Method of sampling, amplifying and quantifying segment of nucleic acid, polymerase chain reaction assembly having nanoliter-sized sample chambers, and method of filling assembly

• US 6,391,559 B1
• Filed: 05/02/2000
• Issued: 05/21/2002
• Est. Priority Date: 04/17/1997
• Status: Expired due to Term

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Cytonix Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Silver, Jonathan E., Kalinina, Olga V., Brown, James F.
• Primary Examiner(s): Chin, Christopher L.
• Application Number:
  US09/563,714
• Time in Patent Office: 749 Days
• Field of Search: 435/6, 435/287.1, 435/287.2, 435/288.3, 435/288.7, 436/164, 436/172, 436/518, 436/524, 436/527, 436/531, 436/805, 436/809, 436/514, 422/50, 422/57, 422/58
• US Class Current: 435/6.11
• 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

Methods of detecting and quantifying genomic nucliec acid molecule sequences are provided using the simultaneous amplification of a plurality of discrete nanoliter-sized samples. A miniaturized closed assembly is also provided for carrying out amplification of a nucleic acid molecule by polymerase chain reaction in multiple nanoliter-sized samples. Methods of filling miniaturized sample chambers are also provided as are methods for determining the number of template molecules in a sample by conducting replicate nucleic acid sequence amplification reactions on a set of terminally diluted samples and counting the number of positive amplification reactions. The methods can be used to detect a single starting nucleic acid target molecule.

Claims

1. An assembly for containing a portion of fluid material, said assembly comprising:

a substrate and a cover having facing surfaces spaced from one another, the facing surface of at least one of said substrate and cover comprising a first material;

a flow-through channel between said substrate and said cover; and

a first fluid retaining means located in said flow-through channel and being in communication with said flow-through channel, said first fluid retaining means having a first affinity to a first fluid and a second affinity to a displacing fluid, said flow through channel having a third affinity to said first fluid and a fourth affinity to said displacing fluid, wherein said first, second, third, and fourth affinities are such that;

(1) the first fluid retaining means retains at least a portion of the first fluid when the first fluid is loaded into the assembly; and

(2) the displacing fluid displaces first fluid from the flow-through channel without substantially displacing first fluid from the first fluid retaining means when the displacing fluid is loaded into the assembly after the first fluid is loaded into the assembly.

2. An assembly as claimed in claim 1, wherein said first fluid retaining means is confined in at least one dimension by opposing barriers separated by a dimension of about 500 microns or less.

3. An assembly as claimed in claim 1, wherein at least one of said cover and said substrate is substantially transparent to visible light.

4. An assembly as claimed in claim 1, wherein at least one of said cover and said substrate is substantially transparent to visible ultraviolet light.

5. An assembly as claimed in claim 1, wherein at least one of said cover and said subtrate is flexible.

6. An assembly as claimed in claim 1, wherein said assembly includes a first fluid and said first fluid is a liquid.

7. An assembly as claimed in claim 1, wherein said assembly includes a first fluid and said first fluid is a chemical or biological sample.

8. An assembly as claimed in claim 1, wherein said assembly includes a first fluid and said first fluid is a gas.

9. An assembly as claimed in claim 1, wherein said assembly includes a displacing fluid and said displacing fluid is a liquid.

10. An assembly as claimed in claim 1, wherein said assembly includes a displacing fluid and said displacing fluid is a gas.

11. An assembly as claimed in claim 1, wherein said assembly includes a first fluid retained by said first fluid retaining means, and a displacing fluid that is a curable adhesive that seals said first fluid retaining means and prevents evaporation of said first fluid from said first fluid retaining means.

12. An assembly as claimed in claim 11, wherein said curable adhesive is cured by electromagnetic energy.

13. An assembly as claimed in claim 1, wherein said assembly includes a first fluid and a displacing fluid, the surface energy of said first fluid is greater than the surface energy of said displacing fluid, and the surface energy of at least a portion of said first fluid retaining means is greater than the surface energy of said flow-through channel.

14. An assembly as claimed in claim 1, wherein said assembly includes a first fluid and the surface energy of said first fluid is less than the surface energy of at least a portion of said first fluid retaining means.

15. An assembly as claimed in claim 1, wherein said assembly includes a first fluid and the surface energy of said first fluid is less than the surface energy of at least a portion of said first fluid retaining means.

16. An assembly as claimed in claim 1, wherein at least a portion of said first fluid retaining means is hydrophilic.

17. An assembly as claimed in claim 1, wherein said assembly includes a first fluid retained by said first fluid retaining means, and a displacing fluid, and wherein the surface energy of said first fluid is less than the surface energy of said displacing fluid, and the surface energy of at least a portion of said first fluid retaining means is less than the surface energy of said flow-through channel.

18. An assembly as claimed in claim 1, wherein at least one of said first, second, third, or fourth affinities results from electrostatic forces.

19. An assembly as claimed in claim 1, wherein at least one of said first, second, third, or fourth affinities result from electromagnetic energy.

20. An assembly as claimed in claim 1, wherein at least a portion of said first fluid retaining means comprises a porous surface.

21. An assembly as claimed in claim 1, wherein said first fluid retaining means comprises a plurality of first fluid retaining means.

22. An assembly as claimed in claim 21, wherein said plurality of first fluid retaining means is at least partially defined by a patterned layer.