Method for separating analyte from a sample

• US 7,569,346 B2
• Filed: 05/03/2005
• Issued: 08/04/2009
• Est. Priority Date: 12/24/1997
• Status: Expired due to Term

• 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:
  US11/121,541
• Publication Number:
  US 20050194316A1
• Time in Patent Office: 1,554 Days
• Field of Search: None
• US Class Current: 435/6.13
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01L 2200/0621 Control of the sequence of chambers filled or emptied
• CPC Class Codes: B01L 2200/0631 Purification arrangements, e.g. solid phase extraction [SPE]
• CPC Class Codes: B01L 2200/0636 Focussing flows, e.g. to laminate flows
• 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 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0883 Serpentine channels
• CPC Class Codes: B01L 2300/1827 using resistive heater
• CPC Class Codes: B01L 2400/0421 electrophoretic flow
• CPC Class Codes: B01L 2400/046 Chemical or electrochemical formation of bubbles
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• 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 2400/086 using baffles or other fixed flow obstructions
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502753 characterised by bulk separation arrangements on lab-on-a-chip devices, e.g. for filtration or centrifugation separation in general B01D; microapparatus for analysis using electrophoresis G01N27/44791; sample preparation G01N1/28
• 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 47/02 Separating microorganisms from the culture medium; Concentration of biomass separating microorganisms from their culture media C12N1/02
• 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: C40B 60/14 : for creating libraries
• CPC Class Codes: G01F 1/708 : Measuring the time taken to traverse a fixed distance
• CPC Class Codes: G01N 30/6091 : Cartridges
• CPC Class Codes: G01N 30/6095 : Micromachined or nanomachined, e.g. micro- or nanosize
• CPC Class Codes: Y10T 436/25375 : Liberation or purification of sample or separation of material from a sample [e.g., filtering, centrifuging, etc.]
• 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 desiccant adjacent to the lysing region; and

iii) at least one waste chamber;

b) contacting the sample with a 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, under conditions where the cells, spores, or microorganisms in the sample are lysed, while drying the sample on the paper or the membrane material by heating and absorbing moisture with the desiccant;

c) binding the nucleic acid released from the cells, spores, or microorganisms to the paper or membrane material;

d) washing the lysing region with wash fluid and forcing the wash fluid to flow from the lysing region into the at least one waste chamber while the nucleic acid remains bound to the paper or membrane material in the lysing region; and

e) eluting the nucleic acid from the paper or membrane material.

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 eluted nucleic acid 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 2, 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 chamber.

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

i) forcing the eluted nucleic acid 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:

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

b) the nucleic acid is eluted from the paper or membrane material by placing fluid into the lysing region and releasing the nucleic acid from the paper or membrane material into the fluid;

c) and the method further comprises the steps of concentrating the nucleic acid by;

i) forcing the fluid containing the nucleic acid to flow out of the lysing region and through the capture region to capture the nucleic acid with the capture material;

ii) forcing the fluid that has flowed through the capture region to flow into at least one waste chamber in the cartridge; and

iii) eluting the nucleic acid from the capture region.

9. The method of claim 8, 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.

10. The method of claim 8, wherein the cartridge has a first flow path that includes the lysing and capture regions, the first flow path leading to the at least one waste chamber, the cartridge has an elution flow path passing through the capture region and diverging from the first flow path, the elution flow path leading to an additional chamber in the cartridge for receiving the nucleic acid, the fluid containing the nucleic acid is forced to flow through the capture region and into the at least one waste chamber via the first flow path, thereby separating the nucleic acid from the fluid in 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 via the diverging elution flow path.

11. The method of claim 8, wherein the cartridge further includes a reaction chamber, and the method further comprises the step of forcing the nucleic acid eluted from the capture region to flow into the reaction chamber and amplifying the nucleic acid in the reaction chamber.

12. The method of claim 8, further comprising the step of forcing the nucleic acid eluted from the capture region to flow into a reaction vessel coupled to the cartridge and amplifying the nucleic acid in the reaction vessel.

13. The method of claim 8, wherein the cartridge has a first flow path that includes the lysing and capture regions, the first flow path leading to the at least one waste chamber, the cartridge has an elution flow path passing through the capture region and diverging from the first flow path, a reaction vessel is coupled to the cartridge for receiving the nucleic acid eluted from the capture region via the elution flow path, the fluid containing the nucleic acid is forced to flow through the capture region and into the at least one waste chamber via the first flow path, thereby separating the nucleic acid from the fluid in the capture region, the nucleic acid is eluted from the capture region by forcing elution fluid to flow through the capture region and along the diverging elution flow path, the nucleic acid eluted from the capture region is forced to flow into the reaction vessel, and the nucleic acid is amplified in the reaction vessel.

14. The method of claim 1, wherein the nucleic acid is eluted from the paper or membrane material by placing fluid in the lysing region, heating the lysing region to release the nucleic acid from the paper or membrane material into the fluid, and forcing the fluid containing the nucleic acid to flow out of the lysing region.

15. The method of claim 14, further comprising the step of binding contaminants or inhibitors to the paper or membrane material prior to releasing the nucleic acid from the paper or membrane material into the fluid, and wherein the contaminants or inhibitors remain bound to the paper or membrane material while the nucleic acid is eluted from the paper or membrane material.

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

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

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