Fluidics station with a mounting system and method of using

• US 6,114,122 A
• Filed: 04/30/1998
• Issued: 09/05/2000
• Est. Priority Date: 03/26/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lobban, Peter E., Norris, Michael C., Besemer, Donald, Muller, Steven V.
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Siew, Jeffrey
• Application Number:
  US09/070,689
• Time in Patent Office: 859 Days
• Field of Search: 435/6, 435/283.1, 435/287.2, 422/100, 422/68.1, 369/77.2, 250/227, 204/411, 204/193, 204/194, 530/24.3, 530/24.31, 530/24.32
• US Class Current: 435/6.14
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/40 Mixers using gas or liquid agitation, e.g. with air supply tubes
• 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 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2200/027 for microfluidic devices
• CPC Class Codes: B01L 2200/143 Quality control, feedback systems
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0877 Flow chambers
• 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 2300/1822 using Peltier elements
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• 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 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: B01L 9/527 : for microfluidic devices, e.g. used for lab-on-a-chip
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: G01N 2035/00158 : Elements containing microarrays, i.e. "biochip"

Abstract

The present invention generally provides novel apparatuses for rapidly and efficiently carrying out repeated hybridizations of a target nucleic acid to an array of nucleic acid probes. The apparatus generally includes a fluid delivery system, a fluid mixing system, a temperature control system and a process control system integrated into a single device.

Claims

1. A fluidics station comprising:

a base frame that is adapted to provide a framework for the fluidics station;

a mounting system coupled to the base frame, the mounting system being adapted to receive a cartridge, and wherein the mounting system is movable between a loading position and a closed position;

at least two injection needles coupled to the base frame; and

at least one fluid source in communication with at least one of the injection needles;

wherein the cartridge is insertable into the mounting system when in the loading position, and wherein the injection needles are adapted to be inserted into the cartridge when in the closed position.

2. A station as in claim 1, wherein the mounting system comprises a mounting frame having a slot which is adapted to receive the cartridge, and wherein the mounting frame is coupled to the base frame by a hinge.

3. A station as in claim 2, wherein the slot is keyed such that the cartridge is insertable into the mounting frame in only one orientation.

4. A station as in claim 1, wherein the mounting system includes a shunt element which in the absence of a cartridge receives the injection needles when in the closed position to allow fluids to flow between the two injection needles.

5. A station as in claim 1, further comprising a temperature controlling element coupled to the base frame, the temperature controlling element being adapted to contact the cartridge when the mounting system is in the closed position.

6. A station as in claim 5, further comprising a tube coupling the fluid source to one of the injection needles, and wherein at least a portion of the tube is disposed near the temperature controlling element.

22. A station as in claim 1, wherein the injection needles each have a blunt distal end and a side port that is spaced above the distal end.

7. A method for introducing a fluid into a cartridge, the method comprising:

providing a frame, at least two injection needles coupled to the frame, and a mounting system that is coupled to the frame, wherein the mounting system is movable between a loading position and a closed position;

placing at least one fluid source in communication with at least one of the injection needles;

inserting a cartridge into the mounting system while in the loading position;

moving the loading system to the closed position to insert the injection needles into the cartridge; and

transferring fluid from the fluid source into the cartridge through one of the injection needles.

8. A method as in claim 7, further comprising removing the fluid from the cartridge with the other injection needle.

9. A method as in claim 8, further comprising discarding the removed fluid.

10. A method as in claim 8, further comprising recirculating the removed fluid through the cartridge.

11. A method as in claim 7, wherein the mounting system further includes a shunt and further comprising removing the cartridge, placing the mounting system in the closed position to insert the injection needles into the shunt of the mounting system, and circulating a washing solution through the shunt.

12. A method as in claim 11, further comprising removing and discarding the shunt.

13. A method as in claim 7, wherein a temperature controlling element is coupled to the frame, and further comprising contacting the temperature controlling element with the cartridge when the mounting system is placed in the closed position.

14. A method as in claim 13, further comprising altering the temperature of the transferred fluid with the temperature controlling element as the fluid is transferred to the cartridge and while the fluid is within the cartridge.

15. A method as in claim 7, further comprising detecting when the cartridge is within the mounting system and the mounting system is in the closed position.

23. A method as in claim 7, wherein the injection needles each have a blunt distal end and a side port that is spaced above the distal end, and further comprising transferring the fluid laterally from the needle through the side port.

16. A fluidics station comprising:

a base frame that is adapted to provide a frame work for the fluidics station;

a mounting system coupled to the base frame, the mounting system being adapted to receive a cartridge, and wherein the mounting system is movable between a loading position and a closed position;

a coupling system which is adapted to couple the cartridge to a fluid source, wherein the coupling system comprises a pair of injection needles and tubing connected to the needles; and

a temperature controlling element coupled to the base frame, the temperature controlling element being adapted to physically contact at least a portion of the cartridge when the mounting system is in the closed position.

17. A station as in claim 16, wherein the temperature controlling element comprises a Peltier device having a face which is adapted to contact a chamber of the cartridge.

18. A station as in claim 16, wherein at least some of the tubing is disposed near the temperature controlling element.

19. A station as in claim 16, further comprising a fluid sensing system which is adapted to detect the presence or absence of a fluid in the cartridge.

20. A station as in claim 19, wherein the sensing system comprises a pair of conductive pins an circuitry to detect a change in the potential difference between the pins.

21. A station as in claim 19, wherein the sensing system comprises a sensing cavity, a light source and a photodetector to detect reflected light from the sensing cavity.

24. A station as in claim 16, wherein the injection needles each have a blunt distal end and a side port that is spaced above the distal end.

25. An apparatus for processing a fluid sample, comprising:

a cartridge having a chamber, said chamber having disposed therein an array of probes, said array of probes including a plurality of different nucleic acid sequences coupled to a solid support in different known locations;

a fluid delivery system for delivering said sample to said chamber; and

a cartridge mounting system comprising a mounting plate and a frame movably coupled to the plate to allow the frame to be moved between an open position and a closed position, the frame including a slot which is adapted to receive the cartridge in a known orientation when the frame is in the open position, wherein the fluid delivery system is adapted to be coupled to the chamber when the frame is in the closed position.

26. The apparatus of claim 25, wherein said fluid delivery system comprises:

a pump in fluid communication with the chamber when the fluid delivery system is coupled to the chamber;

a sample vessel;

a plurality of individual reagent vessels; and

a valve structure in communication with the pump, the valve structure being disposed between the chamber and the sample vessel and reagent vessels to individually connect each of said reagent vessels and said sample vessel to said pump such that operation of the valve structure places the sample vessel or one of the reagent vessels in fluid communication with the pump to allow the pump to deliver a fluid from the sample vessel or the reagent vessel to the chamber; and

wherein said fluid delivery system further comprises;

a first length of tubing connecting said sample vessel to said pump and a second length of tubing connecting said pump to said chamber.

27. The apparatus of claim 26, wherein said pump is a peristaltic pump.

28. The apparatus of claim 26, wherein said pump is a syringe pump.

29. The apparatus of claim 26, further comprising a mixing system positioned to mix said sample in said chamber, wherein said mixing system comprises a piezoelectric element disposed adjacent said chamber, whereby operation of said piezoelectric element produces a convective effect in said chamber.

30. The apparatus of claim 25, further comprising a mixing system positioned to mix said sample in said chamber, wherein said mixing system comprises a reversible pump for removing and redelivering said sample fluid out of and into said chamber.

45. The apparatus of claim 25, further comprising a hinge to couple the frame to the plate.

46. The apparatus of claim 25, wherein said mounting system further comprises alignment structures for aligning said cartridge in said frame.

47. The apparatus of claim 25, wherein said injection system comprises injection needles connected to said fluid delivery system and extending from the plate, said injection needles being adapted for insertion into an inlet and an outlet in said cartridge when said cartridge is mounted in said frame and the frame is moved to the closed position.

48. The apparatus of claim 25, further comprising a temperature control system for monitoring and controlling a temperature of said fluids within said chamber, wherein the temperature control system comprises a temperature controlled block extending from the plate, and wherein the temperature controlled block is placed adjacent an external surface of the array cartridge when the cartridge is in the frame and the frame is moved to the closed position.

49. The apparatus of claim 48, wherein the temperature control system further includes a heat exchange coil disposed near the plate to vary the temperature of the sample just prior to entry of the sample into the cartridge.

50. The apparatus of claim 25, further comprising a window disposed in the frame which is aligned with a window in cartridge when the cartridge is inserted into the frame.

51. The apparatus of claim 25, wherein the cartridge includes a nonflush edge which is adapted to slide into a groove of the frame to allow the cartridge to be inserted into the frame in only one orientation.

31. An apparatus for processing fluids, comprising:

a fluid delivery system adapted to deliver fluids into an array cartridge, said array cartridge including a chamber having a probe array incorporated therein;

a mounting system which is adapted to removably hold said chamber within said array cartridge in fluid communication with said fluid delivery system, said mounting system having an open position for receiving the cartridge and a closed position wherein the cartridge is positioned to be coupled with the fluid delivery system;

a temperature control system for monitoring and controlling a temperature of said fluids within said chamber, wherein the temperature control system comprises a temperature controlled block which is placed adjacent an external surface of the array cartridge when the cartridge is in the mounting system and the mounting system moved to the closed position;

an injection system to couple the fluid delivery system to the array cartridge when the mounting system is moved to the closed position; and

a process control system for monitoring and controlling said fluid delivery system and said temperature control system.

32. The apparatus of claim 31, wherein said pump is a peristaltic pump.

33. The apparatus of claim 31, wherein said pump is a syringe pump.

34. The apparatus of claim 31, wherein said fluid delivery system includes one or more sensors for determining when said chamber is filled or drained.

35. The apparatus of claim 34, wherein said one or more sensors are selected from the group consisting of conductivity sensors and optical sensors.

36. The apparatus of claim 31, wherein said temperature controlled block comprises a thermoelectric temperature controlled element.

37. The apparatus of claim 31, wherein said mounting system comprises a mounting frame and a mounting plate, said mounting plate being adapted to receive said array cartridge, and said mounting frame being operably connected to said mounting plate to hold said mounting plate, said mounting frame and mounting plate being adapted to hold said array cartridge in fluid communication with said fluid delivery system.

38. The apparatus of claim 31, wherein said mounting system comprises alignment structures for aligning said array cartridge on said mounting system.

39. The apparatus of claim 31, wherein said injection system comprises injection needles connected to said fluid delivery system, said injection needles being adapted for insertion into an inlet and an outlet in said array cartridge when said array cartridge is mounted in said mounting system.

52. The apparatus of claim 37, wherein the temperature controlled block is mounted to the plate.

53. The apparatus of claim 37, wherein the temperature controlled block extends into a recess in the cartridge when the mounting system is moved to the closed position.

54. The apparatus of claim 31, wherein said fluid delivery system comprises:

a plurality of reagent vessels, with each vessel containing a fluid;

a valve assembly to connect said injection system to one or more of said plurality of reagent vessels;

a pump to transport said fluid from said one of said plurality of reagent vessels, through said valve assembly, and to said injection system.

40. A method for hybridizing a target nucleic acid to an array of nucleic acid probes, comprising:

providing a hybridization station having a fluid delivery system having a pump and a valving system to deliver fluids from a plurality of vessels into an array cartridge, said array cartridge including a hybridization chamber having said array of nucleic acid probes incorporated therein, a mounting system for holding said hybridization chamber within said array cartridge in fluid communication with said fluid delivery system, a temperature control system for monitoring and controlling a temperature of said fluids within said hybridization chamber, and a process control system for monitoring and controlling said fluid delivery system and said temperature control system;

inserting said array cartridge into said mounting system and moving the mounting system to a closed position to place said array cartridge adjacent a temperature controlled block of the temperature control system;

injecting needles into an inlet and an outlet in said array cartridge to couple the fluid delivery system to said array cartridge;

selecting a fluid sample from said fluids and entering the selection into the process control system, the fluid sample containing said target nucleic acid;

sending a signal from the process control system to operate the valving system and the pump to deliver the fluid sample from the vessel having the fluid sample into said hybridization chamber in said array cartridge;

altering the temperature of the temperature controlled block to transfer heat to or remove heat from said array cartridge; and

washing said hybridization chamber to substantially remove unbound target nucleic acid from said hybridization chamber.

41. The method of claim 40, wherein said delivering step further comprises pumping said sample fluid through a heat exchange coil to control a temperature of said sample fluid.

42. The method of claim 40, wherein said washing step comprises sending signals from the process control system to the valving system to repeatedly fill said hybridization chamber with a wash solution from another one of said vessels and to drain said wash solution from said hybridization chamber.

43. The method of claim 40, further comprising visualizing the fluid sample within the hybridization chamber through windows in the mounting system and the array cartridge.

44. The method of claim 40, further comprising moving the mounting system to the closed position to inject the needles in the inlet and the outlet.

55. A method for hybridizing a target nucleic acid to an array of nucleic acid probes, comprising:

providing a hybridization station having a fluid delivery system having a pump and a valving system to deliver fluids from a plurality of vessels into an array cartridge, said array cartridge including a hybridization chamber having said array of nucleic acid probes incorporated therein, a mounting system for holding said hybridization chamber within said array cartridge in fluid communication with said fluid delivery system, a temperature control system for monitoring and controlling a temperature of said fluids within said hybridization chamber, and a process control system for monitoring and controlling said fluid delivery system and said temperature control system;

inserting said array cartridge into said mounting system and moving the mounting system to a closed position to place said array cartridge adjacent a temperature controlled block of the temperature control system;

coupling the fluid delivery system to said array cartridge;

selecting a fluid sample from said fluids and entering the selection into the process control system, the fluid sample containing said target nucleic acid;

sending a signal from the process control system to operate the valving system and the pump to deliver the fluid sample from the vessel having the fluid sample into said hybridization chamber in said array cartridge;

mixing said target nucleic acids with said nucleic acid probes within said hybridization chamber while controlling the temperature within the array cartridge with said temperature controlled block such that said target nucleic acid hybridizes with said nucleic acid probe; and

moving a fluid through said hybridization chamber to substantially remove unhybridized target nucleic acid or other unwanted materials from said hybridization chamber.