Assays and other reactions involving droplets

• US 10,508,294 B2
• Filed: 10/24/2017
• Issued: 12/17/2019
• 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: Weitz, David A., Agresti, Jeremy, Chu, Liang-Yin, Kim, Jin-Woong, Rowat, Amy, Sommer, Morten, Dantas, Gautam, Church, George
• Primary Examiner(s): Thomas, David C
• Application Number:
  US15/792,218
• Publication Number:
  US 20180119212A1
• Time in Patent Office: 784 Days
• 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 composition comprising a plurality of droplets in an emulsion, wherein a droplet of the plurality of droplets comprises a cell and a particle, wherein the particle comprises one or more reagents for facilitating a reaction on a nucleic acid molecule of the cell.

2. The composition of claim 1, wherein some of the plurality of droplets are unoccupied by a particle.

3. The composition of claim 1, wherein the particle is a gel particle, and wherein the gel particle comprises the one or more reagents for facilitating the reaction on the nucleic acid molecule.

4. The composition of claim 3, wherein the gel particle comprises a hydrogel.

5. The composition of claim 3, wherein the gel particle comprises a polyacrylamide polymer.

6. The composition of claim 1, wherein the one or more reagents comprise a protein or a polypeptide.

7. The composition of claim 1, wherein the one or more reagents comprise a nucleic acid.

8. The composition of claim 1 wherein the one or more reagents comprise a nucleic acid primer.

9. The composition of claim 7, wherein the nucleic acid is coupled to the particle.

10. The composition of claim 9, wherein the nucleic acid is coupled to the particle by an acrydite linkage.

11. The composition of claim 1, wherein the particle is dissolvable such that, when dissolved, the one or more reagents are released into the droplet to carry out the reaction on the nucleic acid molecule from the cell.

12. The composition of claim 1, wherein the reaction is not a polymerase chain reaction.

13. The composition of claim 1, wherein each of at least 75% of the plurality of droplets comprises a particle.

14. The composition of claim 1, wherein the plurality of droplets is monodisperse.

15. The composition of claim 1, wherein the reaction is a nucleic acid extension reaction.

16. The composition of claim 1, wherein the reaction is a reverse transcription reaction.

17. The composition of claim 1, wherein the reaction is a polymerase chain reaction.

18. The composition of claim 1, wherein the droplet further comprises one or more additional reagents selected from the group consisting of a buffer, a salt, dNTPs, a primer, a DNA polymerase, and a reverse transcriptase.

19. The composition of claim 1, wherein at least 90% of the plurality of droplets comprise a particle.

20. The composition of claim 14, wherein the plurality of aqueous droplets is monodisperse with standard deviations less than 20%.

21. The composition of claim 14, wherein the plurality of aqueous droplets is monodisperse with standard deviations less than 15%.

22. The composition of claim 14, wherein the plurality of aqueous droplets is monodisperse with standard deviations less than 10%.

23. The composition of claim 14, wherein the plurality of aqueous droplets is monodispersed with standard deviations less than 2%.

24. The composition of claim 14, wherein the plurality of aqueous droplets is monodispersed with standard deviations less than 1%.

25. The composition of claim 5, wherein the polyacrylamide polymer comprises a cross-linked polyacrylamide polymer.

26. The composition of claim 1, wherein the reaction is whole genome amplification.