Method for separating an analyte from a sample

• US 7,914,994 B2
• Filed: 02/12/2009
• Issued: 03/29/2011
• Est. Priority Date: 12/24/1998
• Status: Expired due to Fees

• Current Assignee: Cepheid (Danaher Corporation)
• Original Assignee: Cepheid (Danaher Corporation)
• Inventors: Kovacs, Gregory T. A., Chang, Ronald, Petersen, Kurt E., Northrup, M. Allen, McMillan, William A., Pourahmadi, Farzad, Christel, Lee A., Ching, Jesus
• Primary Examiner(s): Beisner; William H
• Application Number:
  US12/370,527
• Publication Number:
  US 20100068706A1
• Time in Patent Office: 775 Days
• Field of Search: 435/6, 435/91.2, 435/259, 436/178, 536/25.4
• US Class Current: 435/173.9
• CPC Class Codes: B01D 15/00 Separating processes involving the treatment of liquids with solid sorbents using liquid sorbents B01D11/00; ion exchange processes or materials, sorbent materials in general B01J, e.g. sorbents for chromatography B01J20/281; for investigating or analysing materials G01N30/00; Apparatus therefor
• CPC Class Codes: B01L 2400/0622 distribution valves, valves having multiple inlets and/or outlets, e.g. metering valves, multi-way valves
• CPC Class Codes: B01L 2400/0644 rotary valves
• 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: C12M 47/06 Hydrolysis; Cell lysis; Extraction of intracellular or cell wall material lysis of microorganisms C12N1/06; extracting or separating nucleic acids from biological samples C12N15/1003
• CPC Class Codes: C12N 15/1017 by filtration, e.g. using filters, frits, membranes
• CPC Class Codes: G01N 1/34 Purifying; Cleaning processes or apparatus for extracting or separating nucleic acids from biological samples C12N15/1003
• CPC Class Codes: Y10T 436/255 including use of a solid sorbent, semipermeable membrane, or liquid extraction

Abstract

An analyte is separated from a fluid sample by introducing the sample into a cartridge having a sample port and a first flow path extending from the sample port. The first flow path includes an extraction chamber containing a solid support for capturing the analyte from the sample. The cartridge has a second flow path for eluting the captured analyte from the extraction chamber, the second flow diverging from the first flow path after passing through the extraction chamber. The sample is forced to flow through the extraction chamber and into a waste chamber, thereby capturing the analyte with the solid support as the sample flows through the extraction chamber. The captured analyte is then eluted from the extraction chamber by forcing an elution fluid to flow through the extraction chamber and along the second flow path.

Claims

1. A method for extracting nucleic acid from a sample, the sample containing cells, spores, or microorganisms, the method comprising:

a) introducing the sample into a cartridge having;

i) a lysing region for lysing the cells, spores, or microorganisms to release the nucleic acid therefrom; and

ii) a capture region, the capture region comprising a channel or chamber containing capture material for capturing the nucleic acid;

b) drying the sample on paper or membrane material in the lysing region, the paper or membrane material being impregnated with at least one chemical for lysing the cells, spores, or microorganisms in the sample to release the nucleic acid from the cells, spores, or microorganisms, while binding contaminants or inhibitors in the sample to the paper or membrane material;

c) placing fluid in the lysing region and releasing the nucleic acid from the paper or membrane material into the fluid while the contaminants or inhibitors remain bound to the paper or membrane material;

d) forcing the fluid containing the nucleic acid to flow through the capture region to capture the nucleic acid with the capture material; and

e) eluting the nucleic acid from the capture region.

2. The method of claim 1, wherein the cartridge further includes a reaction chamber, and the method further comprises the steps of:

i) forcing the nucleic acid eluted from the capture region to flow into the reaction chamber;

ii) amplifying the nucleic acid in the reaction chamber; and

iii) detecting the amplified nucleic acid.

3. The method of claim 2, wherein the amplification requires temperature control of the reaction chamber, the portion of the cartridge defining the reaction chamber protrudes from the rest of the cartridge body, and the temperature of the reaction chamber is controlled by inserting the reaction chamber into a thermal sleeve and heating or cooling the reaction chamber according to a time/temperature profile.

4. The method of claim 3, wherein the cartridge further includes a reagent chamber containing dried or lyophilized reagents, and the method further comprises the step of mixing the nucleic acid with the reagents in the reagent chamber prior to forcing the nucleic acid to flow into the reaction chamber.

5. The method of claim 1, further comprising the steps of:

i) forcing the nucleic acid eluted from the capture region to flow into a reaction vessel coupled to the cartridge;

ii) amplifying the nucleic acid in the reaction vessel; and

iii) detecting the amplified nucleic acid.

6. The method of claim 5, wherein the amplification requires temperature control of the reaction vessel, and wherein the temperature of the vessel is controlled by inserting the vessel into a thermal sleeve and heating or cooling the vessel according to a time/temperature profile.

7. The method of claim 5, wherein the cartridge further includes a reagent chamber containing dried or lyophilized reagents, and the method further comprises the step of mixing the eluted nucleic acid with the reagents in the reagent chamber prior to forcing the nucleic acid to flow into the reaction vessel.

8. The method of claim 1, wherein the capture material comprises at least one solid support selected from the group consisting of filters, membranes, beads, fiber, glass wool, filter paper, polymers, and gel.

9. The method of claim 1, wherein the capture region comprises an extraction chamber formed in a microfluidic chip, and wherein the capture material comprises an array of microstructures extending into the extraction chamber, each of the microstructures having an aspect ratio (height to width) of at least 2:

1.

10. The method of claim 1, wherein the cartridge includes at least one waste chamber for receiving waste fluid and at least one additional chamber for receiving the nucleic acid eluted from the capture region, the fluid forced to flow through the capture region in d) is forced to flow into the at least one waste chamber after flowing through the capture region, and the nucleic acid is eluted from the capture region by forcing elution fluid to flow through the capture region and into the additional chamber.

11. The method of claim 10, wherein the volume of sample placed in the lysing region is greater than the volume of elution fluid forced to flow through the capture region, whereby the nucleic acid extracted from the sample is concentrated in the smaller volume of elution fluid.

12. The method of claim 10, wherein the ratio of the volume of fluid forced to flow through the capture region in d) to the volume capacity of the capture region is at least 2:

1.

13. The method of claim 10, wherein the additional chamber comprises a reagent chamber containing reagents, and the method further comprises the mixing the nucleic acid with the reagents in the reagent chamber.

14. The method of claim 10, wherein the additional chamber comprises a reaction chamber, and the method further comprises the step of amplifying the nucleic acid in the reaction chamber.

15. The method of claim 1, wherein the cartridge includes at least one waste chamber for receiving waste fluid, the fluid forced to flow through the capture region in d) is forced to flow into the at least one waste chamber after flowing through the capture region, and the nucleic acid is eluted from the capture region by forcing elution fluid to flow through the capture region and into a reaction vessel coupled to the cartridge.

16. The method of claim 15, wherein the volume of sample placed in the lysing region is greater than the volume of elution fluid forced to flow through the capture region, whereby the nucleic acid extracted from the sample is concentrated in the smaller volume of elution fluid.

17. The method of claim 15, wherein the ratio of the volume of fluid forced to flow through the capture region in d) to the volume capacity of the capture region is at least 2:

1.

18. The method of claim 15, wherein the cartridge includes a reagent chamber, and the method further comprises the step of mixing the nucleic acid eluted from the capture region with reagents in the reagent chamber prior to forcing the nucleic acid to flow into the reaction vessel.

19. The method of claim 15, further comprising the step of amplifying and detecting the nucleic acid in the reaction vessel.

20. The method of claim 1, wherein the cartridge includes a desiccant adjacent the lysing region, and wherein the sample is dried on the paper or membrane material by heating the sample and absorbing moisture with the desiccant.

21. The method of claim 1, wherein the nucleic acid is released from the paper or membrane material into the fluid in the lysing region by heating the paper or membrane material.

22. The method of claim 1, wherein the cartridge includes at least one waste chamber, and wherein c) step (c) is preceded by the additional steps of binding the nucleic acid released from the cells, spores, or microorganisms to the paper or membrane material, washing the lysing region with wash fluid, and forcing the wash fluid to flow out of the lysing region and into the at least one waste chamber while the nucleic acid remains bound to the paper or membrane material.

23. The method of claim 1, wherein the chemical comprises at least one lysing agent selected from the group consisting of enzymes, detergents, and chaotropes.

24. The method of claim 1, wherein the chemical comprises a chaotropic salt.

25. The method of claim 1, wherein the paper or membrane material comprises cellulose, nitrocellulose, polycarbonate, or nylon.