Part I
Microfluidics and Biosensors
1 | Droplet-Based Microfluidics for Biological Sample Preparation and Analysis |
Xuefei Sun and Ryan T. Kelly
CONTENTS
1.1 Introduction
1.2 Droplet-Based Operations
1.2.1 Droplet Generation
1.2.2 In-Droplet Reagent Combination and Mixing
1.2.3 Droplet Readout Strategies
1.3 Perspectives for Droplet-Based Microfluidics
1.3.1 Enhanced LC/MS-Based Proteomic Analysis
1.3.2 Single-Cell Chemical Analysis
1.4 Conclusions
References
1.1 INTRODUCTION
Modern biological research often requires massively parallel experiments to analyze a large number of samples in order to find biomarkers, screen drugs, or elucidate complex cellular pathways. These processes frequently involve time-consuming sample preparation and expensive biochemical measurements. Another constraint frequently encountered in bioanalysis is limited amounts of available sample. Microfluidics or lab-on-a-chip platforms offer promise for addressing the challenges encountered in biological research because a large number of small samples can be handled and processed with different functional elements in an automated fashion.
Droplet-based microfluidics, in which reagents of interest are compartmentalized within femtoliter-to-nanoliter-sized aqueous droplets or plugs that are encapsulated and dispersed in an immiscible oil phase, has emerged as an attractive platform for small-volume bioanalysis [1, 2, 3, 4, 5, 6, 7, 8 and 9]. This new platform elegantly addresses challenges encountered with conventional continuous flow systems by, for example, limiting reagent dilution caused by diffusion and Taylor dispersion and minimizing cross contamination and surface-related adsorptive losses [10]. The microdroplets isolated by the immiscible liquid can serve as microreactors, allowing for high-throughput chemical reaction screening and extensive biological research [1]. Droplet-based microfluidics also offers great promise for reliable quantitative analysis because monodisperse microdroplets can be generated with controlled sizes and preserve temporal information that is easily lost to dispersion in continuous flow systems [11,12].
Biological analysis begins with sample selection and preparation. The initial sampling can comprise cell sorting, tissue dissection, or extraction of protein or other analytes of interest from cells or tissues [13]. The biological samples are then prepared by, for example, combining reagents, mixing, incubating, purifying, and/or enriching. Depending on the complexity of the sample, the subsequent analytical measurements can be very simple employing, for example, laser-induced fluorescence (LIF) to detect a single labeled analyte. With more complex samples having multiple analytes of interest, chemical separations including capillary electrophoresis (CE) and liquid chromatography (LC) and information-rich detection methods such as mass spectrometry (MS) become necessary. To date, many operational components for microdroplets have been well developed to perform most of these basic operations. For example, stable aqueous droplets dispersed in an oil phase can be generated using various droplet generator designs for sampling in a confined small volume, the most common of which are the T-junction [14,15] and flow-focusing [16,17] geometries. Addition of reagents to existing droplets can be realized by fusion with other droplets, enabling the initiation and termination of the compartmentalized reactions confined in the microdroplets [18,19]. Rapid mixing of fluids within droplets enables a homogeneous reactive environment to be achieved and can be enhanced by means of chaotic advection [20]. In addition, droplets can be incubated in delay lines [21] or stored in reservoirs [22,23] or traps [24,25] for extended periods of time to complete reactions or facilitate the biological processes.
Droplet-based microfluidic platforms have been successfully applied in a variety of chemical and biological research areas. For example, a droplet-based platform for polymerase chain reaction (PCR) amplification has proven able to significantly improve amplification efficiency over conventional microfluidic formats [26], which is mainly due to the elimination of both reagent dilution and adsorption on the channel surfaces. Droplets have also been employed to encapsulate, sort, and assay single cells [12,27] or microorganisms [24], study enzyme kinetics [11] and protein crystallization [28], and synthesize small molecules and polymeric micro- and nanoparticles.
Although droplet-based microfluidic technology has developed to a degree where droplets can be generated and manipulated with speed, precision, and control, some real challenges still exist that limit the widespread use of these systems. One challenge is how to extract and acquire the enormous chemical information that may be contained in the picoliter-sized droplets. Detection of droplet contents has historically been limited to optical methods such as LIF, while coupling with chemical separations and nonoptical detection has proven difficult. Combining the advantages of droplet-based platforms with more information-rich analytical techniques including LC, CE, and MS can greatly extend their reach. This often requires that the droplets be extracted from the oil phase for downstream analysis and detection.
This chapter focuses primarily on the integrated droplet-based microsystems having the ability to couple with chemical separations and nonoptical detection, allowing for ex situ analysis and identification of the biochemical components contained in the microdroplets. Some unit operations for microdroplets will be briefly introduced, including droplet generation, fusion, and incubation. All approaches and techniques developed for droplet detection, droplet extraction, coupling CE separation, and electrospray ionization (ESI)-MS detection will be reviewed. An example of integrated droplet-based microfluidics, including on-demand droplet generation and fusion, robust and efficient droplet extraction, and a monolithically integrated nanoelectrospray ionization (nanoESI) emitter, will be given to demonstrate its potential for chemical and biological research.
1.2 DROPLET-BASED OPERATIONS
1.2.1 DROPLET GENERATION
Currently, most planar microfluidic droplet generators are designed using T-junction [14,15] and flow-focusing [16,17] geometries, in which small droplets are spontaneously formed at an intersection taking advantage of the interface instability between oil and aqueous streams. Using these approaches, droplets can be generated over a broad range of frequencies ranging from ~0.1 Hz to 10 kHz and using flow rates on the order of 0.1–100 μL/min [29]. Droplet volume and generation frequency depend on several factors, including the physical properties of the immiscible phases, flow rates, and intersection geometry. For a given geometry and solvent composition, flow-focusing and T-junction interfaces exhibit interdependence between flow rate and droplet generation frequency and cannot be easily modulated over short time scales.
For lower frequencies and applications for which the ability to rapidly change droplet size and generation frequency is desirable, on-demand droplet generation strategies become more favorable, as they ensure precise control and fine manipulation of individual droplets. Various approaches have been developed to generate droplets on demand, for example, by carefully balancing the pressure and flow in the system [27], as well as electrical [30] or laser pulsing [31] and piezoelectric actuation [32]. Pneumatic valving has also been explored and has been found to provide facile, independent control over both droplet size and generation frequency [33, 34, 35 and 36]. Galas et al. utilized a single pneumatic valve that was embedded in an active connector and assembled close to a T-junction to regulate the flow of the dispersed phase [33]. Constant pressures were applied on the inlets of two immiscible liquids to drive the flow in the microchannel. Individual droplets were created by briefly opening the valve. The aqueous droplet size depended on the valve actuation time and frequency, as well as the pressure applied at the oil inlet. Therefore, the droplet volume, spacing, and speed could be controlled accurately and independently. This device not only generated periodic sequences of identical droplets but also enabled the production of nonperiodic droplet trains with different droplet sizes or spacing. Lin et al. also reported a similar platform for pneumatic valve–assisted on-demand droplet generation [34]. Negative pressure was applied at the outlet of the device to drive the flow of the two immiscible liquids through the microchannel. The dependence of droplet size on the valve actuation time and applied pressure was investigated. In addition, they utilized several aqueous flow channels, each with independently controlled microvalves, to ...