. An array, comprising:

a planar support having a surface wherein the surface consists of a hydrophobic surface formed by the support material or by a coating applied to the support;

said surface bearing a microarray of different isolated polynucleotide sequences, wherein the microarray has a density of at least 400 discrete regions of polynucleotide sequences per cm² of support surface, wherein each said region is formed by applying a volume of aqueous reagent solution comprising a polynucleotide sequence reagent selected for said region, wherein said surface is hydrophobic in nature such that it prevents spreading of said volume applied to said surface via reagent bead formation, whereby each said region has a specific polynucleotide sequence reagent selected for said region which is different from polynucleotide reagents of other regions.

2. The array of claim 1, wherein each said polynucleotide sequence is a RNA sequence.

3. The array of claim 1, wherein said support is comprised of glass.

4. The array of claim 1, wherein said polynucleotide sequence is DNA sequence.

5. The array of claim 4, wherein each said polynucleotide sequences is a cDNA sequence.

8. The array of claim 5, wherein said support is comprised of glass.

6. An array comprising:

a planar support having a surface wherein the surface consists of a hydrophobic surface formed by the support material or by a coating applied to the support;

said surface bearing a microarray of different isolated polynucleotide sequences,

wherein the microarray has a density of at least 10,000 discrete regions of polynucleotide sequences per in² of support surface, wherein each said region is formed by applying a volume of aqueous reagent solution comprising a polynucleotide sequence reagent selected for said region, and wherein said surface is hydrophobic in nature such that it prevents spreading of said volume applied to said surface via reagent bead formation, whereby each said region has a specific polynucleotide sequence reagent selected for said region which is different from polynucleotide reagents of other regions.

7. The array of claim 6, wherein each said polynucleotide sequence is a RNA sequence.

9. The array of claim 6, wherein said polynucleotide sequence is a DNA sequence.

10. The array of claim 9, wherein each said polynucleotide sequence is a cDNA sequence.