System for processing polynucleotide-containing samples

• US 10,604,788 B2
• Filed: 08/29/2019
• Issued: 03/31/2020
• Est. Priority Date: 05/03/2004
• Status: Active Grant

• Current Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Original Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Inventors: Wu, Betty, Althaus, John S., Phadke, Nikhil, Brahmasandra, Sundaresh N., Handique, Kalyan, Kehrer, Aaron, Parunak, Gene, Haley, Cecelia, Springer, Ted
• Primary Examiner(s): Forman, Betty J
• Application Number:
  US16/556,067
• Publication Number:
  US 20190390255A1
• Time in Patent Office: 215 Days
• CPC Class Codes: B01F 25/433 Mixing tubes wherein the shape of the tube influences the mixing, e.g. mixing tubes with varying cross-section or provided with inwardly extending profiles
• CPC Class Codes: B01F 25/4331 Mixers with bended, curved, coiled, wounded mixing tubes or comprising elements for bending the flow
• CPC Class Codes: B01F 33/30 Micromixers
• 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 2200/16 Reagents, handling or storing thereof
• CPC Class Codes: B01L 2300/0672 Integrated piercing tool
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0867 Multiple inlets and one sample wells, e.g. mixing, dilution
• CPC Class Codes: B01L 2300/087 Multiple sequential chambers
• CPC Class Codes: B01L 2300/0887 Laminated structure
• CPC Class Codes: B01L 2400/0442 thermal energy, e.g. vaporisation, bubble jet
• CPC Class Codes: B01L 2400/0481 squeezing of channels or chambers
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0633 with moving parts
• CPC Class Codes: B01L 2400/0677 phase change valves; Meltable, freezing, dissolvable plugs; Destructible barriers
• CPC Class Codes: B01L 2400/0683 mechanically breaking a wall or membrane within a channel or chamber
• CPC Class Codes: B01L 2400/0694 vents used to stop and induce flow, backpressure valves
• 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 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502723 characterised by venting arrangements
• 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 3/502753 : characterised by bulk separation arrangements on lab-on-a-chip devices, e.g. for filtration or centrifugation separation in general B01D; microapparatus for analysis using electrophoresis G01N27/44791; sample preparation G01N1/28
• CPC Class Codes: B01L 3/5082 : Test tubes per se
• CPC Class Codes: B01L 3/523 : with means for closing or opening
• CPC Class Codes: B01L 3/565 : Seals in general F16L
• 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: C12N 15/1006 : by means of a solid support carrier, e.g. particles, polymers
• CPC Class Codes: C12N 15/101 : by chromatography, e.g. electrophoresis, ion-exchange, reverse phase
• CPC Class Codes: C12Q 1/6806 : Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2565/629 : being a microfluidic device
• CPC Class Codes: F16K 2099/0084 : Chemistry or biology, e.g. "lab-on-a-chip" technology
• CPC Class Codes: F16K 99/0001 : Microvalves microdevices B81B1/00; manufacture or treatment of devices or systems in or on a substrate B81C1/00; microfluidic structures B01L3/5027; micropumps F04B19/006
• CPC Class Codes: F16K 99/0019 : Valves using a microdroplet or microbubble as the valve member
• CPC Class Codes: F16K 99/0032 : using phase transition or influencing viscosity
• CPC Class Codes: F16K 99/0034 : Operating means specially adapted for microvalves
• CPC Class Codes: F16K 99/0036 : operated by temperature variations
• CPC Class Codes: F16K 99/0044 : using thermo-electric means

Abstract

Methods and systems for processing polynucleotides (e.g., DNA) are disclosed. A processing region includes one or more surfaces (e.g., particle surfaces) modified with ligands that retain polynucleotides under a first set of conditions (e.g., temperature and pH) and release the polynucleotides under a second set of conditions (e.g., higher temperature and/or more basic pH). The processing region can be used to, for example, concentrate polynucleotides of a sample and/or separate inhibitors of amplification reactions from the polynucleotides. Microfluidic devices with a processing region are disclosed.

Claims

1. A system for processing polynucleotides in a biological sample, the system comprising:

a microfluidic device comprising substrate layers that define a microfluidic network, the microfluidic network comprising a first processing region, the microfluidic device further comprising a waste chamber downstream of the first processing region;

a lysing container located external to the substrate layers, wherein the lysing container is configured to receive the biological sample and configured to place the biological sample in contact with a lysing reagent to release polynucleotides from the biological sample into a lysate solution;

a plurality of magnetic binding particles disposed in the lysing container, the plurality of magnetic binding particles comprising polycationic molecules on the surfaces thereof, wherein the plurality of magnetic binding particles are configured to retain at least a portion of the polynucleotides on the surface thereof in the lysate solution at a pH of 8.5 or less;

a first heat source and a second heat source located external to the microfluidic network;

a lysing heater configured to apply heat to the lysate solution and the plurality of magnetic binding particles in the lysing container, wherein the lysing heater is separate and distinct from the first and second heat sources;

an operating system comprising a processor, the processor configured to actuate the first and second heat sources and the lysing heater;

wherein the operating system is configured to actuate the lysing heater to heat the lysate solution in the lysing container to a first temperature;

wherein the first processing region of the microfluidic network is configured to receive the lysate solution and the plurality of magnetic binding particles from the lysing container, wherein the waste chamber is configured to receive excess lysate solution downstream of the first processing region as the plurality of magnetic binding particles are retained in the first processing region;

wherein the microfluidic network is configured to receive a wash solution in the first processing region to remove unbound material not retained by the plurality of magnetic binding particles;

a release solution having a pH of at least 11.4;

wherein the microfluidic network further comprises an inlet for receiving the release solution into the microfluidic network and one or more channels leading from the inlet to the first processing region;

wherein the first processing region is configured to receive the release solution therein, and wherein, in the presence of the release solution in the first processing region, the plurality of magnetic binding particles are configured to release at least a portion of the polynucleotides into an eluate solution in the first processing region;

wherein the first heat source is configured to apply heat to the lysate solution and the plurality of magnetic binding particles in the first processing region, and wherein the operating system is configured to actuate the first heat source to heat the lysate solution in the first processing region to a second temperature greater than the first temperature; and

a second processing region comprising PCR reagents, the second processing region configured to receive the eluate solution containing polynucleotides and configured to place the eluate solution in contact with PCR reagents to form a PCR-ready solution.

2. The system of claim 1, wherein the polycationic molecules are covalently bound to the surfaces of the plurality of magnetic binding particles, and wherein the plurality of magnetic binding particles comprise one or more carboxylic groups to provide an attachment point for the polycationic molecules.

3. The system of claim 1, wherein the release solution comprises NaOH.

4. The system of claim 3, wherein the release solution has a pH between about 11.7 and about 13.

5. The system of claim 1, wherein the plurality of magnetic binding particles are preloaded in the lysing container.

6. The system of claim 5, further comprising a proteinase K enzyme preloaded in the lysing container.

7. The system of claim 1, wherein the PCR reagents contained in the second processing region comprise primers and probes specific to group B streptococcus (GBS) bacteria.

8. The system of claim 1, wherein the PCR reagents in the second processing region are dry PCR reagents.

9. The system of claim 8, wherein the dry PCR reagents have a room-temperature shelf life of at least 12 months.

10. The system of claim 1, wherein the plurality of substrate layers comprise:

an injection molded layer; and

a laminate configured to be secured to another substrate layer to seal components of the microfluidic network.

11. The system of claim 1, wherein the operating system is configured to actuate the lysing heater to heat the lysate solution to between about 30°

C. and about 50°

C.

12. The system of claim 1, wherein the operating system is configured to actuate the lysing heater to heat the lysate solution to about 60°

C.

13. The system of claim 1, wherein the operating system is configured to actuate the first heat source to heat the lysate solution to between about 80°

C. and about 100°

C.

14. The system of claim 1, wherein the operating system is configured to actuate the lysing heater to heat the contents of the lysing container for about 10 minutes.

15. The system of claim 1, wherein the polycationic molecules have a molecular weight of less than about 30,000 Da.

16. The system of claim 1, wherein the polycationic molecules have a molecular weight of less than about 800 Da.

17. The system of claim 1, further comprising an introduction device configured to apply air pressure to move the lysate solution through one or more channels in the microfluidic device into the first processing region.

18. The system of claim 17, wherein the introduction device is configured to apply air pressure through an inlet of the microfluidic device.

19. The system of claim 17, wherein the introduction device comprises a syringe or a pipette.

20. The system of claim 1, further comprising an automated sampling device configured to remove the eluate solution from the first processing region.

21. The system of claim 1, further comprising a syringe or a pipette configured to remove the eluate solution from the first processing region.

22. A system comprising:

a lysing container configured to receive a biological sample;

a plurality of magnetic binding particles disposed in the lysing container, the plurality of magnetic binding particles comprising polycationic molecules on the surfaces thereof, the lysing container configured to place the biological sample in contact with a lysing reagent to release polynucleotides from the biological sample into a lysate solution, the plurality of magnetic binding particles configured to retain at least a portion of the polynucleotides on the surface thereof at a pH of about 8.5 or less in the lysate solution;

substrate layers defining a microfluidic network that comprises a plurality of microfluidic components including a first processing region, wherein the first processing region is configured to receive, from the lysing container, the lysate solution and the plurality of magnetic binding particles retaining the polynucleotides on the surface thereof;

wherein the lysing container is located external to the substrate layers defining the microfluidic network;

a plurality of heat sources having locations that correspond to the plurality of microfluidic components of the microfluidic network, wherein in use, the microfluidic network is disposed in thermal contact with the plurality of heat sources;

wherein the plurality of heat sources are located external to the microfluidic network;

a heater spatially separate and distinct from the plurality of heat sources, the heater configured to heat the lysing container;

an operating system comprising a processor, the processor configured to actuate the plurality of heat sources and the heater;

a waste chamber, the waste chamber configured to receive a wash solution after the wash solution contacts the plurality of magnetic binding particles in the first processing region and removes compounds not retained by the plurality of magnetic binding particles;

a release solution having a pH of at least 11.4;

wherein the microfluidic network further comprises an inlet for receiving the release solution into the microfluidic network and one or more channels leading from the inlet to the plurality of magnetic binding particles retaining the polynucleotides on the surface thereof in the lysate solution in the first processing region;

wherein the plurality of magnetic binding particles are configured to release at least a portion of the polynucleotides into an eluate solution when in the presence of the release solution in the first processing region and when heat is applied by a heat source of the plurality of heat sources to the lysate solution and the plurality of magnetic binding particles in the first processing region; and

a second processing region comprising PCR reagents and configured to receive the eluate solution containing the eluted polynucleotides to reconstitute the PCR reagents and form a PCR-ready solution.

23. The system of claim 22, wherein at least one of the plurality of heat sources comprises a resistive heat source operated by the processor.

24. The system of claim 22, wherein the substrate layers comprise:

an injection molded layer; and

a laminate configured to be secured to another substrate layer to seal components of the microfluidic network.

25. The system of claim 22, further comprising a release solution reservoir, wherein the release solution reservoir is located external to the substrate layers defining the microfluidic network.

26. The system of claim 22, wherein the polycationic molecules are covalently bound to the surfaces of the plurality of magnetic binding particles, and wherein the plurality of magnetic binding particles comprise one or more carboxylic groups to provide an attachment point for the polycationic molecules.

27. The system of claim 22, wherein the release solution comprises NaOH and has a pH between about 11.7 and about 13.

28. The system of claim 22, wherein the plurality of magnetic binding particles are preloaded in the lysing container.

29. The system of claim 28, further comprising a proteinase K enzyme preloaded in the lysing container.

30. The system of claim 22, wherein the PCR reagents in the processing region comprise primers and probes specific to group B streptococcus (GBS) bacteria.

31. The system of claim 22, wherein the PCR reagents in the second processing region are dry PCR reagents.

32. The system of claim 31, wherein the dry PCR reagents have a room-temperature shelf life of at least 12 months.

33. The system of claim 22, further comprising an introduction device configured to apply air pressure to the microfluidic network to move the lysate solution through one or more channels in the microfluidic network.

34. The system of claim 33, wherein the introduction device is configured to apply air pressure through an inlet of the microfluidic network.

35. The system of claim 34, wherein the introduction device comprises a syringe or a pipette.

36. The system of claim 22, further comprising an automated sampling device configured to remove the eluate solution from the microfluidic network.

37. The system of claim 22, further comprising a syringe or a pipette configured to remove the eluate solution from the microfluidic network.

38. The system of claim 22, further comprising an operating system configured to actuate the heater to heat the lysate solution in the lysing container to a temperature between about 30°

C. and about 50°

C.

39. The system of claim 22, further comprising an operating system configured to actuate the heater to heat the lysate solution in the lysing container to a temperature of about 60°

C.

40. A system for processing polynucleotides from a biological sample, the system comprising:

a microfluidic network disposed in a plurality of substrate layers, wherein the microfluidic network comprises a processing region and a detection region;

a lysing container located external to the substrate layers, wherein the lysing container is configured to receive the biological sample and configured to place the biological sample in contact with a lysing reagent to release polynucleotides from the biological sample into a lysate solution;

a plurality of magnetic binding particles disposed in the lysing container, the plurality of magnetic binding particles comprising polycationic molecules on the surfaces thereof, wherein the plurality of magnetic binding particles are configured to retain at least a portion of the polynucleotides on the surface thereof in the lysate solution at a pH of about 8.5 or less;

a first heat source and a second heat source, wherein in use, the processing region of the microfluidic network is disposed in thermal contact with the first heat source and the detection region is disposed in thermal contact with the second heat source;

wherein the first and second heat sources are located external to the microfluidic network;

a heater spatially separate and distinct from the first and second heat sources, the heater configured to heat the lysing container;

wherein the processing region of the microfluidic network is configured to receive the lysate solution and the plurality of magnetic binding particles from the lysing container;

wherein the microfluidic network is configured to receive a wash solution in the processing region to remove unbound material not retained by the plurality of magnetic binding particles;

a release solution having a pH of at least 11.4;

wherein the microfluidic network further comprises an inlet configured to receive the release solution into the microfluidic network and one or more channels leading from the inlet to the processing region, wherein the plurality of magnetic binding particles are configured to release at least a portion of the polynucleotides into an eluate solution in the presence of the release solution and heat applied to the lysate solution and the plurality of magnetic binding particles;

wherein the first heat source is configured to apply heat to the lysate solution and the plurality of magnetic binding particles in the processing region; and

wherein the detection region is configured to receive the eluate solution containing the at least a portion of the polynucleotides and dissolved PCR reagents.

41. The system of claim 40, further comprising a processor, wherein at least one of the first and second heat sources comprises a resistive heat source operated by the processor.

42. The system of claim 40, further comprising an operating system configured to actuate the heater to heat the lysing container for about 10 minutes.

43. The system of claim 40, wherein the plurality of substrate layers comprise:

an injection molded layer; and

a laminate configured to be secured to another substrate layer to seal components of the microfluidic network.

44. The system of claim 40, further comprising:

a release solution reservoir, wherein the release solution reservoir is located external to the microfluidic network; and

a buffer solution reservoir, wherein the buffer solution reservoir is located external to the microfluidic network.

45. The system of claim 40, wherein the polycationic molecules are covalently bound to the surfaces of the plurality of magnetic binding particles, and wherein the plurality of magnetic binding particles comprise one or more carboxylic groups to provide an attachment point for the polycationic molecules.

46. The system of claim 40, wherein the release solution comprises NaOH and has a pH between about 11.7 and about 13.

47. The system of claim 40, wherein the plurality of magnetic binding particles are preloaded in the lysing container.

48. The system of claim 47, further comprising a proteinase K enzyme preloaded in the lysing container.

49. The system of claim 40, wherein the PCR reagents comprise primers and probes specific to group B streptococcus (GBS) bacteria.

50. The system of claim 40, wherein the PCR reagents are dry prior to being dissolved and have a room-temperature shelf life of at least 12 months.

51. The system of claim 40, further comprising an introduction device configured to apply air pressure through an inlet of the microfluidic network to move the lysate solution through one or more channels into the processing region.

52. The system of claim 51, wherein the introduction device comprises a syringe or a pipette.

53. The system of claim 40, further comprising an operating system configured to actuate the heater to heat the lysate solution in the lysing container to a temperature between about 30°

C. and about 50°

C.

54. The system of claim 40, further comprising an operating system configured to actuate the heater to heat the lysate solution in the lysing container to a temperature of about 60°

C.

55. The system of claim 40, further comprising an operating system configured to actuate the first heat source to heat the contents of the processing region to a temperature of between about 80°

C. and about 100°

C.