Device and method for multiple analyte detection

• US 8,247,219 B2
• Filed: 06/11/2007
• Issued: 08/21/2012
• Est. Priority Date: 04/03/1996
• Status: Expired due to Fees

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Woudenberg, Timothy, Albin, Michael, Kowallis, Reid B., Raysberg, Yefim, Ragusa, Robert P., Winn-Deen, Emily S.
• Primary Examiner(s): Yu, Melanie J
• Application Number:
  US11/811,504
• Publication Number:
  US 20080102462A1
• Time in Patent Office: 1,898 Days
• Field of Search: 435/287.2, 435/288.4, 435/288.5, 435/288.7, 436/501, 436/518, 436/164, 436/807, 422/50, 422/82.05, 422/82.08, 422/68.1
• US Class Current: 435/287.2
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00599 Solution-phase processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2200/027 for microfluidic devices
• CPC Class Codes: B01L 2200/0642 Filling fluids into wells by specific techniques
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0864 comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• CPC Class Codes: B01L 2300/1827 using resistive heater
• CPC Class Codes: B01L 2400/049 vacuum
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/50851 specially adapted for heating or cooling samples laboratory heating apparatus B01L7/00; incubators C12M
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: C12Q 1/08 using multifield media
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/08 Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creation; Particular methods of cleavage from the liquid support
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G01N 2035/00148 Test cards, e.g. Biomerieux or McDonnel multiwell test cards
• CPC Class Codes: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: Y10S 436/805 : Optical property
• CPC Class Codes: Y10S 436/807 : Apparatus included in process claim, e.g. physical support structures
• CPC Class Codes: Y10S 436/808 : Automated or kit
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/25 : including sample preparation

Abstract

The invention is directed to a method and device for simultaneously testing a sample for the presence, absence, and/or amounts of one or more of a plurality of selected analytes. The invention includes, in one aspect, a device for detecting or quantitating a plurality of different analytes in a liquid sample. Each chamber may include an analyte-specific reagent effective to react with a selected analyte that may be present in the sample, and detection means for detecting the signal. Also disclosed are methods utilizing the device.

Claims

1. A method for reacting a target nucleic acid and detecting an optical signal, comprising:

providing a substrate comprising a chamber, wherein the chamber is pre-loaded with a first unlabeled oligonucleotide such that the first unlabeled oligonucleotide is immobilized on the substrate, and the chamber is pre-loaded with a second unlabeled oligonucleotide such that the second unlabeled oligonucleotide is immobilized on the substrate;

introducing a target nucleic acid sequence into the chamber;

reacting the target nucleic acid sequence with both the first unlabeled oligonucleotide and the second unlabeled oligonucleotide in the chamber, to form a first reaction product in the chamber;

reacting the first reaction product with an optically detectable detection reagent in the chamber to form a second reaction product; and

detecting an optical signal produced in the chamber by the second reaction product in the chamber,

wherein the substrate further comprises a channel in fluid communication with the chamber.

2. The method of claim 1, wherein reacting the target nucleic acid sequence with both the first unlabeled oligonucleotide and the second unlabeled oligonucleotide in the chamber, to form a first reaction product in the chamber, comprises at least one of a polymerase chain reaction, a ligase chain reaction, an oligonucleotide ligation assay, and a hybridization assay.

3. The method of claim 1, wherein the first unlabeled oligonucleotide and the second unlabeled oligonucleotide comprise a primer pair suitable for amplifying the target nucleic acid sequence.

4. The method of claim 1, wherein at least one of the first unlabeled oligonucleotide and the second unlabeled oligonucleotide comprises a sequence that is complementary to at least a portion of the target nucleic acid sequence.

5. The method of claim 1, wherein the second reaction product is detected through an optically transparent window in the chamber.

6. The method of claim 1, wherein the target nucleic acid sequence is introduced into the chamber by vacuum action.

7. The method of claim 1, wherein at least one of the pre-loaded first unlabelled oligonucleotide and the pre-loaded second unlabelled oligonucleotide are dried in the chamber.

8. The method of claim 1, wherein the optically detectable detection reagent comprises a fluorescent dye.

9. The method of claim 1, wherein the optically detectable detection reagent comprises a fluorescer dye and a quencher dye.

10. The method of claim 1, wherein at least one of the first unlabeled oligonucleotide and the second unlabeled oligonucleotide comprises a polynucleotide analog.

11. The method of claim 1, wherein the first unlabeled oligonucleotide and the second unlabeled oligonucleotide bind to adjacent, contiguous regions of the target nucleic acid sequence.

12. The method of claim 1, wherein the first unlabeled oligonucleotide has a sequence that is complementary to at least a portion of the target nucleic acid sequence.

13. The method of claim 1, wherein the second unlabeled oligonucleotide has a sequence that is complementary to at least a portion of the target nucleic acid sequence.

14. The method of claim 1, wherein the first unlabeled oligonucleotide has a sequence that is complementary to at least a first portion of the target nucleic acid sequence, and where the second unlabeled oligonucleotide has a sequence that is complementary to at least a second portion of the target nucleic acid sequence.

15. The method of claim 1, wherein the reacting of the target nucleic acid sequence with both the first unlabeled oligonucleotide and the second unlabeled oligonucleotide in the chamber, further comprises reacting the target nucleic acid sequence with nucleotide triphosphates, to form the first reaction product in the chamber.

16. The method of claim 1, wherein the chamber comprises a plurality of chambers formed in the substrate, the channel comprises a plurality of channels, and each of the plurality of chambers is in fluid communication with one of the plurality of channels.