Systems and methods for performing reactions in an unsealed environment

• US 6,225,061 B1
• Filed: 03/10/1999
• Issued: 05/01/2001
• Est. Priority Date: 03/10/1999
• Status: Expired due to Term

• Current Assignee: Agena Bioscience Inc. (Mesa Laboratories Inc.)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Koster, Hubert, Becker, Thomas, Cantor, Charles
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): Taylor, Janell E.
• Application Number:
  US09/266,409
• Time in Patent Office: 783 Days
• Field of Search: 435/6, 435/177, 159/1, 159/47.1, 422/63, 422/64, 422/65, 422/66, 422/67, 436/177, 436/43
• US Class Current: 506/16
• CPC Class Codes: B01J 19/16 Preventing evaporation or oxidation of non-metallic liquids by applying a floating layer, e.g. of microballoons in storage tanks B65D90/42
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00367 capillary
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00495 Means for heating or cooling the reaction vessels
• CPC Class Codes: B01J 2219/00603 Making arrays on substantially continuous surfaces
• CPC Class Codes: B01J 2219/0068 Means for controlling the apparatus of the process
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G01N 2035/00287 movable lid/cover for sample or reaction tubes
• CPC Class Codes: Y10T 436/11 Automated chemical analysis
• CPC Class Codes: Y10T 436/25375 Liberation or purification of sample or separation of material from a sample [e.g., filtering, centrifuging, etc.]

Abstract

An open system is provided for performing a submicroliter reaction. An open system can contain a solid support having a target site for performing the reaction; a liquid dispensing system such as a nanoliter dispensing pipette for dispensing a submicroliter amount of a liquid to the target site; a temperature controlling device for regulating the temperature of the support; and means for controlling the amount of liquid dispensed, which corresponds to the amount of liquid that evaporates from the target site. Also provided is an open system, including a solid support having a target site; a liquid dispensing system, which can dispense a liquid to the target site; a temperature controlling system, which regulates the temperature of the solid support; and an interface, which regulates an amount of liquid dispensed from the liquid dispensing system. Also provided is a method for performing a reaction in a submicroliter volume in an unsealed environment by dispensing a submicroliter volume of liquid onto the surface of a support; monitoring the temperature of the support; monitoring an amount or rate of evaporation of the liquid; and dispensing to the surface of the support a further amount of the liquid, which corresponds to the amount lost from the support due to evaporation, thereby maintaining the reaction volume at a predetermined volume throughout the course of the reaction. A method also is provided for maintaining a volume of a reaction mixture, which can be one of a plurality of reaction mixtures, on a solid support in an unsealed environment by monitoring the rate of evaporation of a liquid from the reaction mixture; and dispensing into the reaction mixture an amount of liquid that corresponds to the amount that evaporates.

Claims

1. An open system for performing a reaction while maintaining constant concentrations of reactants, comprising:

a support for performing the reaction in an open environment, wherein;

the support is for containing or retaining biopolymers or biological particles; and

the reaction is a submicroliter volume reaction;

a nanoliter dispensing pipette for dispensing an amount of a liquid onto the surface of the support;

a temperature controlling device for regulating the temperature of the support; and

means for controlling the amount of liquid dispensed, wherein;

the amount of liquid dispensed corresponds to the amount of liquid that evaporates from the support to thereby maintain the concentration of reactants in the reaction; and

the system is not sealed.

2. The open system of claim 1, wherein the controlling means comprises software that calculates the amount of liquid that evaporates and signals the dispensing pipette to deliver an amount of liquid that corresponds to the amount that evaporates.

3. The open system of claim 1, wherein the controlling means comprises manual input.

4. The open system of claim 1, further comprising a means for determining the temperature of a liquid on the support.

5. The open system of claim 1, wherein the support comprises a bead, pin, comb, wafer, well or microchip.

7. The open system of claim 1, wherein the reaction is a submicroliter reaction.

6. An open system for performing a reaction, comprising:

a support functionalized for linking a biopolymer or biological particle and for performing the reaction, wherein the support comprises a bead, pin, comb, wafer, well or microchip;

a nanoliter dispensing pipette for dispensing an amount of a liquid onto the surface of the support;

a temperature controlling device for regulating the temperature of the support; and

means for controlling the amount of liquid dispensed, wherein the amount of liquid dispensed corresponds to the amount of liquid that evaporates from the support, wherein the system is not sealed.

8. A system, comprising:

a solid support having a target site for retaining or containing a liquid;

a liquid dispensing system for dispensing a liquid to the target site;

a temperature controlling system, which regulates the temperature of the solid support; and

an interface for indicating an amount of liquid to be dispensed to the target site, wherein the amount of liquid to be dispensed corresponds to an amount of liquid that evaporates from the target site, wherein;

the interface monitors the level of a liquid on the target site; and

the interface comprises a light source and a photometer.

10. The system of claim 8, wherein the temperature controlling system comprises a Peltier element.

11. The system of claim 8, further comprising a detection system.

9. A system, comprising:

a solid support having a target site for retaining or containing a liquid;

a liquid dispensing system for dispensing a liquid to the target site;

a temperature controlling system, which regulates the temperature of the solid support; and

an interface for indicating an amount of liquid to be dispensed to the target site, wherein the amount of liquid to be dispensed corresponds to an amount of liquid that evaporates from the target site, wherein the interface monitors the concentration of a component in the liquid.

12. A system comprising:

means for dispensing a liquid;

means for containing a reaction volume comprising a microchip or glass slide, wherein the microchip or glass slide comprises on a surface, an array of hydrophilic regions and adjacent hydrophobic regions;

means for controlling the temperature of the reaction volume containing means; and

means for regulating an amount of liquid dispensed from the liquid dispensing means based on the temperature of the reaction volume containing means.

13. A method for performing a reaction in an unsealed environment, comprising the steps of:

a) dispensing a predetermined submicroliter volume of liquid onto a target site on a surface of a support;

b) determining an amount or rate of evaporation of the liquid from the target site; and

c) dispensing a further amount of liquid to the target site, wherein the further amount dispensed corresponds to the amount of liquid that evaporates from the target site, thereby maintaining the reaction volumes and concentration of reactant at a predetermined volume throughout the course of the reaction.

14. The method of claim 13, wherein the reaction is performed in a submicroliter volume.

15. The method of claim 13, wherein the amount or rate of evaporation is determined by monitoring the temperature of the target site and calculating the amount or rate of evaporation.

18. The method of claim 13, wherein the reaction is one of a plurality of reactions.

22. The method of claim 18, wherein each reaction in the plurality is performed at a single target site.

70. The system of claim 14, wherein the temperature controlling system comprises a Peltier element.

71. The system of claim 14, further comprising a detection system.

16. A method for performing a reaction in an unsealed environment, comprising the steps of:

a) dispensing a predetermined submicroliter volume of liquid onto a target site on a surface of a support;

b) determining an amount or rate of evaporation of the liquid from the target site, wherein the amount or rate of evaporation is determined by monitoring the conductance of the liquid at the target site; and

c) dispensing a further amount of liquid to the target site, wherein the further amount dispensed corresponds to the amount of liquid that evaporates from the target site, thereby maintaining the reaction volume at a predetermined volume throughout the course of the reaction.

17. A method for performing a reaction in an unsealed environment, comprising the steps of:

a) dispensing a predetermined submicroliter volume of liquid onto a target site on a surface of a support;

b) determining an amount or rate of evaporation of the liquid from the target site; and

c) dispensing a further amount of liquid to the target site, wherein the further amount dispensed corresponds to the amount of liquid that evaporates from the target site, thereby maintaining the reaction volume at a predetermined volume throughout the course of the reaction, wherein the reaction is a nucleic acid amplification reaction.

19. A method for performing a reaction in an unsealed environment, comprising the steps of:

a) dispensing a predetermined submicroliter volume of liquid onto a target site on a surface of a support;

b) determining an amount or rate of evaporation of the liquid from the target site; and

c) dispensing a further amount of liquid to the target site, wherein the further amount dispensed corresponds to the amount of liquid that evaporates from the target site, thereby maintaining the reaction volume at a predetermined volume throughout the course of the reaction, wherein;

the reaction is one of a plurality of reactions, and

the plurality of reactions are performed at a single target site.

20. The method of claim 19, wherein the reactions are performed simultaneously.

21. The method of claim 20, which is a multiplex reaction.

23. A method for performing a reaction in an unsealed environment, comprising the steps of:

a) dispensing a predetermined submicroliter volume of liquid onto a target site on a surface of a support;

b) determining an amount or rate of evaporation of the liquid from the target site; and

c) dispensing a further amount of liquid to the target site, wherein the further amount dispensed corresponds to the amount of liquid that evaporates from the target site, thereby maintaining the reaction volume at a predetermined volume throughout the course of the reaction, wherein;

the reaction is one of a plurality of reactions;

each reaction in the plurality is performed at a single target site; and

the method comprises synthesis of a combinatorial library.

24. A method for performing a reaction in an unsealed environment, comprising the steps of:

a) dispensing a predetermined submicroliter volume of liquid onto a target site on a surface of a support;

b) determining an amount or rate of evaporation of the liquid from the target site; and

c) dispensing a further amount of liquid to the target site, wherein the further amount dispensed corresponds to the amount of liquid that evaporates from the target site, thereby maintaining the reaction volume at a predetermined volume throughout the course of the reaction; and

d) detecting a component of the reaction, detecting a component of the reaction.

25. A method for maintaining a volume of a reaction mixture on a solid support in an unsealed environment, comprising the steps of:

a) determining the amount of liquid that evaporates from the reaction mixture; and

b) dispensing into the reaction mixture an amount of liquid that corresponds to the amount of liquid that evaporates, thereby maintaining the volume of the reaction mixture, wherein the reaction mixture comprises a biopolymer.

26. The method of claim 25, wherein the reaction mixture comprises a biopolymer sequencing reaction.

27. The method of claim 25, wherein the biopolymer is a polynucleotide.

28. The method of claim 26, wherein the sequencing reaction comprises a chemical cleavage reaction.

29. The method of claim 26, wherein the sequencing reaction comprises an enzymatic reaction.

30. The method of claim 29, wherein the enzymatic reaction is a chain termination reaction comprising a polymerase and a chain terminating nucleoside triphosphate.

31. The method of claim 29, wherein the enzymatic reaction is an exonuclease reaction.

32. The method of claim 26, wherein the biopolymer is a polypeptide.

33. The method of claim 32, wherein the sequencing reaction is selected from the group consisting of a chemical sequencing reaction and an enzymatic sequencing reaction.

34. The method of claim 26, wherein the biopolymer is selected from the group consisting of a carbohydrate, a glycoprotein, a proteoglycan and a lipid.

35. The method of claim 25, wherein the reaction mixture comprises a biopolymer synthesis reaction.

36. The method of claim 35, wherein the biopolymer is a polynucleotide.

37. The method of claim 36, wherein the synthesis reaction is a chemical synthesis reaction.

38. The method of claim 36, wherein the synthesis reaction is an enzymatic synthesis reaction, comprising a polymerase.

39. The method of claim 38, wherein the biopolymer and the polymerase are selected from the group consisting of:

a ribonucleic acid and an RNA dependent RNA polymerase;

a ribonucleic acid and an RNA dependent DNA polymerase; and

a deoxyribonucleic acid and a DNA dependent DNA polymerase.

40. The method of claim 38, comprising a ribonucleic acid, an RNA dependent DNA polymerase, and a DNA dependent DNA polymerase.

41. The method of claim 38, wherein the enzymatic synthesis reaction is a polymerase chain reaction, further comprising a set of primers.

42. The method of claim 41, wherein a primer of the set of primers comprises a peptide nucleic acid sequence.

43. The method of claim 35, wherein the biopolymer is a polypeptide.

44. The method of claim 35, wherein the biopolymer is selected from the group consisting of a carbohydrate, a glycoprotein, a proteoglycan and a lipid.

45. The method of claim 35, wherein the biopolymer is a polynucleotide and the reaction mixture comprises a primer extension reaction.

46. The method of claim 45, wherein the primer extension reaction is selected from the group consisting of:

competitive oligonucleotide single base extension;

primer oligo base extension (PROBE);

loop-PROBE; and

telomeric repeat amplification.

47. The method of claim 25, wherein the reaction mixture comprises an assay for detecting the presence of the biopolymer.

48. The method of claim 47, wherein the biopolymer is obtained from a biological sample.

49. The method of claim 48, wherein the method comprises a diagnostic method for detecting the presence of or predisposition to a genetic disease or condition.

50. The method of claim 48, wherein the method comprises determining a genotype.

51. The method of claim 25, wherein the biopolymer is immobilized to the solid support.

52. The method of claim 47, comprising detecting the biopolymer by identifying a detector oligonucleotide that has hybridized to the biopolymer.

53. The method of claim 52, wherein the detector oligonucleotide comprises a peptide nucleic acid sequence.

54. A method for performing a plurality of reactions in an unsealed environments, comprising the steps of:

a) providing a plurality of reaction mixtures, wherein each reaction in the plurality is at a target site on a surface of a solid support;

b) monitoring the amount of liquid that evaporates from reaction mixtures in the plurality; and

c) dispensing into the reaction mixtures an amount of liquid that corresponds to the amount of liquid that evaporates from the reaction mixtures, thereby maintaining the volume of the reaction mixtures in the plurality at a predetermined volume, wherein one or more of the reaction mixtures in the plurality comprises one or more biopolymers.

55. The method of claim 54, wherein a biopolymer present in a reaction mixture is immobilized to the solid support.

56. The method of claim 54, wherein the solid support comprises a microchip.

57. The method of claim 56, wherein the plurality of reaction mixtures is present in an array on the microchip.

58. A method for performing a plurality of reactions in an unsealed environments, comprising the steps of:

a) providing a plurality of reaction mixtures, wherein each reaction in the plurality is at a target site on a surface of a solid support;

b) monitoring the amount of liquid that evaporates from reaction mixtures in the plurality;

c) dispensing into the reaction mixtures an amount of liquid that corresponds to the amount of liquid that evaporates from the reaction mixtures, thereby maintaining the volume of the reaction mixtures in the plurality at a predetermined volume; and

d) detecting a component of a reaction mixture in the plurality.

59. The method of claim 58, wherein the component is a biopolymer.

60. The method of claim 59, wherein the biopolymer is detected directly.

61. The method of claim 59, wherein the biopolymer is detected indirectly.

62. The method of claim 61, wherein the biopolymer is a polynucleotide, which is detected by detecting an amplification product produced from the polynucleotide.

63. The method of claim 61, wherein the biopolymer is detected by identifying a reagent that binds specifically to the biopolymer.

64. The method of claim 63, wherein the biopolymer is a polynucleotide and the reagent is an oligonucleotide that hybridizes specifically to the polynucleotide.

65. The method of claim 64, wherein the oligonucleotide is a primer, which has been extended due to the activity of a polymerase.

66. The method of claim 63, wherein the biopolymer is a first polypeptide and the reagent is a second polypeptide that binds specifically to the first polypeptide.

67. The method of claim 63, wherein the second polypeptide is an antibody.

68. The method of claim 58, wherein the component is detected by a method selected from mass spectrometry, spectrophotometry, and capillary electrophoresis.

69. A method for performing a plurality of reactions in an unsealed environment, comprising:

a) providing a plurality of reaction mixtures, wherein each reaction in the plurality is performed at a target site on a surface of a solid support that contains or retains the reaction mixtures;

b) monitoring the amount of liquid that evaporates from reaction mixtures in the plurality; and

c) dispensing into the reaction mixtures an amount of liquid that corresponds to the amount of liquid that evaporates from the reaction mixtures, thereby maintaining the volume of the reaction mixtures in the plurality at a predetermined volume, whereby the concentrations of reactants in the reaction mixtures remain constant.