Method for processing polynucleotide-containing samples

• US 10,443,088 B1
• Filed: 07/22/2019
• Issued: 10/15/2019
• Est. Priority Date: 05/03/2004
• Status: Active Grant

• Current Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Original Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Inventors: Wu, Betty, Althaus, John S., Phadke, Nikhil, Brahmasandra, Sundaresh N., Handique, Kalyan, Kehrer, Aaron, Parunak, Gene, Haley, Cecelia, Springer, Ted
• Primary Examiner(s): Forman, Betty J
• Application Number:
  US16/518,735
• Publication Number:
  US 20190338344A1
• Time in Patent Office: 85 Days
• 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 retain 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 method for processing a polynucleotide-containing sample, the method comprising:

retaining polynucleotides from a sample on a plurality of binding particles in a process chamber under a first set of conditions, wherein the retaining step comprises binding the polynucleotides to the surfaces of the plurality of binding particles comprising a poly-cationic substance, wherein the sample has a volume from 0.5 microliters to 3 milliliters;

wherein the first set of conditions includes a first pH of about 8.5 or less and a first temperature, wherein the first temperature is between about 30°

C. and about 50°

C.;

releasing the polynucleotide from the plurality of binding particles under a second set of conditions; and

wherein the second set of conditions includes increasing the pH to a second pH by addition of a hydroxide solution and increasing the temperature to a second temperature, wherein the second temperature is between about 80°

C. and about 100°

C.

2. The method of claim 1, wherein the second pH is about 11.3 or greater.

3. The method of claim 1, wherein the poly-cationic substance is covalently bound to the surfaces of the binding particles.

4. The method of claim 1, wherein the binding particles comprise one or more carboxylic groups to provide an attachment point for the poly-cationic substance.

5. The method of claim 4, further comprising treating magnetic beads with NHS and MAC to form the binding particles.

6. The method of claim 1, wherein the heating step comprises heating the plurality of binding particles in the presence of a liquid, wherein the second temperature is insufficient to boil the liquid.

7. The method of claim 1, further comprising maintaining the second temperature for between about 1 and 10 minutes.

8. The method of claim 1, wherein the sample is heated for about 15 minutes or less while contacting the binding particles with the basic solution thereby releasing the polynucleotides.

9. The method of claim 1, wherein the poly-cationic substance has a molecular weight of less than about 30,000 Da.

10. The method of claim 1, wherein the poly-cationic substance has a molecular weight of less than about 800 Da.

11. The method of claim 1, wherein the ratio of the volume of the sample in the process chamber to the volume of liquid into which the polynucleotides are released is at least about 10.

12. The method of claim 1, wherein the particles occupy about 75 percent or less of the total volume of the process chamber.

13. A method for processing a polynucleotide-containing sample, the method comprising:

retaining polynucleotides from a sample on a plurality of binding particles in a process chamber under a first set of conditions, wherein the retaining step comprises binding the polynucleotides to the surfaces of the plurality of binding particles comprising a poly-cationic substance;

wherein the sample has a volume from 0.5 microliters to 3 milliliters;

wherein the first set of conditions includes a first pH of about 8.5 or less and a first temperature, wherein the first temperature is about 60°

C.;

releasing the polynucleotide from the plurality of binding particles under a second set of conditions; and

wherein the second set of conditions includes increasing the pH to a second pH by addition of a hydroxide solution and increasing the temperature to a second temperature, wherein the second temperature is between about 80°

C. and about 100°

C.

14. The method of claim 13, wherein the second pH is about 11.3 or greater.

15. The method of claim 13, wherein the poly-cationic substance is covalently bound to the surfaces of the binding particles.

16. The method of claim 13, wherein the binding particles comprise one or more carboxylic groups to provide an attachment point for the poly-cationic substance.

17. The method of claim 16, further comprising treating magnetic particles with NHS and EDAC to form the binding particles.

18. The method of claim 13, further comprising maintaining the second temperature for between about 1 and 10 minutes.

19. The method of claim 13, wherein the sample is heated for about 15 minutes or less while contacting the binding particles with the basic solution thereby releasing the polynucleotides.

20. The method of claim 13, wherein the poly-cationic substance has a molecular weight of less than about 30,000 Da.

21. The method of claim 13, wherein the poly-cationic substance has a molecular weight of less than about 800 Da.