Digital Microfluidics for Automated Proteomic Processing

Summary

Digital Microfluidics is a technique characterized by the manipulation of discrete droplets (~nL - mL) on an array of electrodes by the application of electrical fields. It is well-suited for carrying out rapid, sequential, miniaturized automated biochemical assays. Here, we report a platform capable of automating several proteomic processing steps.

Abstract

Clinical proteomics has emerged as an important new discipline, promising the discovery of biomarkers that will be useful for early diagnosis and prognosis of disease. While clinical proteomic methods vary widely, a common characteristic is the need for (i) extraction of proteins from extremely heterogeneous fluids (i.e. serum, whole blood, etc.) and (ii) extensive biochemical processing prior to analysis. Here, we report a new digital microfluidics (DMF) based method integrating several processing steps used in clinical proteomics. This includes protein extraction, resolubilization, reduction, alkylation and enzymatic digestion. Digital microfluidics is a microscale fluid-handling technique in which nanoliter-microliter sized droplets are manipulated on an open surface. Droplets are positioned on top of an array of electrodes that are coated by a dielectric layer - when an electrical potential is applied to the droplet, charges accumulate on either side of the dielectric. The charges serve as electrostatic handles that can be used to control droplet position, and by biasing a sequence of electrodes in series, droplets can be made to dispense, move, merge, mix, and split on the surface. Therefore, DMF is a natural fit for carrying rapid, sequential, multistep, miniaturized automated biochemical assays. This represents a significant advance over conventional methods (relying on manual pipetting or robots), and has the potential to be a useful new tool in clinical proteomics.

Mais J. Jebrail, Vivienne N. Luk, and Steve C. C. Shih contributed equally to this work.

Sergio L. S. Freire's current address is at the University of the Sciences in Philadelphia located at 600 South 43rd Street, Philadelphia, PA 19104.

Protocol

Part 1: Device Fabrication

1. Clean glass substrates in Piranha solution (3:1 conc. sulfuric acid:30% hydrogen peroxide). Leave the substrates in Piranha solution for 10 min with frequent agitation.
2. After rinsing in deionized (DI) water and drying the substrates with N₂ gas, place the substrates inside the electron beam chamber for chromium deposition (thickness of 250 nm).
3. To dehydrate the chromium-coated substrate, rinse in isopropanol and then bake on a hot plate for 5 min at 115°C.
4. Dry the substrates and prime with hexamethyldisilazane (HMDS) by spin-coating (30 s, 3000 rpm). Spin-coat again (using identical param....

Discussion

The lack of standardized sample handling and processing in proteomics is a major limitation for the field. In addition, conventional macroscale sample handling involves multiple containers and solution transfers, which can lead to sample loss and contamination. A potential solution to these problems is to form integrated systems for sample processing relying on digital microfluidics¹ (DMF). In previous work, DMF was shown to be useful for efficient removal of unwanted contaminants in heterogeneous protein-cont.......