Enzyme reactions in nanoporous, picoliter volume containers

Nano-Enabled Approaches to Chemical Imaging in Biosystems

Understanding and predicting how biosystems function require knowledge about the dynamic physicochemical environments with which they interact and alter by their presence. Yet, identifying specific components, tracking the dynamics of the system, and monitoring local environmental conditions without disrupting biosystem function present significant challenges for analytical measurements. Nanomaterials, by their very size and nature, can act as probes and interfaces to biosystems and offer solutions to some of these challenges. At the nanoscale, material properties emerge that can be exploited for localizing biomolecules and making chemical measurements at cellular and subcellular scales. Here, we review advances in chemical imaging enabled by nanoscale structures, in the use of nanoparticles as chemical and environmental probes, and in the development of micro- and nanoscale fluidic devices to define and manipulate local environments and facilitate chemical measurements of complex biosystems. Integration of these nano-enabled methods will lead to an unprecedented understanding of biosystem function.

Resource Sharing Controls Gene Expression Bursting

Episodic gene expression, with periods of high expression separated by periods of no expression, is a pervasive biological phenomenon. This bursty pattern of expression draws from a finite reservoir of expression machinery in a highly time variant way, i.e., requiring no resources most of the time but drawing heavily on them during short intense bursts, that intimately links expression bursting and resource sharing. Yet, most recent investigations have focused on specific molecular mechanisms intrinsic to the bursty behavior of individual genes, while little is known about the interplay between resource sharing and global expression bursting behavior. Here, we confine Escherichia coli cell extract in both cell-sized microfluidic chambers and lipid-based vesicles to explore how resource sharing influences expression bursting. Interestingly, expression burst size, but not burst frequency, is highly sensitive to the size of the shared transcription and translation resource pools. The intriguing implication of these results is that expression bursts are more readily amplified than initiated, suggesting that burst formation occurs through positive feedback or cooperativity. When extrapolated to prokaryotic cells, these results suggest that large translational bursts may be correlated with large transcriptional bursts. This correlation is supported by recently reported transcription and translation bursting studies in E. coli. The results reported here demonstrate a strong intimate link between global expression burst patterns and resource sharing, and they suggest that bursting plays an important role in optimizing the use of limited, shared expression resources.

Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy

Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure-function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2-amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme-substrate interactions, enzyme-substrate active complex formation, and protein folding-binding interactions.

Fabrication of nanoporous membranes for tuning microbial interactions and biochemical reactions

New strategies for combining conventional photo- and soft-lithographic techniques with high-resolution patterning and etching strategies are needed in order to produce multiscale fluidic platforms that address the full range of functional scales seen in complex biological and chemical systems. The smallest resolution required for an application often dictates the fabrication method used. Micromachining and micropowder blasting yield higher throughput, but lack the resolution needed to fully address biological and chemical systems at the cellular and molecular scales. In contrast, techniques such as electron beam lithography or nanoimprinting allow nanoscale resolution, but are traditionally considered costly and slow. Other techniques such as photolithography or soft lithography have characteristics between these extremes. Combining these techniques to fabricate multiscale or hybrid fluidics allows fundamental biological and chemical questions to be answered. In this study, a combination of photolithography and electron beam lithography are used to produce two multiscale fluidic devices that incorporate porous membranes into complex fluidic networks in order to control the flow of energy, information, and materials in chemical form. In the first device, materials and energy were used to support chemical reactions. A nanoporous membrane fabricated with e-beam lithography separates two parallel, serpentine channels. Photolithography was used to pattern microfluidic channels around the membrane. The pores were written at 150 nm and reduced in size with silicon dioxide deposition from plasma enhanced chemical vapor deposition and atomic layer deposition. Using this method, the molecular weight cutoff of the membrane can be adapted to the system of interest. In the second approach, photolithography was used to fabricate 200 nm thin pores. The pores confined microbes and allowed energy replenishment from a media perfusion channel. The same device can be used for study of intercellular communication via the secretion and uptake of signal molecules. Pore size was tested with 750 nm fluorescent polystyrene beads and fluorescein dye. The 200 nm polydimethylsiloxane pores were shown to be robust enough to hold 750 nm beads while under pressure, but allow fluorescein to diffuse across the barrier. Further testing showed that extended culture of bacteria within the chambers was possible. These two examples show how lithographically defined porous membranes can be adapted to two unique situations and used to tune the flow of chemical energy, materials, and information within a microfluidic network.

Fabrication of nanoporous membranes for tuning microbial interactions and biochemical reactions

New strategies for combining conventional photo- and soft-lithographic techniques with high-resolution patterning and etching strategies are needed in order to produce multiscale fluidic platforms that address the full range of functional scales seen in complex biological and chemical systems. The smallest resolution required for an application often dictates the fabrication method used. Micromachining and micropowder blasting yield higher throughput, but lack the resolution needed to fully address biological and chemical systems at the cellular and molecular scales. In contrast, techniques such as electron beam lithography or nanoimprinting allow nanoscale resolution, but are traditionally considered costly and slow. Other techniques such as photolithography or soft lithography have characteristics between these extremes. Combining these techniques to fabricate multiscale or hybrid fluidics allows fundamental biological and chemical questions to be answered. In this study, a combination of photolithography and electron beam lithography are used to produce two multiscale fluidic devices that incorporate porous membranes into complex fluidic networks in order to control the flow of energy, information, and materials in chemical form. In the first device, materials and energy were used to support chemical reactions. A nanoporous membrane fabricated with e-beam lithography separates two parallel, serpentine channels. Photolithography was used to pattern microfluidic channels around the membrane. The pores were written at 150 nm and reduced in size with silicon dioxide deposition from plasma enhanced chemical vapor deposition and atomic layer deposition. Using this method, the molecular weight cutoff of the membrane can be adapted to the system of interest. In the second approach, photolithography was used to fabricate 200 nm thin pores. The pores confined microbes and allowed energy replenishment from a media perfusion channel. The same device can be used for study of intercellular communication via the secretion and uptake of signal molecules. Pore size was tested with 750 nm fluorescent polystyrene beads and fluorescein dye. The 200 nm polydimethylsiloxane pores were shown to be robust enough to hold 750 nm beads while under pressure, but allow fluorescein to diffuse across the barrier. Further testing showed that extended culture of bacteria within the chambers was possible. These two examples show how lithographically defined porous membranes can be adapted to two unique situations and used to tune the flow of chemical energy, materials, and information within a microfluidic network.

Modular microfluidics for point-of-care protein purifications

Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured to suit a variety of fluidic operations or biochemical processes. We demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.

Droplet microfluidics in (bio)chemical analysis

Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation.

Multi-input regulation and logic with T7 promoters in cells and cell-free systems

Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on native host promoters for the construction of circuit elements, such as logic gates, can make the implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell-free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell-free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters function in an E. coli cell-free protein expression system. Our results expand the utility of T7 promoters in cell based as well as cell-free synthetic biology applications.