Mesoscale polynucleotide amplification device and method

• US 6,953,676 B1
• Filed: 12/15/1998
• Issued: 10/11/2005
• Est. Priority Date: 05/01/1992
• Status: Expired due to Fees

• Current Assignee: Trustees Of The University Of Pennsylvania (University of Pennsylvania)
• Original Assignee: Trustees Of The University Of Pennsylvania (University of Pennsylvania)
• Inventors: Kricka, Larry J., Wilding, Peter
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US09/212,029
• Time in Patent Office: 2,492 Days
• Field of Search: 422/50, 422/68.1, 435/283.1, 435/285.1, 435/285.2, 435/286.1, 435/287.1, 435/287.2, 435/287.3, 435/287.9, 435/289.1, 435/299.1, 435/91.2
• US Class Current: 435/91.2
• CPC Class Codes: B01D 2325/028 Microfluidic pore structures
• CPC Class Codes: B01D 61/18 Apparatus therefor
• CPC Class Codes: B01D 67/003 by selective elimination of components, e.g. by leaching
• CPC Class Codes: B01D 67/0031 by elimination of at least one of the blocks of a block copolymer
• CPC Class Codes: B01D 71/02 Inorganic material
• CPC Class Codes: B01D 71/0213 Silicon
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 19/0093 Microreactors, e.g. miniaturised or microfabricated reactors laboratory containers with capillary fluid transport in microfabricated channels or chambers B01L3/5027
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2200/027 for microfluidic devices
• CPC Class Codes: B01L 2200/0647 Handling flowable solids, e.g. microscopic beads, cells, particles
• CPC Class Codes: B01L 2200/10 Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept
• CPC Class Codes: B01L 2200/146 Employing pressure sensors
• CPC Class Codes: B01L 2200/147 Employing temperature sensors
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 2300/0645 Electrodes
• CPC Class Codes: B01L 2300/0681 Filter
• CPC Class Codes: B01L 2300/1822 using Peltier elements
• CPC Class Codes: B01L 2300/185 using a liquid as fluid
• CPC Class Codes: B01L 2300/1861 : using radiation
• CPC Class Codes: B01L 2400/0487 : fluid pressure, pneumatics
• CPC Class Codes: B01L 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502746 : characterised by the means for controlling flow resistance, e.g. flow controllers, baffles B01L3/502738 takes precedence
• CPC Class Codes: B01L 7/525 : with physical movement of samples between temperature zones
• CPC Class Codes: B01L 9/527 : for microfluidic devices, e.g. used for lab-on-a-chip
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: Y10S 436/805 : Optical property
• CPC Class Codes: Y10S 436/806 : Electrical property or magnetic property
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 436/25375 : Liberation or purification of sample or separation of material from a sample [e.g., filtering, centrifuging, etc.]

Abstract

Disclosed are devices for amplifying a preselected polynucleotide in a sample by conducting a polynucleotide polymerization reaction. The devices comprise a substrate microfabricated to define a sample inlet port and a mesoscale flow system, which extends from the inlet port. The mesoscale flow system includes a polynucleotide polymerization reaction chamber in fluid communication with the inlet port which is provided with reagents required for polymerization and amplification of a preselected polynucleotide. In one embodiment the devices may be utilized to implement a polymerase chain reaction (PCR) in the reaction chamber (PCR chamber). The PCR chamber is provided with the sample polynucleotide, polymerase, nucleoside triphosphates, primers and other reagents required for the polymerase chain reaction, and the device is provided with means for thermally controlling the temperature of the contents of the reaction chamber at a temperature controlled to dehybridize double stranded polynucleotide, to anneal the primers, and to polymerize and amplify the polynucleotide.

Claims

1. A device for amplifying a preselected polynucleotide in a sample by conducting a polynucleotide polymerization reaction, the device comprising:

a solid substrate microfabricated to define;

a sample inlet port; and

a mesoscale flow system comprising;

a sample flow channel having a cross-section and extending from said inlet port; and

a polynucleotide polymerization reaction chamber having a cross-section and being in fluid communication with said flow channel, said chamber containing reagents for the polymerization reaction, said flow channel and said reaction chamber having at least one cross-sectional dimension of width or depth which is between about 0.1 to 500 μ

m said reaction chamber cross-section and said flow channel cross-section being dissimilar;

means for thermally regulating the contents of said chamber whereby the temperature is controlled to amplify said preselected polynucleotide; and

means for detecting said amplified polynucleotide.

5. The device of claim 1, wherein said means for detecting said amplified polynucleotide comprises a mesoscale detection region disposed within said substrate in fluid communication with said reaction chamber;

and

wherein the device further includes means for inducing flow through said reaction chamber to transport said amplified polynucleotide to said detection region.

6. The device of claim 5 wherein said detection region includes a polynucleotide probe capable of detectably binding to said amplified polynucleotide.

7. The device of claim 6, wherein said polynucleotide probe is immobilized on a magnetic bead.

8. The device of claim 7 wherein said detection region comprises a fractal flow region, in fluid communication with said flow channel, comprising bifurcations leading to plural secondary flow channels.

9. The device of claim 1, further comprising an appliance for use in combination with said substrate, said appliance comprising:

means for holding said substrate; and

optical means for viewing the contents of said mesoscale flow system in said substrate.

10. The device of claim 9, wherein said optical means comprises magnifying optics and a video camera, and wherein said appliance further comprises:

a tilt mechanism for manually adjusting the angle and location of the device; and

a video screen for viewing the contents of said flow system.

2. A method for amplifying a preselected polynucleotide in a sample by conducting a polynucleotide polymerization reaction, the method comprising:

(i) providing a device comprising;

a solid substrate microfabricated to define;

a sample inlet port; and

a mesoscale flow system comprising;

a sample flow channel having a cross-section and extending from said inlet port; and

a polynucleotide polymerization reaction chamber having a cross-section and being in fluid communication with said flow channel, said flow channel and said reaction chamber having at least one cross-sectional dimension of width or depth which is between about 0.1 to 500 μ

m said reaction chamber cross-section and said flow channel cross-section being dissimilar; and

means for thermally regulating the contents of said chamber at a temperature controlled to amplify said preselected polynucleotide;

(ii) delivering, through said inlet port and said mesoscale flow system to said reaction chamber, said sample polynucleotide and reagents required for the polymerization reaction;

(iii) thermally controlling the contents of said chamber to polymerize said polynucleotide; and

(iv) detecting said amplified polynucleotide.

11. The method of claim 2, wherein said means for detecting said amplified polynucleotide comprises a mesoscale detection region disposed within said substrate in fluid communication with said reaction chamber;

and

wherein said device further includes means for inducing flow through said reaction chamber to transport said amplified polynucleotide to said detection region; and

wherein step (iv) includes the step of delivering said sample from said reaction chamber to said detection region with said transportation means and then detecting said amplified polynucleotide in said detection region.

12. The method of claim 11 wherein the detection region includes a polynucleotide probe capable of detectably binding to said sample polynucleotide;

and

wherein, in step (iv), the binding of said sample polynucleotide to said probe is detected.

13. The method of claim 11 wherein the detection region comprises a fractal flow region in fluid communication with said flow channel comprising bifurcations leading to plural secondary flow channels;

and

wherein, in step (iv), the flow of sample fluid through said fractal flow region is detected.

3. A device for amplifying a preselected polynucleotide in a sample by conducting a polynucleotide polymerization reaction, said device comprising at least one micromachinable solid substrate and including:

a sample inlet port; and

a mesoscale flow system comprising;

a sample flow channel having a cross-section and extending from said inlet port; and

a polynucleotide polymerization reaction chamber having a cross-section and being in fluid communication with said flow channel, said flow channel and said reaction chamber having at least one cross-sectional dimension of width or depth which is between about 0.1 to 500 μ

m said reaction chamber cross-section and said flow channel cross-section being dissimilar;

means for thermally regulating the contents of said chamber whereby the temperature is controlled to amplify said preselected polynucleotide; and

means for detecting said amplified polynucleotide.

4. A method for amplifying a preselected polynucleotide in a sample by conducting a polynucleotide polymerization reaction, the method comprising:

(i) providing a device comprising at least one micromachinable solid substrate and including;

a sample inlet port; and

a mesoscale flow system comprising;

a sample flow system comprising;

a sample flow channel having a cross-section and extending from said inlet port; and

a polynucleotide polymerization reaction chamber having a cross-section and being in fluid communication with said flow channel, said flow channel and said reaction chamber having at least one cross-sectional dimension of width or depth which is between about 0.1 to 500 μ

m said reaction chamber cross-section and said flow channel cross-section being dissimilar; and

means for thermally regulating the contents of said chamber at a temperature controlled to amplify said preselected polynucleotide;

(ii) delivering, through said inlet port and said mesoscale flow system to said reaction chamber, said sample polynucleotide and reagents for the polymerization reaction;

(iii) thermally controlling the contents of said chamber to polymerize said polynucleotide; and

(iv) detecting said amplified polynucleotide.