METHOD FOR PROVIDING MICROARRAYS

• US 20080248971A1
• Filed: 03/10/2008
• Published: 10/09/2008
• Est. Priority Date: 02/12/2004
• Status: Abandoned Application

• Current Assignee: Invitrogen Corp. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Invitrogen Corp. (Thermo Fisher Scientific Incorporated)
• Inventors: Gao, Xiaolian, Wang, Xiaoming, Liu, Jerry
• Application Number:
  US12/045,514
• Publication Number:
  US 20080248971A1
• Time in Patent Office: Days
• US Class Current: 506/24
• CPC Class Codes: B01J 2219/00693 Means for quality control
• CPC Class Codes: B01J 2219/007 Simulation or vitual synthesis
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

Abstract

An interactive method of providing an array of nucleic acid sequences in which a remote user enters a query to generate a listing of desired sequence probes, which are then selected and returned to the host for use in producing a custom microarray designed by a remote user.

Claims

1. An interactive method of providing an array of nucleic acid sequences comprising:

preparing a database of gene probes or probe identifiers wherein each gene probe is effective to identify a specific target gene, and further wherein each of the gene probes is identified by one or more identifiers;

providing an electronic connection to the database effective to allow a user to electronically query the database by the identifiers;

providing means for storing a list of gene probes;

transmitting a collection of selected gene probes from the user to the host; and

producing a nucleic acid probe array that comprises the selected gene probes.

2. The method of claim 1, wherein the identifiers are accession numbers, accession alias numbers, disease names, disease synonym names, gene functions, gene names, gene symbols, gene descriptions, PFAM names, gene ontology (GO) molecular function terms, or locus I.D. numbers.

3. The method of claim 1, wherein the gene probes comprise sets of 1-5 nucleic acid sequences.

4. The method of claim 1, wherein the means for storing a list of gene probes is a storage device on a host server.

5. The method of claim 1, wherein the means for storing a list of gene probes is software that directs storage of the gene probes on the user'"'"'s computer, the host'"'"'s computer, or both.

6. The method of claim 1, wherein the probes are nucleic acid probes of from 40 to 50 bases in length.

7. The method of claim 1, wherein the probes are nucleic acid probes of 10-100 bases in length.

8. The method of claim 1, wherein the probes are designed to hybridize to their respective target genes in a region within 1500 bases of the 3′

end of the coding sequence of the target gene.

9. The method of claim 1, wherein the probes are optimized for Tm, C+G content, probe secondary structure, dimerization tendency, or combinations thereof.

10. The method of claim 1, wherein the microarray further comprises control sequences.

11. The method of claim 1, wherein the nucleotide probes of the array are made by synthesis of the nucleic acid probes in situ on a solid substrate comprising isolated sites.

12. The method of claim 1, wherein the nucleotide probes are synthesized by steps that comprise:

(a) addition of protecting groups to the reactive chemical groups within the isolated sites wherein the protecting groups are not photo-labile;

(b) contacting the isolated sites with photo-generated agent precursors;

(c) irradiating a selected subset of the isolated sites effective to generate active agents from the precursors within the selected subset and to deprotect reactive chemical groups within the selected subset;

(d) contacting the isolated sites with a selected nucleic acid monomer comprising a free reactive chemical group and a protected reactive chemical group under conditions in which the free reactive chemical group of the monomer bonds to the deprotected reactive chemical group of the selected subset; and

(e) repeating steps b-d until the selected nucleic acid probes are synthesized.

13. The method of claim 1, wherein the database comprises gene probes or identifiers for human, mouse, rat, Xenopus, bacteria, Drosophila Arabidopsis, and Caenorhabditis genes.

14. A system for providing custom nucleic acid microarrays comprising:

a host computer comprising a data storage media;

a database of gene probes stored on the storage media wherein each gene probe is associated with one or more identifiers;

a user connection configured to allow remote users to connect to the host computer and to access the database;

software means to allow a remote user to query the database to generate a list of gene probes; and

means for remotely selecting listed gene probes;

wherein the selected gene probes are provided on a microarray.

15. The system of claim 14, wherein the computer interface is a modem connection, T1 line, satellite access, or network access.

16. The system of claim 14, further comprising means for storing selected gene probes on the host computer, on the remote user'"'"'s computer or both.