Assays and other reactions involving droplets

• US 9,029,085 B2
• Filed: 03/07/2008
• Issued: 05/12/2015
• Est. Priority Date: 03/07/2007
• Status: Active Grant

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Agresti, Jeremy, Chu, Liang-Yin, Weitz, David A., Kim, Jin-Woong, Rowat, Amy, Sommer, Morten, Dantas, Gautam, Church, George
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): THOMAS, DAVID C
• Application Number:
  US12/529,926
• Publication Number:
  US 20100136544A1
• Time in Patent Office: 2,622 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: B01F 2101/23 Mixing of laboratory samples e.g. in preparation of analysing or testing properties of materials
• CPC Class Codes: B01F 23/41 Emulsifying
• CPC Class Codes: B01F 23/4105 Methods of emulsifying
• CPC Class Codes: B01F 33/3011 using a sheathing stream of a fluid surrounding a central stream of a different fluid, e.g. for reducing the cross-section of the central stream or to produce droplets from the central stream
• CPC Class Codes: B01F 33/3021 the components to be mixed being combined in a single independent droplet, e.g. these droplets being divided by a non-miscible fluid or consisting of independent droplets
• CPC Class Codes: B01J 13/0052 Preparation of gels
• CPC Class Codes: B01J 13/0065 containing an organic phase
• 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: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C12Q 2563/159 Microreactors, e.g. emulsion PCR or sequencing, droplet PCR, microcapsules, i.e. non-liquid containers with a range of different permeability's for different reaction components
• CPC Class Codes: G01N 15/1404 Handling flow, e.g. hydrodynamic focusing
• CPC Class Codes: G01N 2015/1006 for cytology

Abstract

The present invention generally relates to droplets and/or emulsions, such as multiple emulsions. In some cases, the droplets and/or emulsions may be used in assays, and in certain embodiments, the droplet or emulsion may be hardened to form a gel. In some aspects, a heterogeneous assay can be performed using a gel. For example, a droplet may be hardened to form a gel, where the droplet contains a cell, DNA, or other suitable species. The gel may be exposed to a reactant, and the reactant may interact with the gel and/or with the cell, DNA, etc., in some fashion. For example, the reactant may diffuse through the gel, or the hardened particle may liquefy to form a liquid state, allowing the reactant to interact with the cell. As a specific example, DNA contained within a gel particle may be subjected to PCR (polymerase chain reaction) amplification, e.g., by using PCR primers able to bind to the gel as it forms. As the DNA is amplified using PCR, some of the DNA will be bound to the gel via the PCR primer. After the PCR reaction, unbound DNA may be removed from the gel, e.g., via diffusion or washing. Thus, a gel particle having bound DNA may be formed in one embodiment of the invention.

Claims

1. A method, comprising:

providing a fluidic droplet containing a plurality of species;

causing the fluidic droplet to form a gel droplet containing the plurality of species, wherein the plurality of species are bound to the gel droplet;

exposing the gel droplet to a reactant, thereby exposing the plurality of species within the gel droplet to a reactant which is reactive with at least one of the plurality of species; and

synthesizing a reaction product from at least one of the plurality of species using the reactant wherein the reaction product is bound to the gel droplet.

2. The method of claim 1, wherein the plurality of species are nucleic acids and the reactant is a fluorescent entity able to bind to at least a portion of the nucleic acids.

3. The method of claim 1, wherein the plurality of species are nucleic acids and the reactant is a polynucleotide.

4. The method of claim 3, wherein the nucleic acids are primers.

5. The method of claim 3, wherein the nucleic acids comprise a 5′

acrydite moiety.

6. The method of claim 1, wherein the fluidic droplet forms part of an emulsion.

7. The method of claim 1, wherein the fluidic droplet is contained within a carrying fluid.

8. The method of claim 1, wherein causing the fluidic droplet to form a gel droplet comprises altering the temperature of the fluidic droplet.

9. The method of claim 1, wherein causing the fluidic droplet to form a gel droplet comprises exposing the fluidic droplet to an agent that causes hardening to occur.

10. The method of claim 1, wherein causing the fluidic droplet to form a gel droplet comprises fusing the fluidic droplet with a second fluidic droplet.

11. The method of claim 1, wherein the act of exposing the plurality of species within the gel droplet to a reactant comprises exposing the gel droplet to the reactant, and allowing the reactant to diffuse into the gel droplet to the plurality of species.

12. The method of claim 1, wherein the act of exposing the plurality of species within the gel droplet to a reactant comprises causing the gel droplet to form a liquid state, and causing the reactant to enter the liquefied droplet.

18. The method of claim 1, wherein the plurality of species are polynucleotides.

19. The method of claim 18, wherein the polynucleotides are oligonucleotides.

20. The method of claim 1, wherein the reactant is a polynucleotide template.

21. The method of claim 1, wherein the using the reactant comprises using the reactant as a template to produce the reaction product.

13. A method, comprising:

exposing a gel droplet comprising a plurality of nucleic acids to a polynucleotide different from the plurality of nucleic acids, wherein the plurality of nucleic acids are bound to the gel droplet; and

growing the plurality of nucleic acids within the gel droplet to form an extended nucleic acid using the polynucleotide as a template, wherein the extended nucleic acid is bound to the gel droplet.

14. The method of claim 13, wherein the plurality of nucleic acids are primers.

15. The method of claim 13, wherein the plurality of nucleic acids are primers comprising a 5′

acrydite moiety.

16. The method of claim 13, wherein the act of growing the plurality of nucleic acids within the gel droplet, using the polynucleotide as a template occurs using a PCR chain reaction.

17. The method of claim 13, comprising thermally cycling the gel droplet.