Customized oligonucleotide microchips that convert multiple genetic information to simple patterns, are portable and reusable

• US 6,458,584 B1
• Filed: 03/03/1999
• Issued: 10/01/2002
• Est. Priority Date: 12/23/1996
• Status: Expired due to Term

• Current Assignee: U Chicago Argonne, LLC
• Original Assignee: University of Chicago
• Inventors: Chik, Valentine, Lysov, Yuri, Fotin, Alexander, Guschin, Dmitry Y., Drobyshev, Aleksei, Mirzabekov, Andrei, Yershov, Gennadiy
• Primary Examiner(s): Siew, Jeffrey
• Application Number:
  US09/261,115
• Time in Patent Office: 1,308 Days
• Field of Search: 435/6, 435/7.1, 435/91.1, 435/91.2, 435/287.2, 536/22.1, 536/23.1, 536/24-- 2
• US Class Current: 435/287.2
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design

Abstract

This invention relates to using customized oligonucleotide microchips as biosensors for the detection and identification of nucleic acids specific for different genes, organisms and/or individuals in the environment, in food and in biological samples. The microchips are designed to convert multiple bits of genetic information into simpler patterns of signals that are interpreted as a unit. Because of an improved method of hybridizing oligonucleotides from samples to microchips, microchips are reusable and transportable. For field study, portable laser or bar code scanners are suitable.

Claims

1. A method for using a reuseable microchip to identify at least one nucleic acid sequence in nucleic acids of a sample, said method comprising:

(a) providing a customized matrix of oligonucleotides on the microchip in an arrangement that is an ordered scheme designed to present a detectable pattern as a whole that identifies the sequences of nucleic acids in the sample;

(b) hybridizing nucleic acids from the sample on said microchip; and

(c) identifying at least one nucleic acid sequence in said sample by the pattern detected as a whole on the microchip, said pattern resulting from the locations of oligonucleotides which hybridized to the sample nucleic acids

wherein the customized matrix of oligonucleotides on the reusable microchip is formed by a plurality of gel elements, wherein the number of elements is determined by the number of oligonucleotides in the matrix and wherein each gel element contains one oligonucleotide of a desired nucleic acid sequence length and concentration, each gel element being separated from another by interstitial spaces, said oligonucleotides being positioned in specific locations and wherein said matrix comprises oligonucleotides comprising the base sequences;

2. The method of claim 1, wherein the oligonucleotides are arranged in a matrix wherein I, II, III and IV are columns and “

ABC”

are rows in a microchip;

3. The method of claim 1, further comprising:

adding a label to the nucleic acid sequences in said sample before hybridizing them to oligonucleotides in the microchip.

4. The method of claim 3, wherein the label is a fluorescent dye.

5. The method of claim 3, wherein the label is a plurality of different dyes.

6. A microchip matrix for the detection and classification of nitrifying bacteria wherein said matrix has the following design: