METHOD AND DEVICE FOR DETECTING THE PRESENCE OF TARGET NUCLEIC ACIDS IN A SAMPLE, AND MICROFLUIDIC DEVICE FOR USE IN SUCH METHODS

• US 20080153091A1
• Filed: 08/13/2007
• Published: 06/26/2008
• Est. Priority Date: 04/17/1997
• Status: Abandoned Application

• Current Assignee: United States Department Of Health And Human Services (Government of the United States of America), Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Cytonix, The United States of America As Represented By The Secretary of Agriculture
• Inventors: BROWN, James F., SILVER, Jonathan E.
• Application Number:
  US11/837,613
• Publication Number:
  US 20080153091A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2200/06 Fluid handling related problems
• CPC Class Codes: B01L 2200/0642 Filling fluids into wells by specific techniques
• 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 2200/16 Reagents, handling or storing thereof
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2400/0409 centrifugal forces
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: B01L 3/50851 specially adapted for heating or cooling samples laboratory heating apparatus B01L7/00; incubators C12M
• CPC Class Codes: B01L 3/5088 confining liquids at a location by surface tension, e.g. virtual wells on plates, wires B01L3/50857 takes precedence
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6844 : Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: Y10S 436/805 : Optical property
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

A method comprising loading sample into at least two sample chambers, subjecting the sample portions in each sample chamber to at least a first amplification step, and determining whether each sample portion contains at least one molecule of a target nucleic acid. If a sample portion contains at least a single molecule of the target nucleic acid, it would attain a detectable concentration of the target nucleic acid after a single round of amplification. Also, a method for detecting whether at least one molecule of a first target nucleic acid is present in a first sample and detecting whether at least one molecule of a second target nucleic acid is present in a second sample. Also, a microfluidic device comprising sample chambers comprising respective ingredients which will react with respective target nucleic acids if contacted with the target nucleic acids and subjected to a round of amplification.

Claims

1. A method for detecting whether at least one molecule of a first target nucleic acid is present in a sample and detecting whether at least one molecule of a second target nucleic acid is present in said sample, said method comprising:

loading a first portion of said sample into at least a first sample chamber, whereby if said first portion contains at least a single molecule of said first target nucleic acid, said first portion would attain a detectable concentration of said first target nucleic acid within a portion of said first sample chamber after a single round of amplification;

loading a second portion of said sample into at least a second sample chamber, whereby if said second portion contains at least a single molecule of said second target nucleic acid, said second portion would attain a detectable concentration of said second target nucleic acid within a portion of said second sample chamber after a single round of amplification;

subjecting said first portion in said first sample chamber to at least a first amplification step;

subjecting said second portion in said second sample chamber to at least a first amplification step; and

then

determining whether said first portion contains at least one molecule of said first target nucleic acid and determining whether said second sample portion contains at least one molecule of said second target nucleic acid.

2. A method as recited in claim 1, wherein said first and second sample chambers are provided in an apparatus which comprises more than 1,000 sample chambers.

3. A method as recited in claim 1, wherein said first and second sample chambers are provided in an apparatus which comprises from 10,000 to over 100,000 sample chambers.

4. A method as recited in claim 1, wherein at least said determining whether said first portion contains at least one molecule of said first target nucleic acid is performed by carrying out a procedure which generates signals having magnitude which is higher where said detectable concentration is present than where said detectable concentration is not present.

5. A method as recited in claim 4, wherein said procedure comprises detecting fluorescence from fluor-labeled materials.

6. A method as recited in claim 4, wherein said procedure comprises detecting at least one chemical property which changes upon hybridization.

7. A method as recited in claim 4, wherein said procedure comprises evaluating at least one property selected from among the group consisting of agglutination, turbidity, phosphorescence, light scattering, light absorbance, fluorescence energy transfer, fluorescence quenching, fluorescence dequenching, time-delayed fluorescence, chemiluminescence and calorimetric evaluation.

8. A method as recited in claim 1, wherein said first sample chamber comprises at least a portion of an inside of a first microcapillary device, and wherein peaks are generated by detecting regions within said microcapillary device in which said detectable concentration is present.

9. A method as recited in claim 1, wherein at least one of said sample chambers contains at least one amplification targeting reagent.

10. A method as recited in claim 1, wherein each of said sample chambers contains at least one amplification targeting reagent.

11. A method as recited in claim 10, wherein at least a first of said sample chambers contains at least a first amplification targeting reagent, and at least a second of said sample chambers contains at least a second amplification targeting reagent, said first amplification targeting reagent differing from said second amplification targeting reagent.

12. A method as recited in claim 1, wherein each of said sample chambers has a volume of about 1 picoliter or less.

13. A method as recited in claim 1, wherein each of said sample chambers has a volume in the range of from about 1 picoliter to about 1 microliter.

14. A method as recited in claim 1, wherein each of said sample chambers has a volume of about 10 picoliters or less.

15. A method as recited in claim 1, wherein each of said sample chambers has a volume of about 100 picoliters.

16. A method as recited in claim 1, wherein each of said sample chambers has a volume of about 1 nanoliter.

17. A method as recited in claim 1, wherein each of said sample chambers has a volume of 10 nanoliters or less.

18. A method as recited in claim 1, wherein each of said sample chambers has a volume of about 10 nanoliters.

19. A method as recited in claim 1, wherein each of said sample chambers has at least one dimension of 2 mm or less.

20. A method as recited in claim 1, wherein each of said sample chambers has at least one dimension of 1 mm or less.

21. A method as recited in claim 1, wherein each of said sample chambers has at least one dimension of 100 microns or less.

22. A method as recited in claim 1, wherein each of said sample chambers has at least one dimension of 20 microns or less.

23. A method as recited in claim 1, wherein each of said sample chambers has at least one dimension of a few microns or less.

24. A method as recited in claim 1, wherein each of said sample portions has a volume of about 1 picoliter or less.

25. A method as recited in claim 1, wherein each of said sample portions has a volume in the range of from about 1 picoliter to about 1 microliter.

26. A method as recited in claim 1, wherein each of said sample portions has a volume of about 10 picoliters or less.

27. A method as recited in claim 1, wherein each of said sample portions has a volume which is nanoliter-sized.

28. A method as recited in claim 1, wherein each of said sample portions has a volume of about 1 nanoliter or less.

29. A method as recited in claim 1, wherein each of said sample portions has a volume of about 10 nanoliters or less.

30. A method as recited in claim 1, wherein each of said sample portions has a volume of about 100 nanoliters or less.

31. A method as recited in claim 1, wherein each of said sample portions has a volume of about 1 microliter or less.

32. A method as recited in claim 1, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 2 mm or less.

33. A method as recited in claim 1, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 1 mm or less.

34. A method as recited in claim 1, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 500 microns or less.

35. A method as recited in claim 1, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 100 microns or less.

36. A method as recited in claim 1, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 20 microns or less.

37. A method as recited in claim 1, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by a few microns or less.

38. A method as recited in claim 1, wherein said first sample chamber and said second sample chamber each further comprise constituents for enabling amplification of a target nucleic acid.

39. A method as recited in claim 1, wherein if said first portion contains at least a single molecule of said first target nucleic acid, said first portion would attain a detectable concentration of said first target nucleic acid within a portion of said first sample chamber after a single amplification step.

40. A method for detecting whether at least one molecule of a first target nucleic acid is present in a first sample and detecting whether at least one molecule of a second target nucleic acid is present in a second sample, said method comprising:

loading at least a portion of a first sample into at least a first sample chamber, whereby if said portion of said first sample contains at least a single molecule of said first target nucleic acid, said portion of said first sample would attain a detectable concentration of said first target nucleic acid within part of said first sample chamber after a single round of amplification;

loading at least a portion of a second sample into at least a second sample chamber, whereby if said portion of said second sample contains at least a single molecule of said second target nucleic acid, said portion of said second sample would attain a detectable concentration of said second target nucleic acid within part of said second sample chamber after a single round of amplification;

subjecting said portion of said first sample in said first sample chamber to at least a first amplification step;

subjecting said portion of said second sample in said second sample chamber to at least a first amplification step; and

then

determining whether said portion of said first sample contains at least one molecule of said first target nucleic acid and determining whether said portion of said second sample contains at least one molecule of said second target nucleic acid.

41. A method as recited in claim 40, wherein if said portion of a first sample contains at least a single molecule of said first target nucleic acid, said portion of a first sample would attain a detectable concentration of said first target nucleic acid within a portion of said first sample chamber after a single amplification step.

42. A method as recited in claim 40, wherein said first and second sample chambers are provided in an apparatus which comprises more than 1,000 sample chambers.

43. A method as recited in claim 40, wherein said first and second sample chambers are provided in an apparatus which comprises from 10,000 to over 100,000 sample chambers.

44. A method as recited in claim 40, wherein at least said determining whether said portion of said first sample contains at least one molecule of said first target nucleic acid is performed by carrying out a procedure which generates signals having magnitude which is higher where said detectable concentration is present than where said detectable concentration is not present.

45. A method as recited in claim 44, wherein said procedure comprises detecting fluorescence from fluor-labeled materials.

46. A method as recited in claim 44, wherein said procedure comprises detecting at least one chemical property which changes upon hybridization.

47. A method as recited in claim 44, wherein said procedure comprises evaluating at least one property selected from among the group consisting of agglutination, turbidity, phosphorescence, light scattering, light absorbance, fluorescence energy transfer, fluorescence quenching, fluorescence dequenching, time-delayed fluorescence, chemiluminescence and calorimetric evaluation.

48. A method as recited in claim 40, wherein said first sample chamber comprises at least a portion of an inside of a first microcapillary device, and wherein peaks are generated by detecting regions within said microcapillary device in which said detectable concentration is present.

49. A method as recited in claim 40, wherein at least one of said sample chambers contains at least one amplification targeting reagent.

50. A method as recited in claim 40, wherein each of said sample chambers contains at least one amplification targeting reagent.

51. A method as recited in claim 50, wherein said first sample chamber contains at least a first amplification targeting reagent, and said second sample chamber contains at least a second amplification targeting reagent, said first amplification targeting reagent differing from said second amplification targeting reagent.

52. A method as recited in claim 40, wherein each of said sample chambers has a volume of about 1 picoliter or less.

53. A method as recited in claim 40, wherein each of said sample chambers has a volume in the range of from about 1 picoliter to about 1 microliter.

54. A method as recited in claim 40, wherein each of said sample chambers has a volume of about 10 picoliters or less.

55. A method as recited in claim 40, wherein each of said sample chambers has a volume of about 100 picoliters.

56. A method as recited in claim 40, wherein each of said sample chambers has a volume of about 1 nanoliter.

57. A method as recited in claim 40, wherein each of said sample chambers has a volume of 10 nanoliters or less.

58. A method as recited in claim 40, wherein each of said sample chambers has a volume of about 10 nanoliters.

59. A method as recited in claim 40, wherein each of said sample chambers has at least one dimension of 2 mm or less.

60. A method as recited in claim 40, wherein each of said sample chambers has at least one dimension of 1 mm or less.

61. A method as recited in claim 40, wherein each of said sample chambers has at least one dimension of 100 microns or less.

62. A method as recited in claim 40, wherein each of said sample chambers has at least one dimension of 20 microns or less.

63. A method as recited in claim 40, wherein each of said sample chambers has at least one dimension of a few microns or less.

64. A method as recited in claim 40, wherein each of said sample portions has a volume of about 1 picoliter or less.

65. A method as recited in claim 40, wherein each of said sample portions has a volume in the range of from about 1 picoliter to about 1 microliter.

66. A method as recited in claim 40, wherein each of said sample portions has a volume of about 10 picoliters or less.

67. A method as recited in claim 40, wherein each of said sample portions has a volume which is nanoliter-sized.

68. A method as recited in claim 40, wherein each of said sample portions has a volume of about 1 nanoliter or less.

69. A method as recited in claim 40, wherein each of said sample portions has a volume of about 10 nanoliters or less.

70. A method as recited in claim 40, wherein each of said sample portions has a volume of about 100 nanoliters or less.

71. A method as recited in claim 40, wherein each of said sample portions has a volume of about 1 microliter or less.

72. A method as recited in claim 40, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 2 mm or less.

73. A method as recited in claim 40, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 1 mm or less.

74. A method as recited in claim 40, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 500 microns or less.

75. A method as recited in claim 40, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 100 microns or less.

76. A method as recited in claim 40, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by about 20 microns or less.

77. A method as recited in claim 40, wherein each of said sample portions is confined in at least one dimension by opposing barriers separated by a few microns or less.

78. A microfluidic device comprising:

at least a first sample chamber, said first sample chamber comprising at least a first ingredient which will react with a first target nucleic acid if contacted with said first target nucleic acid and subjected to at least a first round of amplification; and

at least a second sample chamber, said second sample chamber comprising at least a second ingredient which will react with a second target nucleic acid if contacted with said second target nucleic acid and subjected to at least a first round of amplification,

such that;

if a first sample portion contains at least one molecule of said first target nucleic acid and is loaded into said first sample chamber, a reaction product of amplification of said first sample portion will attain a detectable concentration of said first target nucleic acid within at least a portion of said first sample chamber after a single round of amplification, and

if a second sample portion contains at least one molecule of said second target nucleic acid and is loaded into said second sample chamber, a reaction product of amplification of said second sample portion will attain a detectable concentration of said target nucleic acid within at least a portion of said second sample chamber after a single round of amplification.

79. A microfluidic device as recited in claim 78, wherein if said first sample portion contains at least a single molecule of said first target nucleic acid, said first sample portion would attain a detectable concentration of said first target nucleic acid within a portion of said first sample chamber after a single amplification step.

80. A microfluidic device as recited in claim 78, wherein said microfluidic device comprises more than 1,000 sample chambers.

81. A microfluidic device as recited in claim 80, wherein each of said sample chambers comprises at least one of said first ingredient and said second ingredient.

82. A microfluidic device as recited in claim 80, wherein each of said sample chambers comprises at least one ingredient which will react with a corresponding target nucleic acid if contacted with said corresponding target nucleic acid and subjected to at least a first round of amplification.

83. A microfluidic device as recited in claim 80, wherein:

each of said sample chambers contains at least one ingredient for enabling amplification of at least one corresponding target nucleic acid molecule, and

each of said sample chambers contains at least one said ingredient which differs from all of said ingredients in all of said other sample chambers.

84. A microfluidic device as recited in claim 78, wherein said microfluidic device comprises from 10,000 to over 100,000 sample chambers.

85. A microfluidic device as recited in claim 84, wherein each of said sample chambers comprises at least one of said first ingredient and said second ingredient.

86. A microfluidic device as recited in claim 84, wherein each of said sample chambers comprises at least one ingredient which will react with a corresponding target nucleic acid if contacted with said corresponding target nucleic acid and subjected to at least a first round of amplification.

87. A microfluidic device as recited in claim 84, wherein:

each of said sample chambers contains at least one ingredient for enabling amplification of at least one corresponding target nucleic acid molecule, and

each of said sample chambers contains at least one said ingredient which differs from all of said ingredients in all of said other sample chambers.

88. A microfluidic device as recited in claim 78, wherein each of said sample chambers has a volume of about 1 picoliter or less.

89. A microfluidic device as recited in claim 78, wherein each of said sample chambers has a volume in the range of from about 1 picoliter to about 1 microliter.

90. A microfluidic device as recited in claim 78, wherein each of said sample chambers has a volume of about 10 picoliters or less.

91. A microfluidic device as recited in claim 78, wherein each of said sample chambers has a volume of about 100 picoliters.

92. A microfluidic device as recited in claim 78, wherein each of said sample chambers has a volume of about 1 nanoliter.

93. A microfluidic device as recited in claim 78, wherein each of said sample chambers has a volume of 10 nanoliters or less.

94. A microfluidic device as recited in claim 78, wherein each of said sample chambers has a volume of about 10 nanoliters.

95. A microfluidic device as recited in claim 78, wherein each of said sample chambers has at least one dimension of 2 mm or less.

96. A microfluidic device as recited in claim 78, wherein each of said sample chambers has at least one dimension of 1 mm or less.

97. A microfluidic device as recited in claim 78, wherein each of said sample chambers has at least one dimension of 100 microns or less.

98. A microfluidic device as recited in claim 78, wherein each of said sample chambers has at least one dimension of 20 microns or less.

99. A microfluidic device as recited in claim 78, wherein each of said sample chambers has at least one dimension of a few microns or less.