Apparatus for high throughput chemical reactions

• US 20080176290A1
• Filed: 01/22/2008
• Published: 07/24/2008
• Est. Priority Date: 01/22/2007
• Status: Active Grant

• Current Assignee: Takara Bio Usa, Inc. (Ningbo Junsheng Investment Group Co., Ltd.)
• Original Assignee: WaferGen, Inc.
• Inventors: Joseph, Victor, Huda, Amjad, Shivji, Alnoor
• Granted Patent: US 8,252,581 B2
• Time in Patent Office: Days
• US Class Current: 435/91.2
• 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 2200/147 Employing temperature sensors
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2300/0829 Multi-well plates; Microtitration plates
• CPC Class Codes: B01L 2300/0893 having a very large number of wells, microfabricated wells
• CPC Class Codes: B01L 2300/1805 Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks
• CPC Class Codes: B01L 2300/1827 using resistive heater
• CPC Class Codes: B01L 2300/1844 using fans
• CPC Class Codes: B01L 2300/1894 Cooling means; Cryo cooling
• CPC Class Codes: B01L 7/525 with physical movement of samples between temperature zones
• CPC Class Codes: B01L 7/5255 by moving sample containers
• CPC Class Codes: B01L 7/54 using spatial temperature gradients
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: G01N 21/0332 with temperature control control of temperature G05D23/00; cryostats F17C3/08
• CPC Class Codes: G01N 21/253 for batch operation, i.e. multisample apparatus analytical automats G01N35/00

Abstract

Apparatus, systems, chips, and methods of performing a large number of simultaneous chemical reactions are provided herein. The chips of the invention comprise addressable units that can be addressed according to the temperature of the reaction to be run. The subject apparatus, systems, and chips are particularly suited for performing polymerase chain reactions on thousands of nucleic acid sequences, up to and including sequences of an entire genome of an organism of interest.

Claims

1. An apparatus comprising at least one heating element, configured to be in thermal contact with a chip said chip comprising a substrate and an array of nanowells, wherein the at least one heating element is configured to move relative to the chip.

2. The apparatus of claim 1, wherein the at least one heating element is in thermal contact with the chip from above and below the chip, and wherein the heating element in thermal contact from below the chip is set at a temperature lower than the temperature of the heating element in thermal contact from above the chip.

3. The apparatus of claim 1, wherein the chip comprises an upper surface and a bottom surface and wherein a first series of nanowells is arranged along one orientation on the upper surface and a second series of nanowells is oriented perpendicular to the first series of nanowells.

4. The apparatus claim 1, wherein the heating element is positioned above or below a stationary chip comprising an array of nanowells.

5. The apparatus of claim 1, wherein the heating element is capable of heating and cooling.

6. The apparatus of claim 1, comprising a plurality of heating elements corresponding to a plurality of temperature zones.

7. The apparatus of claim 6, wherein the plurality of temperature zones a range from about 52°

C. to about 95°

C.

8. The apparatus of claim 7, wherein the plurality of temperature zones provides a temperature gradient.

9. The apparatus of claim 6, wherein at least one of the temperature zones is set at a temperature ranging from about 52°

C. to about 65°

C. and at least one other temperature zone is set at a temperature ranging from about 90°

C. to about 95°

C.

10. The apparatus of claim 9, further comprising at least one other temperature zone set at temperature ranging from about 68°

C. to about 72°

C.

11. The apparatus of claim 1, wherein the at least one heating element is configured to provide an output comprising a spike waveform of temperature over time.

12. The apparatus of claim 1, wherein an individual nanowell in said array has a dimension of about 250 μ

m in length, about 250 μ

m in width, and a depth of about 525 μ

m, or less.

13. The apparatus of claim 1, wherein the chip is operatively coupled to an optical system that detects optical signals.

14. The apparatus of claim 13, wherein the optical system comprises a plurality of optical detectors.

15. The apparatus of claim 1, wherein the number of nanowells is greater than about 30,000.

16. The apparatus of claim 1, wherein the nanowells are configured to contain about 100 nl.

17. A method of conducting a chemical reaction comprising:

providing a chip configured to receive a reaction sample;

providing at least one heating element positionable in relation to the chip to provide thermal contact between the at least one heating element and the chip; and

conducting the chemical reaction in the reaction sample by varying the temperature of the chip, wherein said varying the temperature is effected by moving the at least one heating element in relation to the chip such that the heating element is in thermal contact with the chip.

18. The method of claim 17, wherein the chemical reaction is a nucleic acid amplification reaction.

19. The method of claim 17, wherein movement of the at least one heating element is controlled by signals generated from a temperature sensor that is operatively linked to the chip.

20. The method of claim 18, wherein the reaction sample is capable of producing an optical signal, and, wherein the chip is operatively coupled to an optical system configured to detect optical signals emitted from the reaction sample.

21. The method of claim 20, wherein the optical signals are proportional to the amount of product of the chemical reaction.

22. The method of claim 21, wherein said varying the temperature is effected by moving a plurality of heating elements, each of which is set at a different temperature.

23. The method of claim 21, wherein at least one heating element is set at a temperature ranging from about 52°

C. to about 65°

C. and at least one other heating element is set at a temperature ranging from about 90°

C. to about 95°

C.

24. A chip for running a reaction comprising an array of addressable units, each unit being configured for running a chemical reaction, wherein the array of the addressable units is configured to correspond to a predetermined temperature zone, and wherein an individual unit in said array is dimensioned to hold a chemical reaction mixture of less than about 1 μ

l.

25. The chip of claim 24 comprising a plurality of arrays.

26. The chip of claim 24 comprising a plurality of arrays, each of which corresponding to a different temperature zone.

27. The chip of claim 24 comprising a plurality of arrays wherein at least one of the arrays is set at an annealing temperature for supporting a nucleic acid amplification reaction and at least one other array is set at a denaturing temperature for supporting a nucleic acid amplification reaction.

28. The chip of claim 24, wherein the zone is addressed to indicate the predetermined temperature zones.

29. The chip of claim 24, wherein the array of addressable units are configured to correspond to six or more predetermined temperature zones.

30. The chip of claim 24, wherein the chip is in thermal contact with a heating element.

32. The apparatus of claim 24 or claim 31, wherein the array of addressable units is greater than about 30,000.

37. The apparatus of claim 24 or claim 31, wherein an individual unit within the array comprises a nanowell for receiving and confining a sample, said well being sealed when filled with the sample.

38. The apparatus of claim 24 or claim 31, wherein the chemical reaction is a nucleic acid amplification reaction.

39. The apparatus of claim 38, wherein the predetermined temperature of a unit is configured to yield at least 90% of homogeneous product from the chemical reaction.

31. An apparatus for conducting a chemical reaction requiring cycling at least two temperature levels, comprising:

(a) chip for running a reaction comprising an array of addressable units, each unit being configured for a chemical reaction, wherein the array of the addressable units is configured to correspond to a predetermined temperature zone, and wherein an individual unit in said array is dimensioned to hold a chemical reaction mixture of less than about 1 μ

l; and

(b) a heating element in thermal contact with the chip.

33. The apparatus of claim 31, further comprising (c) an optical system operatively coupled to the chip, wherein the optical system detects an optical signal coming from an addressed thermo-controllable unit.

34. The apparatus of claim 33, wherein the optical system comprises a plurality of optical detectors.

35. The apparatus of claim 31, further comprising a plurality of heating elements.

36. The apparatus of claim 35, wherein the plurality of heating elements comprises six or more heating elements.

40. A method of conducting a reaction that involves a plurality of reaction samples and requires cycling at least two temperature levels, comprising:

(a) providing a chip for running a reaction comprising an array of addressable units, each unit being configured for a chemical reaction, wherein the array of the addressable units is configured to correspond to a predetermined temperature zone, and wherein an individual unit in said array is dimensioned to hold a chemical reaction mixture of less than about 1 μ

l;

(b) placing the plurality of reaction samples into the units of the chip according to the set of predetermined temperatures; and

(c) controlling a heating element to effect cycling at least two temperature levels.

41. The method of claim 40, wherein an individual unit within the array of the chip comprises a nanowell for receiving and confining a sample, said well being sealed when filled with the sample.

42. The method of claim 40, wherein the chemical reaction is a nucleic acid amplification reaction.

43. The method of claim 42, wherein the predetermined temperature of a unit is configured to yield at least 90% of homogeneous product from the chemical reaction.

44. An apparatus for conducting a chemical reaction involving cycling at least two temperature levels, comprising:

(a) a body configured to receive a chip comprising a plurality of nanowells, for containing the chemical reaction; and

(b) a first heater providing a first temperature and a second heater providing a second temperature;

wherein the first heater and the second heater are configured to be movable between a first and a second orientation, and wherein the first orientation places the heater in thermal contact with the sample holder and the second orientation does not place the heater in thermal contact with the sample holder.

45. The apparatus of claim 44, wherein the plurality of nanowells are addressable, wherein the nanowells are arranged according to a predetermined set of temperatures such that at least one of the nanowells is addressed to indicate the predetermined temperature for running the chemical reaction within said nanowell.

46. The apparatus of claim 44, wherein the plurality of nanowells comprises over about 30,000 nanowells.

47. The apparatus of claim 44, wherein the first heater comprises a plurality of temperature zones.

48. The apparatus of claim 47, wherein the temperature zones comprise six or more temperature zones.

49. The apparatus of claim 48, wherein the plurality of temperature zones correspond to the predetermined set of temperatures according to which the thermo-controllable units are arrayed.

50. The apparatus of claim 44, wherein the first and second heaters move between the first and second orientations according to a protocol.

51. The apparatus of claim 44 further comprising a motor for moving the first and second heaters between the first and second orientations.

52. The apparatus of claim 44, wherein the first heater provides a temperature gradient.

53. The apparatus of claim 44, further comprising a heat sink in thermal contact with the first heater.

54. The apparatus of claim 44, further comprising a heat sink in thermal contact with the second heater.

55. The apparatus of claim 53 or claim 54, further comprising a fan for removing heat from the heat sink.

56. The apparatus of claim 44, further comprising a plurality of temperature sensors operably connected to the chip.

57. The apparatus of claim 56, wherein the plurality of temperature sensors has at least one temperature sensor assigned to measure the temperature of each temperature zone.