Droplet-based nucleic acid amplification in a temperature gradient

• US 8,951,732 B2
• Filed: 06/23/2008
• Issued: 02/10/2015
• Est. Priority Date: 06/22/2007
• Status: Active Grant

• Current Assignee: Advanced Liquid Logic, Inc. (Illumina Incorporated)
• Original Assignee: Advanced Liquid Logic, Inc. (Illumina Incorporated)
• Inventors: Pollack, Michael G., Paik, Philip, Eckhardt, Allen, Pamula, Vamsee K.
• Primary Examiner(s): Kim, Young J
• Application Number:
  US12/665,788
• Publication Number:
  US 20100323405A1
• Time in Patent Office: 2,423 Days
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6846 Common amplification features
• CPC Class Codes: C12Q 2527/101 Temperature
• CPC Class Codes: C12Q 2527/15 Gradients

Abstract

A method of amplifying a nucleic acid, the method comprising cycling an amplification-ready droplet through a temperature gradient to locations within the temperature gradient suitable for effecting steps in an amplification reaction.

Claims

1. A method of amplifying a nucleic acid, the method comprising:

(a) providing an amplification-ready droplet loaded operations gap of a droplet actuator, wherein the droplet actuator comprises;

(i) two substrates separated to provide the droplet operations gap therebetween;

(ii) electrodes associated with the substrates and arranged for transporting droplets in the droplet operations gap by electrowetting, the electrodes including an electrode path comprising electrodes arranged to transport droplets along the electrode path; and

(iii) an oil-based filler fluid in the droplet operations gap at least partially surrounding the amplification-ready droplet;

(b) applying heat to the droplet actuator to establish a temperature gradient of gradually varying temperature in the droplet operations gap, wherein the temperature gradient is established using a heating element arranged to heat filler fluid at a locus of the electrode path; and

(c) cycling the amplification-ready droplet by using the electrodes to transport the amplification-ready droplet through the temperature gradient to locations within the temperature gradient having temperatures suitable for effecting steps in an amplification reaction, wherein the droplet is shuttled along the electrode path to different locations within the temperature gradient, and improved amplification patterns based on the results of varying the locations are identified.

2. The method of claim 1 wherein the droplet is shuttled through the oil-based filler fluid along the electrode path to the locations by using the electrodes to conduct electrowetting-mediated droplet operations on the droplet.

3. The method of claim 1 wherein the locations comprise locations having temperatures suitable for:

(a) adjusting the droplet to a temperature selected to denature double stranded nucleic acid in the droplet into single-stranded DNA;

(b) adjusting the droplet temperature selected to permit primers to anneal to their complementary sequences on the nucleic acid template strands; and

(c) adjusting the droplet temperature selected to facilitate extension of the double stranded segment of the nucleic acid to be extended by incorporation of additional nucleotides.

4. The method of claim 1 comprising independently varying anneal location to identify an improved anneal location or temperature.

5. The method of claim 1 comprising independently varying extension location to identify an improved extension location or temperature.

6. The method of claim 1 comprising independently varying denaturation location to identify an improved denaturation location or temperature.

7. The method of claim 1 further comprising executing an improved PCR amplification protocol using the newly identified locations.

8. The method of claim 1 further comprising minimizing denaturation and annealing/extension times to reduce analysis time.

9. The method of claim 1 wherein the temperature gradient is established comprising:

(a) using a heating element arranged to heat filler fluid at a first locus of the electrode path; and

(b) a heat sink element arranged to heat filler fluid at a second locus of the electrode path.

10. The method of claim 1 further comprising mapping the temperature gradient.

11. The method of claim 1 further comprising mapping the temperature gradient to specific electrodes of the electrode path.