Device, system, and method for depositing processed immiscible-fluid-discrete-volumes

• US 9,285,297 B2
• Filed: 08/22/2006
• Issued: 03/15/2016
• Est. Priority Date: 08/22/2005
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Schroeder, Benjamin G., Cox, David M., Oldham, Mark F., Reel, Richard T., Wiyatno, Willy
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US11/507,733
• Publication Number:
  US 20070039866A1
• Time in Patent Office: 3,493 Days
• Field of Search: 435/6.12, 435/91.2, 210/265, 204/182.8
• US Class Current: 1/1
• CPC Class Codes: B01J 2219/00353 Pumps
• CPC Class Codes: B01J 2219/0036 Nozzles
• CPC Class Codes: B01J 2219/00364 Pipettes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01L 2200/0673 Handling of plugs of fluid surrounded by immiscible fluid
• 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 2300/0864 comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• CPC Class Codes: B01L 2300/0867 Multiple inlets and one sample wells, e.g. mixing, dilution
• CPC Class Codes: B01L 2400/0421 electrophoretic flow
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 3/0293 for liquids
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502784 : specially adapted for droplet or plug flow, e.g. digital microfluidics automatic analysis using a stream of discrete samples in a tube system G01N35/08
• 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: C12Q 1/6806 : Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6869 : Methods for sequencing
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2535/101 : Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: F15C 5/00 : Manufacture of fluid circuit elements; Manufacture of assemblages of such elements integrated circuits
• 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 99/0011 : Gate valves or sliding valves
• CPC Class Codes: F16K 99/0013 : Rotary valves
• CPC Class Codes: G01N 1/14 : Suction devices, e.g. pumps; Ejector devices
• CPC Class Codes: G01N 27/44743 : Introducing samples
• CPC Class Codes: G01N 27/44769 : Continuous electrophoresis, i.e. the sample being continuously introduced, e.g. free flow electrophoresis [FFE]
• CPC Class Codes: G01N 35/08 : using a stream of discrete samples flowing along a tube system, e.g. flow injection analysis
• CPC Class Codes: Y10T 137/0318 : Processes
• CPC Class Codes: Y10T 137/4259 : With separate material addition
• CPC Class Codes: Y10T 137/85978 : With pump
• CPC Class Codes: Y10T 137/85986 : Pumped fluid control
• CPC Class Codes: Y10T 137/86863 : Rotary valve unit
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

Various embodiments relate to systems and/or methods for sample preparation that can be used for biochemical and/or molecular biology procedures involving small volumes, for example, micro volumes or smaller. Methods and systems that can reduce sample size requirements and increase the number of samples on a substrate are provided. Samples can be applied to a plate or other appropriate substrate and can be used for, inter alia, sequencing reactions. In some embodiments, apparatuses, systems, and/or methods for charged analyte collection are provided. Charged analytes in a sample can be electrokinetically collected or extracted from a conduit through a hole formed in a sidewall of the conduit, by application of an electric field that causes the charged analytes to migrate in a direction that is transverse to the conduit.

Claims

1. A method comprising:

diluting a sample into sample portions wherein at least one sample portion contains a single fragment of target analyte;

forming in a conduit a plurality of aqueous sample slugs spaced apart from one another by slugs of spacing fluid, and at least one of the aqueous sample slugs comprising at least one target analyte, wherein the forming includes;

flowing the sample portions and the spacing fluid from an aqueous sample injection unit and a spacing fluid injection unit, respectively, and

injecting volumes of the sample portions and the spacing fluid respectively to form the aqueous sample slugs in the conduit;

amplifying a target analyte located in at least one aqueous sample slug;

dispensing the aqueous sample slugs one-at-a-time from the conduit onto a substrate to form a pattern of spaced apart aqueous samples on the substrate, the substrate comprising an electrically conductive surface and an immersion fluid configured to have the dispensed aqueous sample slugs immersed therein, and the dispensing onto the substrate comprising dispensing the aqueous sample slugs directly onto the electrically conductive surface of said substrate;

reacting the at least one target analyte with a reagent mixture to form at least one target analyte product;

imaging the electrically conductive surface to differentiate a target analyte product from non-target analyte products;

positioning a collection device comprising a capillary of a capillary electrophoretic analyzer, adjacent the at least one target analyte product on the substrate;

injecting at least a portion of the at least one target analyte product into the collection device, wherein the injecting comprises applying a potential to the electrically conductive surface and the capillary; and

performing nucleic acid sequencing on the at least one target analyte product with the capillary electrophoretic analyzer.

2. The method of claim 1, wherein the electrically conductive surface comprises at least one linker moiety bound thereto, wherein the at least one linker moiety is adapted to bind the at least one target analyte.

3. The method of claim 2, further comprising:

capturing the at least one target analyte with the at least one linker moiety to form at least one bound target analyte; and

solubilizing the bound target analyte or a reaction product thereof prior to injection.

4. The method of claim 2, further comprising contacting the electrically conductive surface with a mixture of sequencing reaction components.

5. The method of claim 1, wherein the electrically conductive surface comprises a gold-coated surface.

6. The method of claim 2, wherein the at least one target analyte comprises at least one target nucleic acid sequence.

7. The method of claim 1, further comprising:

binding the at least one target analyte to the substrate to form at least one bound target analyte;

reacting the at least one bound target analyte with a reagent mixture to form at least one target analyte product; and

solubilizing the target analyte product prior to injection.

8. The method of claim 3, further comprising reacting the at least one bound target analyte with a reagent mixture to form at least one target analyte product.

9. The method of claim 1, wherein forming the pattern of spaced apart aqueous samples comprises forming a plurality of rows of aqueous samples.

29. The method of claim 1, wherein the electrically conductive surface is in electrical communication with a voltage source for application of an electrical potential to the electrically conductive surface.

30. The method of claim 1, wherein the conduit comprises tubing.

34. The method of claim 1, further comprising flowing the plurality of spaced apart aqueous sample plugs containing the at least one nucleic acid and the at least one target analyte through the conduit to the substrate where said dispensing occurs, through or by one or more intervening sample processors selected from the group consisting of an amplification thermo-cycler, an excitation source, a spectrophotometric detector, and a discriminating/waste collector device.

36. The method of claim 1, wherein the substrate includes a plurality of hydrophilic regions corresponding to the pattern, and each aqueous sample slug is dispensed onto a hydrophilic region of the plurality of hydrophilic regions.

37. The method of claim 36, wherein each hydrophilic region includes an electrically conductive surface.

10. A method comprising:

diluting a sample into sample portions wherein at least one sample portion contains a single fragment of target analyte;

forming in a conduit a plurality of spaced apart aqueous sample slugs comprising at least one target analyte comprising at least one respective linkage group, wherein the forming includes;

flowing the sample portions and the spacing fluid from an aqueous sample injection unit and a spacing fluid injection unit, respectively, and

injecting volumes of the sample portions and the spacing fluid respectively to form the aqueous sample slugs in the conduit;

amplifying a target analyte located in at least one aqueous sample slug;

dispensing the aqueous sample slugs one-at-a-time from the conduit onto a substrate to form a pattern of aqueous samples on the substrate, the substrate comprising an electrically conductive surface adapted to bind the at least one respective linkage group to form an attached analyte and an immersion fluid configured to have the dispensed aqueous sample slugs immersed therein, and the dispensing onto the substrate comprising dispensing the aqueous sample slugs directly onto the electrically conductive surface of said substrate;

reacting the at least one target analyte with a reagent mixture to form at least one target analyte product;

imaging the electrically conductive surface to differentiate a target analyte product from non-target analyte products;

positioning a collection device comprising a capillary of a capillary electrophoretic analyzer, adjacent the at least one target analyte product;

injecting at least a portion of the at least one target analyte product into the collection device wherein the injecting comprises applying a potential to the electrically conductive surface and the capillary; and

performing nucleic acid sequencing on the at least one target analyte product with the capillary electrophoretic analyzer.

11. The method of claim 10, further comprising:

bonding the at least one linkage group to the electrically conductive surface to form at least one captured target analyte; and

solubilizing the bound target analyte or a reaction product thereof prior to injection.

12. The method of claim 11, further comprising contacting the electrically conductive surface with a mixture of sequencing reaction components after the bonding.

13. The method of claim 10, wherein the electrically conductive surface comprises a metal coated surface.

14. The method of claim 10, wherein the electrically conductive surface comprises a goldcoated surface.

15. The method of claim 10, wherein the at least one target analyte comprises at least one target nucleic acid sequence.

16. The method of claim 10, wherein forming the pattern of aqueous samples comprises forming a plurality of rows of aqueous samples.

31. The method of claim 10, wherein the conduit comprises tubing.

35. The method of claim 10, further comprising flowing the plurality of spaced apart aqueous sample plugs containing the at least one nucleic acid and the at least one target analyte through the conduit to the substrate where said dispensing occurs, through or by one or more intervening sample processors selected from the group consisting of an amplification thermocycler, an excitation source, a spectrophotometric detector, and a discriminating/waste collector device.

17. A method comprising:

diluting a sample into sample portions wherein at least one sample portion contains a single fragment of target analyte;

flowing the sample portions and the spacing fluid from an aqueous sample injection unit and a spacing fluid injection unit, respectively, and

injecting volumes of the sample portions and the spacing fluid respectively to form aqueous sample slugs in the conduit;

amplifying target analyte in a plurality of aqueous sample slugs in a conduit to form amplicons, each aqueous slug separated from an adjacent aqueous slug by at least one oil slug;

depositing the amplicons from the conduit onto the substrate, the substrate comprising an electrically conductive surface and an immersion fluid configured to have the deposited amplicons immersed therein, and the depositing comprising depositing the amplicons directly onto the electrically conductive substrate;

attaching the amplicons to the electrically conductive surface;

contacting the substrate with a sequencing reaction mixture to form at least one dye-labeled spot;

imaging the electrically conductive surface to differentiate a target analyte product from non-target analyte products;

positioning a capillary of a capillary electrophoretic analyzer over the at least one dye-labeled spot;

electrically contacting the dye-labeled spot with the capillary;

injecting one or more components from the dye-labeled spot into the capillary wherein the injecting comprises applying a potential to the electrically conductive surface and the capillary; and

performing nucleic acid sequencing on the at least one target analyte product with the capillary electrophoretic analyzer.

18. The method of claim 17, wherein the amplifying comprises incorporating a 5′

-sulfhydryl group into a DNA molecule.

19. The method of claim 17, wherein the surface comprises an electrically conductive surface.

20. The method of claim 19, wherein the electrically conductive surface comprises a gold surface.

21. The method of claim 17, wherein the surface comprises a binding moiety.

22. The method of claim 17, further comprising washing the electrically conductive surface with a denaturing solution after depositing the amplicons from the conduit onto the electrically conductive surface.

23. The method of claim 17, wherein the sequencing reaction mixture comprises a primer and a dye-labeled terminator and the method comprises reacting the amplicons with the primer and the dye-labeled terminator to form the dye-labeled spot.

24. The method of claim 17, further comprising imaging the electrically conductive surface and determining a location of the dye-labeled spot.

25. The method of claim 17, further comprising analyzing the one or more components in the capillary electrophoretic analyzer.

26. The method of claim 17, wherein the electrically conductive surface comprises reactive groups.

27. The method of claim 26, wherein the reactive groups comprise one or more of carboxy groups, amino groups, and hydroxyl groups.

32. The method of claim 17, wherein the electrically conductive surface is in electrical communication with a voltage source for application of an electrical potential to the electrically conductive surface.

28. A method comprising:

diluting a sample into sample portions wherein at least one sample portion contains a single fragment of target analyte;

flowing the sample portions and the spacing fluid from an aqueous sample injection unit and a spacing fluid injection unit, respectively, and

injecting volumes of the sample portions and the spacing fluid respectively to form aqueous sample slugs in a conduit, each aqueous slug separated from an adjacent aqueous slug by at least one non-aqueous slug;

moving the conduit comprising the target analyte over a substrate and depositing the target analyte from the conduit onto the substrate, the substrate comprising an electrically conductive surface and an immersion fluid configured to have the dispensed aqueous sample slugs immersed therein, and the depositing comprising depositing the aqueous sample slugs directly onto the electrically conductive substrate;

attaching the target analyte to the electrically conductive surface;

contacting the electrically conductive surface with a reaction mixture;

imaging the electrically conductive surface to differentiate a target analyte product from non-target analyte products;

positioning a second conduit of a capillary electrophoretic analyzer over the target analyte product;

electrically contacting the target analyte product with the second conduit;

injecting the target analyte product into the second conduit wherein the injecting comprises applying a potential to the electrically conductive surface and the second conduit; and

performing nucleic acid sequencing on the at least one target analyte product with the capillary electrophoretic analyzer.

33. The method of claim 28, wherein the electrically conductive surface is in electrical communication with a voltage source for application of an electrical potential to the electrically conductive surface.