Analying polynucleotide sequences

• US 6,054,270 A
• Filed: 09/09/1997
• Issued: 04/25/2000
• Est. Priority Date: 05/03/1988
• Status: Expired due to Fees

• Current Assignee: Oxford Gene Technology Limited (Sysmex Corporation)
• Original Assignee: Oxford Gene Technology Limited (Sysmex Corporation)
• Inventors: Southern, Edwin
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/925,676
• Time in Patent Office: 959 Days
• Field of Search: 435/6, 435/810, 422/50, 422/68.1, 436/501, 536/23.1, 536/24.1, 536/24.3-24.33, 536/25.3, 935/77, 935/78
• US Class Current: 435/6.12
• 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 2219/00385 Printing
• CPC Class Codes: B01J 2219/0043 for direct application of reagents, e.g. through openings in a shutter
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• 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 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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: 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 60/14 for creating libraries

Abstract

This invention provides an apparatus and method for analyzing a polynucleotide sequence; either an unknown sequence or a known sequence. A support, e.g. a glass plate, carries an array of the whole or a chosen part of a complete set of oligonucleotides which are capable of taking part in hybridization reactions. The array may comprise one or more pair of oligonucleotides of chosen lengths. The polynucleotide sequence, or fragments thereof, are labelled and applied to the array under hybridizing conditions. Applications include analyses of known point mutations, genomic fingerprinting, linkage analysis, characterization of mRNAs, mRNA populations, and sequence determination.

Claims

1. A method of making an array of oligonucleotides, which comprises:

attaching a plurality of oligonucleotides to an impermeable surface of a support, the oligonucleotides having different predetermined sequences and being attached at different known locations on the surface of the support through a computer-controlled printing device.

2. The method as claimed in claim 1, wherein stripes of oligonucleotides, corresponding to allelic variants of a polynucleotide to be probed, are attached to the impermeable surface of the support.

3. A method for constructing an array of oligonucleotides of length s and composed of different nucleotides, which method comprises:

a) applying precursors for the different nucleotides separately to a plurality of different regions of a surface,

b) applying precursors for the different nucleotides separately to a plurality of different regions amongst the plurality of different regions defined in a),

c) repeating the process until each of said regions contains oligonucleotides of length s.

4. The method as claimed in claim 3, wherein the number of different nucleotides utilized is 4.

5. The method as claimed in claim 3, where s is 8-20.

6. The method as claimed in claim 3, wherein the regions are organized on the surface in rows and columns.

7. The method as claimed in claim 3, wherein the precursors are applied through a computer-controlled printing device.

8. The method as claimed in claim 3, wherein each region is at least 100 microns wide.

9. A method of analysing a polynucleotide, which method comprises:

applying a labelled polynucleotide to be analysed or fragments thereof to an array of oligonucleotides under hybridisation conditions, wherein the array comprises a support having an impermeable surface to which a plurality of oligonucleotides having different predetermined sequences are attached to different known regions on the surface, and

analysing the polynucleotide by observing the regions where the polynucleotide or fragment thereof hybridizes and the regions where the polynucleotide or fragment thereof does not hybridize.

10. A method of comparing polynucleotide sequences, which method comprises:

applying the polynucleotides to an array of oligonucleotides under hybridizing conditions, wherein the oligonucleotides have different predetermined sequences and are attached at different known locations on an impermeable surface of a support, and

observing the differences between the patterns of hybridisation.

11. A method for analysing multiple sequences in multiple polynucleotides, which comprises:

a) laying down stripes of oligonucleotides corresponding to each sequence on the surface of an impermeable solid support,

b) applying the polynucleotides to the surface under hybridisation conditions in stripes orthogonal to those of the oligonucleotides,

c) observing hybridisation at a site of intersection as an indication of the presence of a sequence in the polynucleotide.

12. An array of oligonucleotides comprising a support having an impermeable surface to which a plurality of oligonucleotides are attached, the oligonucleotides having different nucleotide sequences and being attached at different known locations on the surface of the support, wherein each oligonucleotide has the sequence N_m AATAAAN_n or its complement where N is any nucleotide residue and m+n is at least about 8.