Device and method for multiple analyte detection

• US 20030152994A1
• Filed: 02/24/2003
• Published: 08/14/2003
• Est. Priority Date: 04/03/1996
• Status: Active Grant

• Current Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Kowallis, Reid B., Albin, Michael, Winn-Deen, Emily S., Ragusa, Robert P., Raysberg, Yefim, Woudenberg, Timothy W.
• Granted Patent: US 7,211,443 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2300/0887 Laminated structure
• CPC Class Codes: B01L 2400/049 vacuum
• CPC Class Codes: B01L 3/5025 for parallel transport of multiple samples
• 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 3/50273 characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502738 characterised by integrated valves microvalves F16K99/0001
• 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: G01N 2035/00148 Test cards, e.g. Biomerieux or McDonnel multiwell test cards
• CPC Class Codes: G01N 2035/00356 Holding samples at elevated temperature (incubation)
• CPC Class Codes: G01N 2035/1032 Dilution or aliquotting
• CPC Class Codes: G01N 2035/1034 Transferring microquantities of liquid
• CPC Class Codes: G01N 35/08 using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
• CPC Class Codes: G01N 35/10 Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices G01N35/0099 takes precedence
• CPC Class Codes: Y10S 436/807 Apparatus included in process claim, e.g. physical support structures

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 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. The device includes a substrate which defines a sample-distribution network having (i) a sample inlet, (ii) one or more detection chambers, and (iii) channel means providing a dead-end fluid connection between each of the chambers and the inlet. 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 detecting or quantitating one or more of a plurality of polynucleotide sequences in a sample, said method comprising

providing a device comprising a substrate defining a sample-distribution network including (i) a sample inlet, (ii) two or more detection chambers, and (iii) channel means providing a dead-end fluid connection between each of said chambers and said inlet, wherein at least two of said detection chambers each contain a different, sequence-specific polynucleotide binding polymer for detecting or quantitating different polynucleotide sequences that may be present in such sample, to produce a detectable signal,

applying a liquid sample to the sample inlet and delivering the sample to the network by action of a force whereby the sample is delivered to the detection chambers,

allowing the delivered sample to react with at least one sequence-specific polynucleotide binding polymer in each detection chamber under conditions effective to produce a detectable signal in each detection chamber when a specific sequence is present in the sample, and

measuring the signals produced in the reaction chambers to detect or quantitate specific target sequences in the sample.

2. The method of claim 1, wherein said channel means comprises a single channel to which said detection chambers are connected by said fluid connections.

3. The method of claim 1, wherein said channel means comprises a first channel to which a first group of detection chambers are connected by such fluid connections, and a second channel to which a second group of detection chambers are connected.

4. The method of claim 1, wherein said channel means comprises an individual channel for each detection chamber, for providing a dead-end fluid connection between said inlet and each detection chamber.

5. The method of claim 1, wherein said device further comprises a port connected to the channel means at a site in fluid communication with the sample inlet and detection chambers.

6. The method of claim 5, wherein said port is connected to the channel means at a site that is downstream of said sample inlet and said detection chambers.

7. The method of claim 1, wherein said device further comprises a non-flowthrough reservoir in fluid communication with said channel means.

8. The method of claim 1, wherein at least one binding polymer comprises an oligonucleotide primer pair suitable for amplifying, by polymerase chain reaction, a specific polynucleotide sequence which is flanked by sequences complementary to the primer pair.

9. The method of claim 8, wherein at least one binding polymer further comprises a fluorescer-quencher oligonucleotide capable of hybridizing to the specific polynucleotide sequence in a region downstream of one of the primers, for producing a detectable fluorescent signal when the selected sequence is present in the sample.

10. The method of claim 1, wherein at least one binding polymer comprises first and second oligonucleotides effective to bind to adjacent, contiguous regions of a specific polynucleotide sequence.

11. The method of claim 10, wherein the at least one binding polymer comprises a second pair of oligonucleotides which are effective to bind to adjacent, contiguous regions complementary to the regions bound by the first pair of oligonucleotides, for amplification of the regions by ligase chain reaction.

12. The method of claim 1, wherein at least one of the detection chambers comprises an intercalating compound which produces an optically detectable signal upon intercalating a double-stranded polynucleotide.

13. The method of claim 1, wherein said substrate further comprises a temperature regulator for controlling the temperature of each detection chamber.

14. The method of claim 1, wherein said substrate defines at least two such sample-distribution networks.

15. The method of claim 1, wherein said providing comprises filling said network with carbon dioxide gas.

16. The method of claim 1, wherein at least one of the binding polymers contains a fluorescent dye.

17. The method of claim 1, wherein at least one of the binding polymers comprises a fluorescent dye moiety which produces a detectable signal upon hybridization of the binding polymer to a target polynucleotide sequence.

18. The method of claim 1, wherein at least one binding polymer comprises first and second oligonucleotides effective to bind to adjacent regions of a specific polynucleotide sequence which are separated from each other by one or more intervening bases.

19. The method of claim 1, wherein the dead-end fluid connection provides sole fluid access to each of said detection chambers, such that fluid cannot enter or exit the detection chamber by any other way than through the dead-end fluid connection.

20. A method for analyzing one or more polynucleotide sequences in a sample, said method comprising

providing a device comprising a substrate defining a (i) a sample inlet, (ii) a plurality of detection chambers, and (iii) channel structure providing a fluid connection between each of said chambers and said inlet, wherein two or more of said detection chambers contain one or more sequence-specific polynucleotide binding polymers for the analysis of one or more polynucleotide sequences that may be present in such sample, to produce a detectable signal,

applying a sample to the sample inlet and delivering the sample to the detection chambers,

allowing the delivered sample to react with at least one sequence-specific polynucleotide binding polymer in at least one of said detection chambers under conditions effective to produce a detectable signal when a specific sequence is present in the sample, and

detecting for said signal.

21. A device for detecting or quantitating one or more of a plurality of different polynucleotide sequences in a liquid sample, said device comprising

a substrate defining a sample-distribution network including (i) a sample inlet, (ii) two or more detection chambers, and (iii) channel means providing a dead-end fluid connection between each of said chambers and said inlet, wherein at least two of said detection chambers each contain a different, sequence-specific polynucleotide binding polymer for detecting or quantitating different polynucleotide sequences that may be present in such sample, to produce a detectable signal,

whereby, application of such sample to said inlet and a change in pressure within said network, is effective to provide each of said chambers with a portion of said sample therein.

22. The device of claim 21, wherein said channel means comprises a single channel to which said detection chambers are connected by said fluid connections.

23. The device of claim 21, wherein said channel means comprises a first channel to which a first group of detection chambers are connected by such dead-end fluid connections, and a second channel to which a second group of detection chambers are connected by such dead-end fluid connections.

24. The device of claim 21, wherein said channel means comprises an individual channel for each detection chamber, for providing a dead-end fluid connection between said inlet and each detection chamber.

25. The device of claim 21, which further comprises a port connected to said channel means at a site in fluid communication with the sample inlet and detection chambers.

26. The device of claim 25, wherein said port is connected to said channel means at a site that is downstream of said detection chambers.

27. The device of claim 21, which further comprises a non-flowthrough reservoir in fluid communication with said channel means.

28. The device of claim 21, wherein said detection means comprises an optically transparent window associated with each detection chamber, through which such signal can be optically detected.

29. The device of claim 21, wherein at least one binding polymer includes first and second oligonucleotide primers having sequences effective to hybridize to opposite end regions of complementary strands of a selected polynucleotide sequence, for amplifying the sequence by primer-initiated polymerase chain reaction.

30. The device of claim 29, wherein at least one binding polymer further comprises a fluorescer-quencher oligonucleotide capable of hybridizing to the selected polyucleotide sequence in a region downstream of one of the primers, for producing a detectable fluorescent signal when the selected sequence is present in the sample.

31. The device of claim 21, wherein at least one binding polymer comprises first and second oligonucleotides effective to bind to adjacent, contiguous regions of a selected polynucleotide sequence.

32. The device of claim 31, wherein the at least one binding polymer comprises a second pair of oligonucleotides which are effective to bind to adjacent, contiguous regions complementary to the regions bound by the first pair of oligonucleotides, for amplification of the regions by ligase chain reaction.

33. The device of claim 21, wherein at least one of the detection chambers additionally comprises an intercalating compound which produces an optically detectable signal upon intercalating a double-stranded polynucleotide.

34. The device of claim 21, wherein said substrate further comprises a temperature regulator for controlling the temperature of each detection chamber.

35. The device of claim 21, wherein said substrate defines at least two such sample-distribution networks.

36. The device of claim 21, wherein the interior of said network is under vacuum.

37. The device of claim 21, wherein at least one of the binding polymers contains a fluorescent dye.

38. The device of claim 21, wherein at least one binding polymer contains a fluorescent dye moiety which produces a detectable signal upon hybridization of the binding polymer to a target polynucleotide sequence.

39. The device of claim 21, wherein at least one binding polymer comprises first and second oligonucleotides effective to bind to adjacent regions of a selected polynucleotide sequence which are separated from each other by one or more intervening bases.