REAL-TIME PCR OF TARGETS ON A MICRO-ARRAY

• US 20120053068A1
• Filed: 03/31/2008
• Published: 03/01/2012
• Est. Priority Date: 11/18/2004
• Status: Abandoned Application

• Current Assignee: Eppendorf AG
• Original Assignee: Eppendorf Array Technologies SA (Eppendorf Se)
• Inventors: Remacle, Jose, Alexandre, Isabelle, De Roeck, Sven, Zammatteo, Nathalie, Koehn, Heinz, Husar, Dieter
• Application Number:
  US12/060,022
• Publication Number:
  US 20120053068A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2547/101 by confinement to a single tube/container
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides

Abstract

The present invention relates to a method, apparatus, cartridge and kit for monitoring on a micro-array a real-time PCR amplification of a polynucleotide molecule being present in a solution.

Claims

1. A method for PCR amplification and detection of a polynucleotide molecule being present in a solution contained in a chamber having a surface bearing the capture molecules for the detection of the amplified sequences comprising:

providing a rotating holder and a reaction chamber having fixed upon one of its surface at least a capture molecule being immobilized in a localized areas of a flat surface of said reaction chamber,

introducing a solution containing said polynucleotide molecule into said reaction chamber and reagents for polynucleotide molecule amplification and labelling,

submitting the solution to at least 2 thermal cycles having at least 2 and preferably 3 different temperature steps in order to obtain labelled target polynucleotide molecule by PCR amplification, wherein the change in temperatures is obtained by changing the temperature of the air around the reaction chamber and wherein the reaction chamber is subjected to a rotating movement,

performing at least a measurement of the labelled target polynucleotide molecule in the following way,

incubating said labelled target polynucleotide molecule present in said solution under conditions allowing a specific hybridization between said target polynucleotide molecule and its corresponding capture molecule (20),

measuring a signal originating from the surface having the bound labelled target polynucleotide molecule in response to illumination of said flat surface, wherein the signal is measured outside the chamber, and wherein the surface of signal emission comprises at least one localized area having a surface of between about 0.1 μ

m² and about 75 mm², wherein the said surface has a homogeneous interface during the measurement of the signal and

processing the data obtained in order to detect and/or quantify the amount of polynucleotide molecule present in the solution before the amplification.

2. The method of claim 1, wherein the measurement of the labelled target polynucleotide molecule is performed with the reaction chamber being on said rotating holder.

3. The method of claim 1, wherein the measurement of the labelled target polynucleotide molecule is performed at least once during the PCR amplification.

4. The method of claim 1, wherein the surface bearing the bound capture molecules has a homogeneous interface after a PCR cycle.

5. The method of claim 1, wherein the interface between the said surface containing bound target and the solution is homogeneous in at least 90% of the surface.

6. The method of claim 1, wherein the height of the liquid in the detection part of the chamber is preferably comprised between 0.1 and 5 mm, and even more preferably between 0.2 and 2 mm.

7. The method of claim 1, wherein the signal is the result of light emission from the bound labelled target polynucleotide molecule in response to excitation light.

8. The method of claim 1, wherein the measurement of the labelled target polynucleotide molecule is performed in presence of the amplification solution containing the labelled target polynucleotide molecules.

9. The method of claim 7, wherein the surface of the reaction chamber having fixed capture molecule is transparent to the excitation and/or emission light.

10. The method of claim 7, wherein at least one side and/or the top of the reaction chamber is in a material transparent to the excitation and/or emission light.

11. The method of claim 7, wherein light emission is due to evanescence excitation.

12. The method of claim 7, wherein the detected signal is light due to evanescence emission.

13. The method of claim 7, wherein the excitation light is totally internally reflected inside the transparent support.

14. The method of claim 7, wherein the detected emitted light is totally internally reflected inside the transparent support.

15. The method of claim 7, wherein the excitation light is the result of a light beam focused on the surface of the chamber having bound capture molecules.

16. The method of claim 1, wherein the detected signal is the measured through the support bearing the bound capture molecules at an observation angle θ

obin relative to the normal to the said solid support surface in the support, such that 90°

>

θ

obin>

sin<sup>−

1</sup> (n2/n1), whereby the optically transparent solid support having a refractive index n1 and being in contact with a medium having refractive index n2, whereby n1>

n2.

17. The method of claim 16, wherein, the observation angle is within the forbidden angle and being in the range of the critical angle plus 10°

, preferably plus 5° and

more preferably plus 3°

.

18. The method of claim 1, wherein the signal is a scattered light from the bound labelled target polynucleotide molecule in response to illumination.

19. The method of claim 1, wherein the signal is the result of light diffraction from the bound labelled target polynucleotide molecule in response to illumination.

20. The method of claim 1, wherein the PCR and the detection are performed in a closed cartridge.

21. The method of claim 1 wherein the PCR is performed with the support being rotated at a speed of at least 100 and preferably 400 and still preferably 1000 rpm.

22. The method of claim 1, wherein the measurement of the labelled target polynucleotide molecule is performed when the chamber is subjected to a rotating movement.

23. The method of claim 1, wherein the measurement of the labelled target polynucleotide molecule is performed when the chamber is not subjected to a rotating movement.

24. The method of claim 1, wherein the measurement of the labelled target polynucleotide molecule is performed in at least 5, preferably at least 10 thermal cycles and even preferably at least 20 thermal cycles.

25. The method of claim 1, wherein subjecting the reaction chamber to a rotating movement during the thermal cycles prevents a presence of bubbles on the localized areas.

26. The method of claim 1, wherein the solution containing the labelled target polynucleotide molecules is moved from the reaction chamber to a second reaction chamber by centrifugation.

27. The method of claim 26, wherein reading of the bound labelled target polynucleotide molecules is performed in the reaction chamber in absence of solution comprising the labelled target polynucleotide molecules.

28. The method of claim 1, wherein the reagents for polynucleotide molecule amplification comprise a primer pair, dNTPs, a thermostable DNA polymerase, a hot start PCR system and buffer.

29. The method of claim 28, further comprising a salt composition having at least 100 and preferably 150 mM and even more preferably 200 mM of cations.

30. The method of claim 28, further comprising a salt composed of a cation and an anion, wherein the said anion has two carboxylic groups and one amine group, wherein the salt concentration in the composition is comprised between 10 mM and 400 mM and from 1% to 20% by weight of an exclusion agent.

31. The method of claim 30, wherein the anion is glutamate.

32. The method of claim 1, wherein the steps of denaturation, annealing, elongation are performed in 1 min or less.

33. The method of claim 1, wherein the Tm of the primers (Tmp) for a target are within a range of the temperature of annealing (Ta) −

2 to +8°

C. and preferably 0 to +4°

C.

34. The method of claim 1 wherein the Tm of the capture molecule for a target is within a range of temperature of the hybridization +4 to 16°

C. preferably +8 to 12°

C.

35. The method of claim 1 wherein the Tm of the two capture molecules differing from one base and use for the discrimination of a SNP in a target sequence have a Tm within a range of temperature of hybridization plus 4 to 8°

C.

36. The method of claim 1 wherein the Tm of the primer is at least 4°

C. and preferably 8°

C. lower than the Tm of the capture molecule.

37. The method of claim 1, wherein the capture molecule has a spacer of at least 6.8 nm long being preferably a sequence of at least 20 nucleotides and preferably more than 40 nucleotides long.

38. The method of claim 1, wherein the hybridization and the annealing are performed in the same step.

40. The method of either claim 1 or claim 39, wherein the hybridization, annealing and elongation are performed in the same step.

41. The method of either claim 1 or claim 39, wherein the steps of annealing and hybridization are performed in 2 min or less.

42. The method of either claim 1 or claim 39, wherein the Tm of the capture molecule for a target is at least 4°

C. and preferably 6°

C. higher than the Tm of the two primers specific of said target.

43. The method of either claim 1 or claim 39, wherein the Tm of the primers (Tmp) for a target are within a range of the temperature of annealing (Ta) −

2 to +8°

C. and preferably 0 to +4°

C., wherein the Tm of the capture molecule for a target is within a range of temperature of the hybridization +4 to 16°

C. preferably +8 to 12°

C., and wherein the Tm of the two capture molecules differing from one base and used for the discrimination of a SNP in a target sequence have a Tm within a range of temperature of hybridization plus 4 to 8°

C.

44. The method of either claim 1 or claim 39, wherein the reagents for polynucleotide molecule amplification comprise a primer and/or dNTP labelled with a fluorescent dye.

45. The method of claim 1, wherein the flat surface is at least 0.04 cm² or preferably at least 1 cm2 or even more preferably more than 2 cm².

46. The method of claim 1, wherein the flat surface is at least 0.25 mm thick and preferably 0.5 mm thick.

47. The method of claim 1 wherein at least one part of the device is a conductive material.

48. The method of claim 1, wherein the flatness of the surface is changed by less than 0.05 mm after at least 20 amplification cycles.

49. The method of claim 1, wherein the localized area is comprised between about 10 μ

m² and about 1 mm² and preferably between about 1 μ

m² and about 100 μ

m².

50. The method of claim 1, wherein the capture molecules are bound to a localized area of the flat surface in the form of a micro-array.

51. The method of claim 50, wherein the micro-array comprises more than 5 different capture molecules, preferably more than 20 and even more than 50.

52. The method of claim 1, wherein the rotating holder bears several micro-arrays separated by physical boundaries.

53. The method of claim 1, wherein the rotating holder has a disk shape.

54. The method of claim 1, wherein the rotating holder has a multi-well plate or strip format.

55. The method of claim 54, wherein the multi-well plate is submitted to a temperature gradient during the measurement of light emission.

56. The method of claim 1, wherein the light emission is measured at a defined timing from the beginning of a temperature step.

57. The method of claim 1, wherein the light emission is measured at within 5 min and even within 2 min and more preferably within 1 min after the beginning of the annealing temperature step.

58. The method of claim 1, wherein the light emission is measured at the end of at least one of the 3 temperature steps used for the PCR amplification.

59. The method of claim 1, wherein the light emission is measured at the end of the PCR amplification.

60. The method of claim 1, wherein the data are processed in order to obtain a signal value for each of the localized area.

61. The method of claim 1, wherein the data are processed in order to obtain a signal value for each of the localized area and for the local background.

62. The method of claim 1, wherein the data are further processed by subtracting the background from the signal value for each of the localized area.

63. The method of claim 1, wherein the quantification of the amount of polynucleotide molecule is performed by comparing the signal value of the localized area with a fixed value.

64. The method of claim 1, wherein the quantification of the amount of polynucleotide molecule is performed by comparing the number of thermal cycles necessary to reach a fixed value (CT) with the CT of a reference polynucleotide molecule.

65. The method of claim 64, wherein the reference polynucleotide molecule is amplified in the same solution and detected on the same micro-array as the target polynucleotide molecule.

66. The method of claim 64, wherein the polynucleotide molecule is labelled with a first fluorescent dye and the reference polynucleotide molecule is labelled with a second fluorescent dye different from the first fluorescent dye.

67. The method of claim 1, wherein the quantification of the amount of polynucleotide molecule is performed by comparing the number of thermal cycles necessary to reach a fixed value (CT) with a standard curve wherein the CT are plotted against standard concentrations.

68. The method of claim 1, wherein two fluorescent dyes are used in the same solution.

69. The method of claim 1, wherein the solution composition is adapted for performing the annealing of the primers on the polynucleotide molecule and the hybridization of the labelled target molecule on the capture molecule during the same temperature step.

70. The method of claim 1, wherein the capture molecules bound to the labelled target polynucleotide molecules are elongated during the temperature step of elongation.

71. The method of claim 1, wherein the capture molecules elongated are detected during the temperature step of denaturation.

72. The method of claim 1, wherein, the reagents for polynucleotide molecule amplification comprises at least 5 primer pairs, preferably at least 10 primer pairs, more preferably at least 20 primer pairs et even at least 40 primer pairs.

73. The method of claim 1, wherein between 1 and 4 polynucleotide molecules and preferably between 1 and 20 polynucleotide molecules present in a solution are amplified and detected and/or quantified in the same assay.

74. The method of claim 1, wherein between 20 and 1000 polynucleotide molecules present in a solution are amplified and detected and/or quantified in the same assay.

75. The method of claim 1, wherein an excitation light (7) from a light source is directed on the surface of the support.

76. The method of claim 1, wherein the detected light is the light emitted by the bound target molecule under excitation from a light source.

77. The method of claim 1, wherein a thermal cycle is performed within 10 min and preferably within 3 min and even more preferably within 2 min.

78. The method of claim 1, wherein 30 thermal cycles are performed within 5 h and preferably within 3 h and even more preferably within 1.5 h.

79. The method of claim 1, wherein the capture molecule is a single stranded polynucleotide containing a sequence able to specifically bind the labelled target polynucleotide molecule and a spacer of at least 20 nucleotides.

80. The method of claim 1, wherein changing the temperature of the air around the chamber is obtained by pulsed air.

39. A method for PCR amplification and detection of a polynucleotide molecule being present in a solution contained in a chamber having a surface bearing the capture molecules for the detection of the amplified sequences comprising the steps of:

providing a rotating holder (1) and a reaction chamber (2) having fixed upon one of its surface at least a capture molecule (20) being immobilized in a localized areas (21) of a flat surface of said reaction chamber,

introducing a solution containing said polynucleotide molecule into said reaction chamber (2) and reagents for polynucleotide molecule amplification and labelling,

submitting the solution to at least 2 thermal cycles comprising a denaturation, annealing and elongation steps in order to obtain labelled target polynucleotide molecule by PCR amplification,

performing at least a measurement of the labelled target polynucleotide molecule in the following way,

incubating said labelled target polynucleotide molecule present in said solution under conditions allowing a specific hybridization between said target polynucleotide molecule and its corresponding capture molecule (20),

measuring a signal originating from the surface having the bound labelled target polynucleotide molecule in response to illumination of said flat surface, wherein the signal is measured outside the chamber, and wherein the surface of signal emission comprises at least one localized area having a surface of between about 0.1 μ

m² and about 75 mm², wherein the said surface has a homogeneous interface during the measurement of the signal,

wherein the hybridization and the annealing steps occur at the same temperature and wherein the Tm of the primers for a target are within a range of the temperature of annealing plus 0-4°

C. and the Tm of the probe for said target is within a range of temperature of the hybridization plus 6-12°

C. and

Processing the data obtained in order to detect and/or quantify the amount of polynucleotide molecule present in the solution before the amplification.

81. An apparatus for monitoring on a micro-array a PCR amplification of a polynucleotide molecule being present in a solution comprising:

a rotating holder and a reaction chamber having fixed upon its surface a micro-array, comprising at least one capture molecule being immobilized in specifically localized areas of a flat surface of said chamber, which is in fluid communication in a chamber with said polynucleotide molecule and reagents for polynucleotide molecule amplification and labelling,

a thermal cycler for carrying out an automated PCR process, said thermal cycler capable of changing the temperature of the air around the chamber for producing labelled target polynucleotide molecule,

a rotor for rotating said holder and said reaction chamber,

an illumination light source,

a detector for measuring a signal from the bound labelled target polynucleotide molecule, with said solution being present in the chamber and containing the labelled target polynucleotide molecule wherein the surface of emission for a localized area is comprised between about 0.1 μ

m² and about 75 mm² and has a homogeneous interface,

wherein the different parts are integrated into the same apparatus in order to read the signal of the bound labelled target polynucleotide molecule during the PCR amplification.

82. The apparatus of claim 81, further comprising:

a storage system for storing the data of the different measurements for at least 5 localized areas of the support at a defined timing of a thermal cycle,

a controller repeating the steps of illumination, detection and storage at least one time in at least one thermal cycle for each localized area of the micro-array,

a program for processing the data obtained in at least one thermal cycle in order to detect and/or quantify the amount of polynucleotide molecule present in the sample before the amplification.

83. The apparatus of claim 81, wherein the rotating holder has a disk shape.

84. The apparatus of claim 81, wherein the rotating holder is the rotor.

85. The apparatus of claim 81, wherein the rotating holder comprises a plurality of reaction chambers.

86. The apparatus of claim 81, wherein the detector comprises an optic lens.

87. The apparatus of claim 81, wherein the micro-array comprises more than 5 different capture molecules, preferably more than 20 and even more than 50.

88. The apparatus of claim 81, wherein changing the temperature of the air around the chamber is performed by pulsed air at a ramp rate of 5°

C. per sec.

89. The apparatus of claim 81, wherein the localized area is comprised between about 10 μ

m² and about 1 mm² and preferably between about 1 μ

m² and about 100 μ

m².

90. The apparatus of claim 81, wherein said illumination light source produces an excitation light which is directly focused on the flat surface of the reaction chamber, wherein the excitation light reaches the micro-array surface within an angle comprised between 45 and 135°

.

91. The apparatus of claim 81, wherein the illumination light source produces an evanescent field.

92. The apparatus of claim 81, wherein the evanescent field is generated by an incident light source illuminating the surface of the reaction chamber with an incidence angle comprised between about 60°

and 90°

.

93. The apparatus of claim 81, wherein the detector comprises a CCD camera.

94. The apparatus of claim 81, wherein the detector is positioned at an observation angle θ

obin relative to the normal to the said flat surface of the reaction chamber, such that 90°

>

θ

obin>

sin<sup>−

1</sup> (n2/n1).

95. The apparatus of claim 94, wherein the observation angle is within the forbidden angle and being in the range of the critical angle plus 10°

, preferably plus 5° and

more preferably plus 3°

.

96. A cartridge for monitoring on a micro-array a PCR amplification of a polynucleotide molecule being present in a solution, said cartridge comprising:

a substrate (optic bloc) comprising a first flat surface and a flat second surface, said first flat surface comprising a micro-array comprising at least 20 different capture molecules being immobilized in specifically localized areas; and

an airlock comprising an inlet port, a mounting surface and a reaction chamber (2);

said reaction chamber comprising a channel constructed to permit fluid flow from said inlet port into said reaction chamber, wherein said first flat surface of said substrate is mounted with respect to said mounting surface thereby covering said reaction chamber and whereby said micro-array is located inside said reaction chamber.

97. The cartridge of claim 96, further comprising a cap for sealing said inlet port, preferably a screwing cap.

98. The cartridge of claim 96, further comprising:

a second reaction chamber said second reaction chamber comprising a channel constructed to permit fluid flow from said inlet port into said second reaction chamber, said channel being connected to the channel constructed to permit fluid flow from said inlet port into said reaction chamber.

99. A kit for monitoring on a micro-array a PCR amplification of a polynucleotide molecule being present in a solution, said kit comprising a cartridge having a substrate (optic bloc) comprising a first flat surface and a flat second surface, said first flat surface comprising a micro-array comprising at least 20 different capture molecules being immobilized in specifically localized areas and primers for the amplification of target, wherein the Tm of the immobilized probes for said target is at least 4°

C. and preferably 6°

C. higher than the Tm of the two primers specific of said target and a solution for the PCR including glutamate.