Device and method for multiple analyte detection

• US 7,381,569 B2
• Filed: 01/27/2006
• Issued: 06/03/2008
• Est. Priority Date: 04/03/1996
• Status: Expired due to Fees

• Current Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Raqusa, Robert P., Kowallis, Reid B., Albin, Michael, Winn-Deen, Emily S., Raysberg, Yefim, Woudenberg, Timothy M.
• Primary Examiner(s): Le; Long V.
• Assistant Examiner(s): DIRAMIO, JACQUELINE A
• Application Number:
  US11/341,732
• Publication Number:
  US 20060127939A1
• Time in Patent Office: 858 Days
• Field of Search: 422/50, 422/55, 422/57, 422/58, 422/68.1, 422/102, 422/82.05, 422/82.08, 435/6, 435/7.1, 435/287.2, 435/288.5, 435/288.4, 435/288.7, 436/164, 436/501, 436/807
• US Class Current: 436/518
• 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 system comprising:

a device comprising

a plurality of detection chambers,

channel means in fluid communication with each of the plurality of detection chambers, wherein the channel means provides a plurality of dead-end fluid connections to the plurality of detection chambers, wherein one dead-end fluid connection is provided to each of the plurality of detection chambers, and each dead-end fluid connection provides the sole fluid access to its respective detection chamber such that fluid cannot enter or exit the respective detection chamber by any other way than through the respective dead-end fluid connection,

non-immobilized detection reagents provided in each of the plurality of detection chambers, the non-immobilized detection reagents comprising at least one binding polymer, wherein the non-immobilized detection reagents are effective to selectively bind with a target nucleic acid sequence under conditions effective to produce a detectable fluorescent signal when a target nucleic acid sequence is present in a liquid sample in at least one of the plurality of detection chambers; and

a fluorescence detector for detecting a fluorescent signal, the fluorescence detector configured for optical communication with one or more of the plurality of detection chambers.

2. The system of claim 1, wherein the plurality of detection chambers further comprise a liquid sample provided therein, the liquid sample comprising a target nucleic acid sequence.

3. The system of claim 2, wherein the target nucleic acid sequence comprises a single stranded nucleic acid sequence.

4. The system of claim 1, wherein the at least one binding polymer comprises a first unlabeled oligonucleotide and a second unlabeled oligonucleotide, each of which are effective to bind selectively to different regions of a target nucleic acid sequence.

5. The system of claim 4, the detection reagents further comprising a third oligonucleotide for providing a detectable fluorescent signal when a target nucleic acid sequence is present in a liquid sample.

6. The system of claim 5, wherein the third oligonucleotide comprises a fluorescently-labeled oligonucleotide.

7. The system of claim 6, wherein the fluorescently-labeled oligonucleotide comprises a fluorescer-quencher oligonucleotide.

8. The system of claim 6, wherein the detection reagents further comprise at least one enzyme.

9. A device comprising:

a plurality of detection chambers;

channel means in fluid communication with each of the plurality of detection chambers, wherein the channel means provides a plurality of dead-end fluid connections to the plurality of detection chambers, wherein one dead-end fluid connection is provided to each of the plurality of detection chambers, and each dead-end fluid connection provides the sole fluid access to its respective detection chamber such that fluid cannot enter or exit the respective detection chamber by other way than through the respective dead-end fluid connection; and

non-immobilized detection reagents provided in each of the plurality of detection chambers, the non-immobilized detection reagents comprising at least one binding polymer, wherein the non-immobilized detection reagents are effective to selectively bind with a target nucleic acid sequence under conditions effective to produce a detectable fluorescent signal when a target nucleic acid sequence is present in a liquid sample in at least one of the plurality of detection chambers.

10. The device of claim 9, further comprising temperature regulating means adapted to regulate the temperature of each of the plurality of detection chambers by heating and cooling each of the plurality of detection chambers.

11. The device of claim 9, wherein the at least one binding polymer comprises a first unlabeled oligonucleotide and a second unlabeled oligonucleotide, wherein the first unlabeled oligonucleotide and the second unlabeled oligonucleotide are each effective to bind selectively to different regions of a target nucleic acid.

12. The device of claim 11, further comprising a third oligonucleotide for providing a detectable fluorescent signal when a target nucleic acid sequence is present in a liquid sample.

13. The device of claim 12, wherein the third oligonucleotide comprises a fluorescently-labeled oligonucleotide.

14. The device of claim 13, wherein the fluorescently labeled oligonucleotide comprises a fluorescer-quencher oligonucleotide.

15. The device of claim 12, further comprising a liquid sample comprising a target nucleic acid sequence, provided in each of the plurality of detection chambers.

16. The device of claim 15, wherein the target nucleic acid sequence comprises a single-stranded nucleic acid sequence.

17. A system for detecting or quantitating one or more target nucleic acid sequences in a liquid sample, the system comprising:

a device comprising

a plurality of detection chambers,

a channel network in fluid communication with each of the plurality of detection chambers, the channel network comprising a plurality of dead-end fluid connections to the plurality of detection chambers, wherein one dead-end fluid connection is provided to each of the plurality of detection chambers, and each dead-end fluid connection provides the sole fluid access to its respective detection chamber such that fluid cannot enter or exit the respective detection chamber by any other way than through the respective dead-end fluid connection,

non-immobilized detection reagents provided in at least one of the plurality of detection chambers, the non-immobilized detection reagents comprising an unlabeled oligonucleotide primer pair effective to selectively bind with a target nucleic acid sequence under conditions effective to amplify the target nucleic acid sequence by polymerase chain reaction when the target nucleic acid sequence is present in the liquid sample in the at least one of the plurality of detection chambers;

a fluorescent detection reagent provided in the at least one of the plurality of detection chambers; and

a fluorescence detector for detecting a fluorescent signal, the fluorescence detector configured for optical communication with one or more of the plurality of detection chambers.

18. The system of claim 17, wherein the fluorescent detection reagent comprises a nucleic acid binding dye that exhibits a fluorescence increase or decrease upon binding to a double-stranded nucleic acid.

19. A system for detecting or quantitating one or more target polynucleotide sequences in a liquid sample, comprising:

a device comprising a substrate defining a sample-distribution network including (i) a sample inlet, (ii) two or more detection chambers, (iii) a channel providing a fluid communication to said inlet, and (iv) a plurality of dead-end fluid connections, wherein said two or more detection chambers are each pre-loaded with an oligonucleotide primer pair suitable for polymerase chain reaction;

a temperature-controller adapted to heat the two or more detection chambers; and

a fluorescence detector configured for optical communication with one or more of the two or more detection chambers, for detecting fluorescence produced therein.

20. The system of claim 19, wherein the temperature-controller comprises:

means for modulating the temperature of the two or more detection chambers to effect thermal cycling of a liquid sample within each detection chamber.

21. The system of claim 19, wherein each of the two or more detection chambers are pre-loaded with a different oligonucleotide primer pair suitable for polymerase chain reaction, compared to the oligonucleotide primer pair pre-loaded in at least one other of the two or more detection chambers.