Processing Polynucleotide-Containing Samples

• US 20080262213A1
• Filed: 05/03/2005
• Published: 10/23/2008
• Est. Priority Date: 05/03/2004
• Status: Active Grant

• Current Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Original Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Inventors: Handique, Kalyan, Brahmasandra, Sundaresh N., Wu, Betty, Althaus, John S., Phadke, Nikhil
• Granted Patent: US 8,470,586 B2
• Time in Patent Office: Days
• US Class Current: 536/25.4
• CPC Class Codes: B01F 25/433 Mixing tubes wherein the shape of the tube influences the mixing, e.g. mixing tubes with varying cross-section or provided with inwardly extending profiles
• CPC Class Codes: B01F 25/4331 Mixers with bended, curved, coiled, wounded mixing tubes or comprising elements for bending the flow
• CPC Class Codes: B01F 33/30 Micromixers
• 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 2300/0672 Integrated piercing tool
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0867 Multiple inlets and one sample wells, e.g. mixing, dilution
• CPC Class Codes: B01L 2300/087 Multiple sequential chambers
• CPC Class Codes: B01L 2300/0887 Laminated structure
• CPC Class Codes: B01L 2400/0442 thermal energy, e.g. vaporisation, bubble jet
• CPC Class Codes: B01L 2400/0481 squeezing of channels or chambers
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0633 with moving parts
• CPC Class Codes: B01L 2400/0677 phase change valves; Meltable, freezing, dissolvable plugs; Destructible barriers
• CPC Class Codes: B01L 2400/0683 mechanically breaking a wall or membrane within a channel or chamber
• CPC Class Codes: B01L 2400/0694 vents used to stop and induce flow, backpressure valves
• CPC Class Codes: B01L 3/502707 characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502723 characterised by venting arrangements
• CPC Class Codes: B01L 3/50273 : characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502738 : characterised by integrated valves microvalves F16K99/0001
• 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 3/5082 : Test tubes per se
• CPC Class Codes: B01L 3/523 : with means for closing or opening
• CPC Class Codes: B01L 3/565 : Seals in general F16L
• 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: C12N 15/1006 : by means of a solid support carrier, e.g. particles, polymers
• CPC Class Codes: C12N 15/101 : by chromatography, e.g. electrophoresis, ion-exchange, reverse phase
• 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 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2565/629 : being a microfluidic device
• CPC Class Codes: F16K 2099/0084 : Chemistry or biology, e.g. "lab-on-a-chip" technology
• CPC Class Codes: F16K 99/0001 : Microvalves microdevices B81B1/00; manufacture or treatment of devices or systems in or on a substrate B81C1/00; microfluidic structures B01L3/5027; micropumps F04B19/006
• CPC Class Codes: F16K 99/0019 : Valves using a microdroplet or microbubble as the valve member
• CPC Class Codes: F16K 99/0032 : using phase transition or influencing viscosity
• CPC Class Codes: F16K 99/0034 : Operating means specially adapted for microvalves
• CPC Class Codes: F16K 99/0036 : operated by temperature variations
• CPC Class Codes: F16K 99/0044 : using thermo-electric means

Abstract

Methods and systems for processing polynucleotides (e.g., DNA) are disclosed. A processing region includes one or more surfaces (e.g., particle surfaces) modified with ligands that regain polynucleotides under a first set of conditions (e.g., temperature and pH) and release the polynucleotides under a second set of conditions (e.g., higher temperature and/or more basic pH). The processing region can be used to, for example, concentrate polynucleotides of a sample and/or separate inhibitors of amplification reactions from the polynucleotides. Microfluidic devices with a processing region are disclosed.

Claims

1. A sample preparation device, comprising:

a surface comprising a poly-cationic polyamide bound thereto; and

a sample introduction passage in communication with the surface for contacting the surface with a fluidic sample.

2. The sample preparation device of claim 1, further comprising a heat source configured to heat an aqueous liquid in contact with the surface to at least about 65°

C.

3. The sample preparation device of claim 1, further comprising a reservoir of liquid having a pH of at least about 10, wherein the device is configured to contact the surface with the liquid.

4. The sample preparation device of claim 1, wherein in the surface comprises surfaces of a plurality of particles.

5. The sample preparation device of claim 1, wherein the surface can be removed from the device.

6. The sample preparation device of claim 1, wherein the poly-cationic polyamide comprises at least one of poly-L-lysine and poly-D-lysine.

7. A method for processing a sample, comprising:

providing a mixture comprising a liquid and an amount of polynucleotide;

contacting a retention member with the mixture, the retention member configured to preferentially retain polynucleotides as compared to polymerase chain reaction inhibitors;

separating substantially all of the liquid in the mixture from the retention member; and

releasing polynucleotides retained by the retention member therefrom.

8. The method of claim 7, wherein the polynucleotide has a size of less than about 7.5 Mbp.

9. The method of claim 7, wherein the liquid is a first liquid and separating substantially all of the liquid comprises contacting the retention member with a second liquid.

10. The method of claim 9, wherein contacting the retention member with a second liquid comprises actuating a thermally actuated pressure source to apply a pressure to the second liquid.

11. The method of claim 10, wherein contacting the retention member with a second liquid comprises opening a thermally actuated valve to place the second liquid in fluid communication with the retention member.

12. The method of claim 10, wherein the second liquid has a volume of less than about 50 microliters.

13. The method of claim 10, wherein the retention member comprises a surface comprising a compound configured to bind polynucleotides preferentially to polymerase chain reaction inhibitors.

14. The method of claim 13, wherein the inhibitors comprise at least one of hemoglobin, peptides, faecal compounds, humic acids, mucousol compounds, DNA binding proteins, or a saccharide.

15. The method of claim 13, wherein surface comprises a poly-lysine.

16. The method of claim 15, wherein poly-lysine comprises at least one of poly-L-lysine and poly-D-lysine.

17. The method of claim 15, wherein separating comprises replacing the first liquid with a second liquid.

18. The method of claim 17, wherein the second liquid comprises a detergent.

19. The method of claim 9, wherein releasing comprises heating the retention member to a temperature of at least about 50°

C.

20. The method of claim 19, wherein the retention member is heated in the presence of a liquid and the temperature is insufficient to boil the liquid in the presence of the retention member during heating.

21. The method of claim 20, wherein the temperature is 100°

C. or less.

22. The method of claim 19, wherein the temperature is maintained for less than about 10 minutes.

23. The method of claim 19, wherein the method does not comprise centrifugation of the retention member.