Thermal cycling by positioning relative to fixed-temperature heat source

• US 8,945,880 B2
• Filed: 07/29/2009
• Issued: 02/03/2015
• Est. Priority Date: 07/31/2008
• Status: Active Grant

• Current Assignee: Genomadix Incorporated
• Original Assignee: Spartan Bioscience, Inc.
• Inventors: Cloake, Martin, Harder, Chris, Shayanpour, Alan, Perreault, Michael, Lem, Paul
• Primary Examiner(s): Wilder, Cynthia B
• Application Number:
  US12/462,098
• Publication Number:
  US 20100075296A1
• Time in Patent Office: 2,015 Days
• Field of Search: 435/91.2, 435/285
• US Class Current: 435/91.2
• CPC Class Codes: B01L 2200/142 Preventing evaporation
• CPC Class Codes: B01L 2200/147 Employing temperature sensors
• CPC Class Codes: B01L 2300/042 Caps; Plugs
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/1844 using fans
• CPC Class Codes: B01L 3/5082 Test tubes per se
• 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 9/06 Test-tube stands; Test-tube holders

Abstract

The thermal cycling system for performing a biological reaction at two or more different temperatures comprises: a) a heat source for setting at a fixed temperature; b) a reaction vessel containing material upon which the biological reaction is to be performed; c) mechanically-operable structure for altering the relative position of the heat source and the reaction vessel so that reaction vessel first achieves and maintains a desired first temperature in the reaction vessel for starting the carrying out of the biological reaction, and then for altering the relative position of the heat source and the reaction vessel so that the reaction vessel then achieves and maintains a second temperature for continuing the carrying out of the biological reaction on the biological material, and d) temperature-sensing structure operatively associated with the reaction vessel for controlling the altering of the relative position of the heat source and the reaction vessel so that the reaction vessel achieves and maintains the desired second temperature in the reaction vessel.

Claims

1. A thermal cycling system for performing a biological reaction at two or more different temperatures, the thermal cycling system comprising:

a) a heat source for setting at a fixed temperature;

b) a metal sleeve capable of receiving a reaction vessel containing material upon which the biological reaction is to be performed, wherein the sleeve includes a temperature-sensing means for sensing the temperature of the sleeve; and

c) moving means operatively associated with the sleeve for altering the relative position of the heat source and the sleeve based on the temperature of the sleeve sensed by the temperature-sensing means, the thermal cycling system arranged and configured such that,

i) in a first configuration the relative positions of the sleeve and the heat source, with respect to each other, are such that the sleeve achieves and maintains a first temperature; and

ii) in a second configuration the relative positions of the sleeve and the heat source, with respect to each other, are adjusted such that the sleeve achieves and maintains a second temperature.

3. The thermal cycling system of claim 1, wherein said heat source is a block of heat retentive material including means to heat said block to, and maintain said block at a fixed temperature.

4. The thermal cycling system of claim 3, wherein said block is configured and arranged to be movable.

5. The thermal cycling system of claim 3, wherein said sleeve is configured and arranged to be movable.

6. The thermal cycling system of claim 5, wherein said temperature-sensing means is operatively associated with a processor which is downloaded with an algorithm to predict the temperature being experienced by said reaction vessel, said algorithm being based on a program to achieve and maintain a desired temperature in the reaction vessel.

7. The thermal cycling system of claim 5, wherein the positions of said sleeve relative to said heat source for achieving and maintaining the first and second temperatures were determined empirically to provide an empirical formula, and wherein said temperature-sensing means is operatively associated with a processor which is downloaded with an algorithm defining said empirical formula.

8. The thermal cycling system of claim 1, wherein said sleeve is provided with openings that are capable of allowing material inside said reaction vessel to be excited and imaged as part of a fluorescence detection apparatus.

9. The thermal cycling system of claim 1, further comprising a reaction vessel, wherein said reaction vessel includes a plug-style cap which is situated within said reaction vessel and wherein said sleeve extends up the sides of said reaction vessel, so that said plug will be heated and will minimize evaporation into the top of the reaction vessel.

10. A method for performing a biological reaction at two or more different temperatures, the method comprising the steps of:

a) providing the thermal cycling system of claim 1 and placing a reaction vessel containing a biological mixture in the sleeve of the system;

b) positioning the sleeve in a position relative to the heat source that is set at a fixed temperature to allow the sleeve to achieve and maintain a first temperature of said biological reaction;

c) altering the relative position of the sleeve with respect to the heat source based on the temperature of the sleeve sensed by the temperature sensing means, so that the sleeve achieves and maintains a second different temperature of said biological reaction;

d) and thereby performing said biological reaction on the biological mixture at two or more different temperatures.

12. The method of claim 10, which comprises maintaining said heat source fixed in place and moving said sleeve.

13. The method of claim 10, which comprises moving said heat source and maintaining said sleeve fixed in place.

14. The method of claim 10, wherein the sleeve is a metal sleeve with a temperature sensor.

15. The method of claim 14, including the step of altering the relative position of said sleeve with respect to said heat source to achieve and maintain said reaction vessel at a template denaturation temperature when said temperature sensor senses that the temperature of said sleeve approaches said template denaturation temperature.

16. The method of claim 15, including the step of altering the relative position of said sleeve with respect to said heat source to achieve and maintain the reaction vessel at a primer annealing temperature when said temperature sensor senses that the temperature of said sleeve approaches said primer annealing temperature.

17. The method of claim 16, including the step of altering the relative position of said sleeve with respect to said heat source to achieve and maintain the reaction vessel at a primer extension temperature when said temperature sensor senses that the temperature of said sleeve approaches said primer extension temperature.

18. The method of claim 16, which comprises the steps of providing a processor with an algorithm to predict the temperature being experienced by said reaction vessel, and altering the relative position of said sleeve with respect to said heat source to achieve and maintain the temperature of said reaction vessel at a primer annealing temperature when said algorithm predicts that the temperature of said reaction vessel approaches a primer annealing temperature.

19. The method of claim 17, which comprises the steps of providing a processor with an algorithm to predict the temperature being experienced by said reaction vessel, and altering the relative position of said sleeve with respect to said heat source to achieve and maintain the temperature of said reaction vessel at a primer extension temperature when said algorithm predicts that the temperature of said reaction vessel approaches a primer extension temperature.

20. The method of claim 14, which comprises the steps of empirically determining the positions of said sleeve relative to said heat source for each desired temperature, providing an empirical formula thereof and converting said empirical formula into an algorithm, and altering the relative position of said sleeve with respect to said heat source to achieve and maintain a desired temperature in said reaction vessel when said algorithm determines that the temperature of said reaction vessel approaches the desired temperature.

21. The method of claim 20, which comprises the steps of empirically determining the positions of said sleeve relative to said heat source for a desired template denaturation temperature, providing an empirical formula thereof and converting said empirical formula into an algorithm and changing the relative position of said sleeve with respect to said heat source to achieve and maintain the desired template denaturation temperature in said reaction vessel when said algorithm determines that the temperature of said reaction vessel approaches the desired template denaturation temperature.

22. The method of claim 20, which comprises the steps of empirically determining the positions of said sleeve relative to said heat source for a desired primer annealing temperature, providing an empirical formula thereof and converting said empirical formula into an algorithm, and changing the relative position of said sleeve with respect to said heat source to achieve and maintain a desired primer annealing temperature in said reaction vessel when said algorithm determines that the temperature of said reaction vessel approaches a desired primer annealing temperature.

23. The method of claim 20, which comprises the steps of empirically determining the positions of said sleeve relative to said heat source for a desired primer extension temperature, providing an empirical formula thereof and converting said empirical formula into an algorithm, and changing the relative position of said sleeve with respect to said heat source to achieve and maintain a desired primer extension temperature in said reaction vessel when said algorithm determines that the temperature of said reaction vessel approaches a desired primer extension temperature.

24. The method of claim 20, which comprises providing said sleeve with small openings that allow material inside the reaction vessel to be excited and imaged as part of a fluorescence detection apparatus.

25. The method of claim 20, which comprises minimizing evaporation into the top of said vessel by placing a plug-style cap reaction vessel into said reaction vessel and by positioning said sleeve to extend up the sides of the reaction vessel, so that said plug will be heated.

33. The thermal cycling system of claim 1, wherein the thermal cycling system comprises a single heat source.

2. A thermal cycling system for performing a polymerase chain reaction amplification protocol comprising multiple cycles of three temperature-dependent stages of template denaturation, primer annealing and primer extension that constitute a single cycle of PCR, the thermal cycling system comprising:

a) a heat source that is set at a fixed temperature;

b) a metal sleeve capable of receiving a reaction vessel containing material upon which a polymerase chain reaction amplification protocol is to be performed, wherein the sleeve includes a temperature-sensing means for sensing the temperature of the sleeve; and

c) moving means operatively associated with the sleeve for altering the relative position of the heat source and the sleeve based on the temperature of the sleeve sensed by the temperature-sensing means, the thermal cycling system arranged and configured such that,

i) in a first configuration the relative positions of the sleeve and the heat source, with respect to each other, are such that the sleeve achieves and maintains a first temperature for carrying out template denaturation on the material;

ii) in a second configuration the relative positions of the sleeve and the heat source, with respect to each other, are adjusted such that the sleeve achieves and maintains a second temperature for carrying out primer annealing on the material; and

iii) in a third configuration the relative positions of the sleeve and the heat source, with respect to each other, are adjusted such that the sleeve achieves and maintains a third temperature for carrying out primer extension on the material.

11. A method for performing a polymerase chain reaction amplification protocol comprising multiple cycles of three sequential temperature-dependent stages that constitute a single cycle of PCR:

comprising template denaturation, primer annealing; and

primer extension on a biological material, the method comprising the steps of;

a) providing the thermal cycling system of claim 2 and placing a reaction vessel containing a biological material and reagents for PCR in the sleeve of the system;

b) positioning the sleeve in a position relative to a heat source that is set at a fixed temperature to allow the sleeve to achieve and maintain a temperature for carrying out template denaturation;

c) altering the relative position of the sleeve with respect to the heat source based on the temperature of the sleeve sensed by the temperature-sensing means, so that the sleeve achieves and maintains a temperature for carrying out primer annealing;

d) altering the relative position of the sleeve with respect to the heat source based on the temperature of the sleeve sensed by the temperature-sensing means, so that the sleeve achieves and maintains a temperature for carrying out primer extension; and

e) repeating the steps b), c) and d) to perform multiple cycles of PCR on the biological material.

26. The thermal cycling system, of claim 2, wherein said heat source is a block of heat retentive material including means to heat said block to, and maintain said block at a fixed temperature.

27. The thermal cycling system of claim 26, wherein said sleeve is configured and arranged to be movable.

28. The thermal cycling system of claim 27, wherein said temperature-sensing means is operatively associated with a processor which is downloaded with an algorithm to predict the temperature being experienced by said reaction vessel, said algorithm being based on a program to achieve and maintain a desired temperature in the reaction vessel.

29. The thermal cycling system of claim 27, wherein the positions of said sleeve relative to said heat source for achieving and maintaining the first and second temperatures were determined empirically to provide an empirical formula, and wherein said temperature-sensing means is operatively associated with a processor which is downloaded with an algorithm defining said empirical formula.

30. The thermal cycling system of claim 26, wherein said block is configured and arranged to be movable.

31. The thermal cycling system of claim 2, wherein said sleeve is provided with openings that are capable of allowing material inside said reaction vessel to be excited and imaged as part of a fluorescence detection apparatus.

32. The thermal cycling system of claim 2, further comprising a reaction vessel, wherein said reaction vessel includes a plug-style cap which is situated within said reaction vessel and wherein said sleeve extends up the sides of said reaction vessel, so that said plug will be heated and will minimize evaporation into the top of the reaction vessel.

34. The thermal cycling system of claim 2, wherein the thermal cycling system comprises a single heat source.