Sequence-independent and reversible photocontrol of transcription/expression systems using a photosensitive nucleic acid binder

Linking genotype and phenotype in protein synthesizing liposomes with external supply of resources

Reconstituting an elementary gene expression system inside self-assembled lipid vesicles to mimic the cellular synthesis machinery is at the core of the development of a minimal cell following a bottom-up synthetic biology approach. The ability to operate the expression of multiple genes in a controlled manner and to generate the output proteins with predictable dynamics in liposomes relies on the link between genotype and phenotype. Here, we established this link in surface-tethered liposomes producing proteins from a linear DNA template using a reconstituted transcription/translation/aminoacylation apparatus fuelled by external supply of feedstock. The amounts of entrapped DNA molecules and synthesized proteins were visualized by fluorescence confocal microscopy in individual vesicles. We showed that there exists no linear correlation between the amount of encapsulated genes and the level of output proteins, which is a consequence of the compositional heterogeneity between liposomes due to the low-copy number of some constituents, as well as interfacing differences with the nutrient-containing environment. In order to decouple gene activity from those sources of variability and, thus, infer the probabilistic occupancy of transcriptionally active genes in protein synthesizing liposomes, we developed a dual gene expression assay consisting of the production of two fluorescent reporter proteins of distinguishable colors from two different DNA templates. The stochastic color-coding of the vesicles was analyzed and compared to the color pattern expected from a Poisson distribution of encapsulated genes. Unexpectedly, we found that the apparent number of transcriptionally active DNA molecules in liposomes corresponds only to ca. 10% of the bulk concentration. We believe that our study provides new insights about the relationship between the genotype and phenotype in protein synthesizing liposomes, which is of primary importance toward the construction of a programmable artificial cell implemented with regulatory gene networks of predictable dynamics.

Modification-free photocontrol of β-lactam conversion with spatiotemporal resolution

β-Lactams can be converted into β-amino acids by β-lactamase, a bacterial enzyme, leading to significant change in the biological function of the substrate molecules. Here we describe a method for photocontrol of β-lactam conversion without gene nor enzyme modification. This is achieved by the addition of a cationic photosensitive surfactant, AzoTAB, to a gene expression medium containing DNA coding for β-lactamase, the enzyme capable of the desired conversion. In the absence of UV (365 nm) or after illumination by blue light (480 nm) for 4 min, conversion of β-lactam is strongly reduced while the application of UV for 4 min results in a strong enhancement of substrate conversion. Several cycles of activation/inhibition are obtained upon successive UV/blue light illuminations. When both reconstituted photoresponsive gene expression medium and β-lactamase substrate are encapsulated in independent microfluidic chambers, selective UV illumination results in spatially resolved activation of substrate conversion.

Photo-actuation of liquids for light-driven microfluidics: state of the art and perspectives

Using light to control liquid motion is a new paradigm for the actuation of microfluidic systems. We review here the different principles and strategies to induce or control liquid motion using light, which includes the use of radiation pressure, optical tweezers, light-induced wettability gradients, the thermocapillary effect, photosensitive surfactants, the chromocapillary effect, optoelectrowetting, photocontrolled electroosmotic flows and optical dielectrophoresis. We analyze the performance of these approaches to control using light many kinds of microfluidic operations involving discrete pL- to μL-sized droplets (generation, driving, mixing, reaction, sorting) or fluid flows in microchannels (valve operation, injection, pumping, flow rate control). We show that a complete toolbox is now available to control microfluidic systems by light. We finally discuss the perspectives of digital optofluidics as well as microfluidics based on all optical fluidic chips and optically reconfigurable devices.

Light-controlled tools

Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.

UV-induced bursting of cell-sized multicomponent lipid vesicles in a photosensitive surfactant solution

We study the behavior of multicomponent giant unilamellar vesicles (GUVs) in the presence of AzoTAB, a photosensitive surfactant. GUVs are made of an equimolar ratio of dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) and various amounts of cholesterol (Chol), where the lipid membrane shows a phase separation into a DPPC-rich liquid-ordered (L(o)) phase and a DOPC-rich liquid-disordered (L(d)) phase. We find that UV illumination at 365 nm for 1 s induces the bursting of a significant fraction of the GUV population. The percentage of UV-induced disrupted vesicles, called bursting rate (Y(burst)), increases with an increase in [AzoTAB] and depends on [Chol] in a non-monotonous manner. Y(burst) decreases when [Chol] increases from 0 to 10 mol % and then increases with a further increase in [Chol], which can be correlated with the phase composition of the membrane. We show that Y(burst) increases with the appearance of solid domains ([Chol] = 0) or with an increase in area fraction of L(o) phase (with increasing [Chol] ≥ 10 mol %). Under our conditions (UV illumination at 365 nm for 1 s), maximal bursting efficiency (Y(burst) = 53%) is obtained for [AzoTAB] = 1 mM and [Chol] = 40 mol %. Finally, by restricting the illumination area, we demonstrate the first selective UV-induced bursting of individual target GUVs. These results show a new method to probe biomembrane mechanical properties using light as well as pave the way for novel strategies of light-induced drug delivery.

Enhancement of DNA compaction by negatively charged nanoparticles: effect of nanoparticle size and surfactant chain length

We study the compaction of genomic DNA by a series of alkyltrimethylammonium bromide surfactants having different hydrocarbon chain lengths n: dodecyl-(DTAB, n=12), tetradecyl-(TTAB, n=14) and hexadecyl-(CTAB, n=16), in the absence and in the presence of negatively charged silica nanoparticles (NPs) with a diameter in the range 15-100 nm. We show that NPs greatly enhance the ability of all cationic surfactants to induce DNA compaction and that this enhancement increases with an increase in NP diameter. In the absence of NP, the ability of cationic surfactants to induce DNA compaction increases with an increase in n. Conversely, in the presence of NPs, the enhancement of DNA compaction increases with a decrease in n. Therefore, although CTAB is the most efficient surfactant to compact DNA, maximal enhancement by NPs is obtained for the largest NP diameter (here, 100 nm) and the smallest surfactant chain length (here, DTAB). We suggest a mechanism where the preaggregation of surfactants on NP surface mediated by electrostatic interactions promotes cooperative binding to DNA and thus enhances the ability of surfactants to compact DNA. We show that the amplitude of enhancement is correlated with the difference between the surfactant concentration corresponding to aggregation on DNA alone and that corresponding to the onset of adsorption on nanoparticles.

Photoreversible fragmentation of a liquid interface for micro-droplet generation by light actuation

We describe a method to induce by light a reversible switch from a continuous two-phase laminar flow to a droplet generating regime, in microfluidic devices with a usual water-in-oil flow focusing geometry. It consists in adding a photosensitive surfactant to the aqueous phase to modulate using light the interfacial energy between flowing liquids and the microfluidic substrate. We show that UV irradiation induces liquid fragmentation into monodisperse water microdroplets and that many cycles of reversible and rapid switches (<2 s) between continuous laminar flows and stable droplet regimes can be realized. By spatially controlling the application of the light stimulus, we also demonstrate the first spatially resolved remote induction of droplet generation.

Azobenzene photoswitches for biomolecules

The photoisomerization of azobenzene has been known for almost 75 years but only recently has this process been widely applied to biological systems. The central challenge of how to productively couple the isomerization process to a large functional change in a biomolecule has been met in a number of instances and it appears that effective photocontrol of a large variety of biomolecules may be possible. This critical review summarizes key properties of azobenzene that enable its use as a photoswitch in biological systems and describes strategies for using azobenzene photoswitches to drive functional changes in peptides, proteins, nucleic acids, lipids, and carbohydrates (192 references).

Oil microsealing: a robust micro-compartmentalization method for on-chip chemical and biological assays

A simple and robust method to compartmentalize aqueous solutions into an array of independent microchambers is presented. The array of microchambers fabricated in poly(dimethylsiloxane) are filled with the sample solution through a microfluidic channel and then sealed with oil to isolate the microchambers from each other. A water reservoir close to the microchambers allows the maintainance and incubation of sub-nanoliter solutions (e.g., at 37 °C) within the chambers for hours without any problem of evaporation. Once assembled, the device is self-sustainable and can be used for different application purposes. As a demonstration, the device configuration is shown to be suitable for spatiotemporal control of the inner solution conditions by light stimulation through a photomask. This method was applied for the generation of regular EmGFP (emerald green fluorescent protein) expression arrays, selective photobleaching, photopatterning of calcium concentration, and cell culture in independent microchambers.