Arrays

• US 20040002078A1
• Filed: 12/05/2002
• Published: 01/01/2004
• Est. Priority Date: 12/05/2001
• Status: Abandoned Application

• Current Assignee: Sengenics Corporation Pte., Ltd.
• Original Assignee: Sense Proteomic Ltd. (Sysmex Corporation)
• Inventors: Boutell, Jonathan Mark, Hart, Darren James, Blackburn, Jonathan Michael, Godber, Benjamin Leslie James
• Application Number:
  US10/313,963
• Publication Number:
  US 20040002078A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/005 Beads
• 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 2219/00585 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 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• 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 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00691 using robots
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 30/04 : by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• 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 2500/00 : Screening for compounds of potential therapeutic value
• CPC Class Codes: G01N 33/6845 : Methods of identifying protein-protein interactions in protein mixtures

Abstract

Protein arrays and their use to assay, in a parallel fashion, the protein products of highly homologous or related DNA coding sequences and described. By highly homologous or related it is meant those DNA coding sequences which share a common sequence and which differ only by one or more naturally occurring mutations such as single nucleotide polymorphisms, deletions or insertions, or those sequences which are considered to be haplotypes. Such highly homologous or related DNA coding sequences are generally naturally occurring variants of the same gene. Arrays according to the invention have two or more individual proteins deposited in a spatially defined pattern on a surface in a form whereby a property such as an activity or function of the proteins can be investigated or assayed in parallel by interrogation of the array.

Claims

1. A protein array comprising a surface upon which are deposited at spatially defined locations at least two protein moieties characterised in that said protein moieties are those of naturally occurring variants of a DNA sequence of interest.

2. A protein array as claimed in claim 1 wherein said variants map to the same chromosomal locus.

3. A protein array as claimed in claim 1 or 2 wherein the one or more protein moieties are derived from synthetic equivalents of naturally occurring variants of a DNA sequence of interest.

4. A protein array as claimed in claim 1 or claim 2 wherein said at least two protein moieties comprise a protein moiety expressed by a wild type gene of interest together with at least one protein moiety expressed by one or more genes containing one or more naturally occurring mutations thereof.

5. A protein array as claimed in claim 4 wherein said mutations are selected from the group consisting of, a mis-sense mutation, a single nucleotide polymorphism, a deletion mutation, and an insertion mutation.

6. A protein array as claimed in any of the preceding claims wherein the protein moieties comprise proteins associated with a disease state, drug metabolism or those which are uncharacterised.

7. A protein array as claimed in any of the preceding claims wherein the protein moieties encode wild type p53 and allelic variants thereof.

8. A protein array as claimed in any of the claims 1 to 6 wherein the protein moieties encode a drug metabolising enzyme.

9. A protein array as claimed in claim 8 wherein the drug metabolising enzyme is wild type p450 and allelic variants thereof.

17. Use of an array as claimed in any of claims 1 to 9 in the determination of the phenotype of a naturally occurring variant of a DNA sequence of interest wherein said DNA sequence is represented by at least one protein moiety derived therefrom and is present on said array.

18. A method of screening a set of protein moieties for molecules which interact with one or more proteins comprising the steps of

a) bringing one or more test molecules into contact with an array as claimed in any one of claims 1 to 9;

which carries said set of protein moieties; and

b) detecting an interaction between one or more test molecules and one or more proteins on the array.

19. A method of simultaneously determining the relative properties of members of a set of protein moieties, comprising the steps of:

a) bringing an array as claimed in any one of claims 1 to 9 which carries said set of protein moieties into contact with one or more test substances, and

b) observing the interaction of said test substances with the set members on the array.

20. The method of claim 19 wherein one or more of said protein moieties are drug metabolising enzymes and wherein said enzymes are activated by contact with an accessory protein or by chemical treatment.

10. A method of making a protein array comprising the steps of

a) providing DNA coding sequences which are those of two or more naturally occurring variants of a DNA sequence of interest

b) expressing said coding sequences to provide one or more individual protein moieties

c) purifying said protein moieties

d) depositing said protein moieties at spatially defined locations on a surface to give an array.

11. The method as claimed in claim 10, wherein steps c) and d) are combined in a single step by the simultaneous purification and isolation of the protein moieties on the array via an incorporated tag.

12. The method as claimed in claim 10, wherein step c) is omitted and said individual protein moieties are present with other proteins from an expression host cell.

13. The method as claimed in claim 10, wherein said DNA sequence of interest encodes a protein associated with a disease state, drug metabolism or is uncharacterised.

14. The method as claimed in claim 13, wherein said DNA sequence of interest encodes p53.

15. The method as claimed in claim 13, wherein said DNA sequence of interest encodes a drug metabolising enzyme.

16. The method as claimed in claim 15, wherein said drug metabolising enzyme is wild type p450 and allelic variants thereof.