Manipulation of Microparticles In Microfluidic Systems

• US 20110118139A1
• Filed: 01/27/2011
• Published: 05/19/2011
• Est. Priority Date: 02/23/1999
• Status: Active Grant

• Current Assignee: Caliper Life Sciences Incorporated (Revvity, Inc.)
• Original Assignee: Caliper Life Sciences Incorporated (Revvity, Inc.)
• Inventors: Knapp, Michael R., Kopf-Sill, Anne R., Mehta, Tammy Burd, Gallagher, Steve, Bousse, Luc J., Nikiforov, Theo T., Chow, Andrea W., Parce, J. Wallace
• Granted Patent: US 9,101,928 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2400/0409 centrifugal forces
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/043 magnetic forces
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502715 characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• 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 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: C12Q 2563/173 staining/intercalating agent, e.g. ethidium bromide
• CPC Class Codes: C12Q 2565/629 : being a microfluidic device
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2035/00574 : Means for distributing beads
• CPC Class Codes: G01N 27/44756 : Apparatus specially adapted therefor
• CPC Class Codes: G01N 35/0098 : involving analyte bound to insoluble magnetic carrier, e.g. using magnetic separation magnetic particles used in immunoassays G01N33/54326; magnetic separation in general B03C
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]

Abstract

An array of transportable particle sets is used in a microfluidic device for performing chemical reactions in the microfluidic device. The microfluidic device comprises a main channel and intersecting side channels, the main channel and side channels forming a plurality of intersections. The array of particle sets is disposed in the main channel, and the side channels are coupled to reagents. As the particle sets are transported through the intersections of the main channel and the side channels, reagents are flowed through the side channels into contact with each array member (or selected array members), thereby providing a plurality of chemical reactions in the microfluidic system.

Claims

1. A method of performing a plurality of chemical reactions in a microfluidic device, the method comprising:

providing a microfluidic device comprising an interior cavity, the cavity comprising a main channel and first and second side channels, the first and second side channels intersecting the main channel, thereby forming first and second channel intersections;

providing an array comprising first and second sets of particles within the interior cavity;

providing first and second liquid reagents within the interior cavity;

transporting the first set of particles through the main channel into the first channel intersection;

flowing the first liquid reagent through the first side channel into the first channel intersection, wherein the first liquid reagent contacts the first set of particles in the main channel, thereby providing a first chemical reaction in the microfluidic device;

transporting the first set of particles through the main channel into the second channel intersection; and

flowing the second liquid reagent through the second side channel into the second channel intersection, wherein the second liquid reagent contacts the first set of particles in the main channel, thereby providing a second chemical reaction in the microfluidic device.

2. The method of claim 1, the method further comprising:

transporting the second set of particles through the main channel into the first channel intersection; and

flowing the first liquid reagent through the first side channel into the first channel intersection, wherein the first reagent contacts the second set of particles in the main channel.

3. The method of claim 1, the method further comprising detecting a signal resulting from contact of the first set of particles by one of the first and the second liquid reagents.

4. The method of claim 1, the method further comprising detecting a plurality of signals resulting from contact of the first set of particles by the first and the second liquid reagents.

5. The method of claim 2, the method further comprising detecting a plurality of signals resulting from contact of the first and second sets of particles by the first liquid reagent.

6. The method of claim 5, wherein detecting a plurality of signals resulting from contact of the first and second sets of particles by the first liquid reagent comprises detecting simultaneous or sequential signal emissions from the first and second sets of particles.

7. The method of claim 1, wherein at least one of the first and second liquid reagents is a nucleic acid sequencing reagent selected from the group consisting of a liquid solution comprising a nucleotide, a liquid solution comprising a polymerase, a liquid solution comprising a dNTP or ddNTP, a liquid solution comprising a fluorescently labeled nucleotide, a liquid solution comprising a nucleotide analog, a liquid solution comprising a sufurylase, a liquid solution comprising an apyrase, a liquid solution comprising inorganic phosphate, a liquid solution comprising ATP, a liquid solution comprising a thermostable polymerase, a liquid solution comprising an endonuclease, a liquid solution comprising an exonuclease, a liquid solution comprising Mg++, a liquid solution comprising a molecular crowding agent, a liquid solution comprising a buffer, a liquid solution comprising an intercalating dye, a liquid solution comprising a reducing agent, a liquid solution comprising a phosphatase or an enzyme with phosphatase activity, a liquid solution comprising a salt, and combinations thereof.

8. The method of claim 1, wherein at least one of the first and second liquid reagents is a binding reagent selected from the group consisting of a first nucleic acid that is fully or partially complementary to a second nucleic acid complexed with at least one of the first and second particle sets, a first protein that specifically binds to one or more component of at least one of the first and second particle sets, a first antibody that specifically binds to one or more component of at least one of the first and second particle sets, a binding buffer, a blocking reagent, an immunoassay reagent, a labeled probe nucleic acid, and combinations thereof;

and wherein the method further comprises flowing the at least one of the first and second liquid reagents into contact with at least one of the first and second sets of particles and detecting resulting binding of the liquid reagent to the at least one of the first and second sets of particles.

9. The method of claim 1, wherein at least one of the first and second sets of particles comprises at least one set of nucleic acid templates and at least one set of nucleic acid primers, wherein at least one of the first and second liquid reagents comprises one or more nucleotide analogs, and wherein at least one of the first and the second chemical reactions comprises adding at least one of the one or more nucleotide analogs to at least one member of the set of primers.

10. The method of claim 9, wherein the one or more nucleotide analogs comprise reversible chain-terminating nucleotide analogs.

11. The method of claim 10, wherein the reversible chain-terminating nucleotide analogs comprise a compound having formula (I) or formula (II):

12. The method of claim 1, wherein at least one of the first and second sets of particles comprises at least one set of nucleic acid templates and at least one set of nucleic acid primers, wherein at least one of the liquid reagents comprises one or more nucleotides, and wherein at least one of the first and second chemical reactions results in a double-stranded nucleic acid region, the method further comprising flowing an intercalating dye into contact with the double-stranded nucleic acid region, which intercalating dye intercalates into the double-stranded region.

13. The method of claim 1, further comprising adding an intercalating dye to a nucleic acid complementary to a template molecule bound to one or more of the first and second sets of particles, the method further comprising detecting the intercalating dye.

14. The method of claim 1, the cavity further comprising third and fourth side channels, the third and fourth side channels intersecting the main channel, thereby forming third and fourth channel intersections, the method further comprising:

providing third and fourth liquid reagents, wherein each of the first, second, third, and fourth liquid reagents comprises one of A, G, C, or T nucleotides;

transporting the first set of particles through each of the third and fourth channel intersections;

flowing the third reagent through the third side channel into the third channel intersection; and

flowing the fourth reagent through the fourth side channel into the fourth channel intersection,

wherein each of the third and fourth liquid reagents contacts the first set of particles in the main channel.

15. The method of claim 2, the cavity further comprising third and fourth side channels, the third and fourth side channels intersecting the main channel, thereby forming third and fourth channel intersections, the method further comprising:

providing third and fourth liquid reagents, wherein each of the first, second, third, and fourth liquid reagents comprises one of A, G, C, or T nucleotides;

transporting the second set of particles through each of the second, third, and fourth channel intersections;

flowing the second reagent through the second side channel into the third channel intersection;

flowing the third reagent through the third side channel into the third channel intersection; and

flowing the fourth reagent through the fourth side channel into the fourth channel intersection,

wherein each of the second, third, and fourth liquid reagents contacts the second set of particles in the main channel.

16. The method of claim 1, further comprising sequencing by synthesis, the sequencing by synthesis method comprising addition of an intercalating dye to a nucleic acid complementary to a template molecule bound to an array member, the method further comprising detecting the intercalating dye.

17. The method of claim 1, further comprising sequencing by synthesis, the method comprising addition of a chain terminator to a nucleic acid complementary to a template molecule bound to an array member, the chain terminator comprising a label.

18. The method of claim 1, further comprising sequencing by synthesis, the method comprising addition of a reversible chain terminator to a nucleic acid complementary to a template molecule bound to an array member, the reversible chain terminator comprising a label, and the method further comprising cleavage of the reversible chain terminator.

20. The method of claim 16, the method further comprising:

providing a second set of particles within the interior cavity;

transporting the second set of particles through the main channel into the first channel intersection;

flowing the first liquid reagent through the first side channel into the first channel intersection, wherein the first liquid reagent contacts the second set of particles in the main channel;

transporting the second set of particles through the main channel into the second channel intersection;

flowing the second liquid reagent through the second side channel into the second channel intersection, wherein the second liquid reagent contacts the second set of particles in the main channel;

transporting the second set of particles through the main channel into the third channel intersection;

flowing the third liquid reagent through the third side channel into the third channel intersection, wherein the third liquid reagent contacts the second set of particles in the main channel;

transporting the second set of particles through the main channel into the fourth channel intersection; and

flowing the fourth liquid reagent through the fourth side channel into the fourth channel intersection, wherein the fourth liquid reagent contacts the second set of particles in the main channel.

19. A method of performing a plurality of chemical reactions in a microfluidic device, the method comprising:

providing a microfluidic device comprising an interior cavity, the cavity comprising a main channel and first, second, third, and fourth side channels, the first, second, third, and fourth side channels intersecting the main channel, thereby forming first, second, third, and fourth channel intersections;

providing a first set of particles within the interior cavity;

providing first, second, third, and fourth liquid reagents within the interior cavity, the reagents comprising one of A, G, C, or T nucleotides;

transporting the first set of particles through the main channel into the first channel intersection;

flowing the first liquid reagent through the first side channel into the first channel intersection, wherein the first liquid reagent contacts the first set of particles in the main channel;

transporting the first set of particles through the main channel into the second channel intersection;

flowing the second liquid reagent through the second side channel into the second channel intersection, wherein the second liquid reagent contacts the first set of particles in the main channel;

transporting the first set of particles through the main channel into the third channel intersection;

flowing the third liquid reagent through the third side channel into the third channel intersection, wherein the third liquid reagent contacts the first set of particles in the main channel;

transporting the first set of particles through the main channel into the fourth channel intersection; and

flowing the fourth liquid reagent through the fourth side channel into the fourth channel intersection, wherein the fourth liquid reagent contacts the first set of particles in the main channel;

thereby providing a plurality of chemical reactions in the microfluidic device.