Light-controlled tools

Optical control and study of biological processes at the single-cell level in a live organism

Living organisms are made of cells that are capable of responding to external signals by modifying their internal state and subsequently their external environment. Revealing and understanding the spatio-temporal dynamics of these complex interaction networks is the subject of a field known as systems biology. To investigate these interactions (a necessary step before understanding or modelling them) one needs to develop means to control or interfere spatially and temporally with these processes and to monitor their response on a fast timescale (< minute) and with single-cell resolution. In 2012, an EMBO workshop on 'single-cell physiology' (organized by some of us) was held in Paris to discuss those issues in the light of recent developments that allow for precise spatio-temporal perturbations and observations. This review will be largely based on the investigations reported there. We will first present a non-exhaustive list of examples of cellular interactions and developmental pathways that could benefit from these new approaches. We will review some of the novel tools that have been developed for the observation of cellular activity and then discuss the recent breakthroughs in optical super-resolution microscopy that allow for optical observations beyond the diffraction limit. We will review the various means to photo-control the activity of biomolecules, which allow for local perturbations of physiological processes. We will end up this review with a report on the current status of optogenetics: the use of photo-sensitive DNA-encoded proteins as sensitive reporters and efficient actuators to perturb and monitor physiological processes.

Lipid Phase Separation and Protein-Ganglioside Clustering in Supported Bilayers Are Induced by Photorelease of Ceramide

Photolysis of 6-bromo-7-hydroxycoumarinyl-caged ceramide was used to generate ceramide with spatial and temporal control in supported lipid bilayers prepared from mixtures of caged ceramide and phospholipids. The caged ceramide molecules are randomly distributed in fluid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers, and upon photolysis with long wavelength UV light small ordered ceramide domains are formed that phase separate from the bulk fluid membrane. Irradiation of a spatially restricted area leads to the transient formation of ceramide-enriched gel phase domains that equilibrate via lipid diffusion with the surrounding unirradiated membrane. Photorelease of C16-ceramide in supported bilayers prepared from POPC, caged ceramide and the ganglioside GM1 (90:10:1 molar ratio) results in partitioning of a ganglioside-protein complex into the ceramide-enriched domains, modeling some aspects of ceramide's behavior in cells. The photo-uncaging strategy used here for delivery of ceramide in bilayers provides a novel and useful alternative to the enzymatic generation of ceramide in sphingomyelin-containing membranes. The ability to control membrane phase separation behavior and the clustering of membrane-anchored proteins illustrates the potential of photo-uncaging for studying the compartmentalization of ceramide in cellular membranes.

Single-molecule FRET studies of RNA folding: a Diels-Alderase ribozyme with photolabile nucleotide modifications

Enzymology at the single-molecule level by using fluorescence resonance energy transfer (smFRET) offers unprecedented insight into mechanistic aspects of catalytic reactions. Implementing spatiotemporal control of the reaction by using an external trigger is highly valuable in these challenging experiments. Here, we have incorporated a light-cleavable caging moiety into specific nucleotides of the Diels-Alderase (DAse) ribozyme. In this way, the folding energy landscape was significantly perturbed, and the catalytic activity was essentially suppressed. A careful smFRET efficiency histogram analysis at various Mg(2+) ion concentrations revealed an additional intermediate state that is not observed for the unmodified DAse ribozyme. We also observed that only a fraction of DAse molecules returns to the native state upon cleavage of the caged group by UV light. These constructs are attractive model RNA systems for further real-time single-molecule observation of the coupling between conformational changes and catalytic activity.

Mechanism-based design of a photoactivatable firefly luciferase

We developed a photoactivatable firefly luciferase (pfLuc) whose activation can be controlled by light. A photocaged Lys analogue was site-specifically incorporated into fLuc to replace its key catalytic Lys residue, Lys529, rendering fLuc inactive until light-triggered removal of the caging group. This photoinduced gain of luminescence provides a facile approach for assessing the photolysis efficiency of this valuable photosensitive Lys analogue within the context of its carrier protein in vitro and in living cells. We further took advantage of the spatial and temporal activation feature of pfLuc for intracellular measurement of labile ATP levels without impairment of cellular physiology.

Nucleobase-caged peptide nucleic acids: PNA/PNA duplex destabilization and light-triggered PNA/PNA recognition

The 2-(o-nitrophenyl)-propyl (NPP) group is used as caging group to mask the nucleobases adenine and cytosine in N-(2-aminoethyl)glycine peptide nucleic acids (aeg-PNA). The adeninyl and cytosinyl nucleo amino acid building blocks Fmoc-a(NPP) -aeg-OH and Fmoc-c(NPP) -aeg-OH were synthesized and incorporated into PNA sequences by Fmoc solid phase synthesis relying on high stability of the NPP nucleobase protecting group toward Fmoc-cleavage, coupling, capping, and resin cleavage conditions. Removal of the nucleobase caging group was achieved by UV-LED irradiation at 365 nm. The nucleobase caging groups provided sterical crowding effecting the Watson-Crick base pairing, and thereby, the PNA double strand stabilities. Duplex formation can completely be suppressed for complementary PNA containing caging groups in both strands. PNA/PNA recognition can be completely restored by UV light-triggered release of the photolabile protecting group.

Highly discriminating photorelease of anticancer drugs based on hypoxia activatable phototrigger conjugated chitosan nanoparticles

An ultimately selective photorelease system of chitosan-nanoparticles is constructed. Only under unique aspects of tumor-hypoxia physiological conditions, the preliminary locked phototrigger is unlocked by biological reduction to enable the release of the caged drug either by visible light or two-photon near-IR (NIR) excitation. This approach provides a highly discriminating photorelease of anticancer drug to hypoxic tumor cells, but not to healthy normal cells.

Light at the end of the channel: optical manipulation of intrinsic neuronal excitability with chemical photoswitches

Ion channels are transmembrane proteins that control the movement of ions across the cell membrane. They are the molecular machines that make neurons excitable by enabling the initiation and propagation of action potentials (APs). Rapid signaling within and between neurons requires complex molecular processes that couple the sensing of membrane voltage or neurotransmitter release to the fast opening and closing of the ion channel gate. Malfunction of an ion channel's sensing or gating module can have disastrous pathological consequences. However, linking molecular changes to the modulation of neural circuits and ultimately to a physiological or pathological state is not a straightforward task. It requires precise and sophisticated methods of controlling the function of ion channels in their native environment. To address this issue we have developed new photochemical tools that enable the remote control of neuronal ion channels with light. Due to its optical nature, our approach permits the manipulation of the nervous system with high spatial, temporal and molecular precision that will help us understand the link between ion channel function and physiology. In addition, this strategy may also be used in the clinic for the direct treatment of some neuronal disorders.

Photouncaging of ceramides promotes reorganization of liquid-ordered domains in supported lipid bilayers

6-Bromo-7-hydroxycoumarin (Bhc)-caged ceramide (Cer) analogs were incorporated into supported lipid bilayers containing a mixture of coexisting liquid-ordered (Lo) and liquid-disordered (Ld) phases. The release of N-palmitoyl and N-butanoyl-D-erythro-sphingosine (C16- and C4-Cer) by the photolysis of caged Cers using long-wavelength UV light was studied using a combination of atomic force microscopy and fluorescence microscopy. This approach demonstrated the ability to generate Cer with spatial and temporal control, providing an alternative method to the enzymatic generation of Cer. The generation of C16-Cer from Bhc-C16-Cer disrupted the Lo domains, with the incorporation of small fluid-phase regions and the disappearance of some smaller domains. Cer-rich gel-phase domains were not observed, in contrast to results reported by either direct Cer incorporation or enzymatic Cer generation. The photorelease of C4-Cer from Bhc-C4-Cer resulted in qualitatively similar changes in bilayer morphology, with the disappearance of some Lo domains and no evidence of Cer-rich gel domains but with a smaller height difference between the ordered and disordered phases.

Interactions of a photochromic spiropyran with liposome model membranes

The interactions between anionic or zwitterionic liposomes and a water-soluble, DNA-binding photochromic spiropyran are studied using UV/vis absorption and linear dichroism (LD) spectroscopy. The spectral characteristics as well as the kinetics of the thermal isomerization process in the absence and presence of the two different liposome types provide information about the environment and whether or not the spiropyran resides in the liposome membrane. By measuring LD on liposomes deformed and aligned by shear flow, further insight is obtained about interaction and binding geometry of the spiropyran at the lipid membranes. We show that the membrane interactions differ between the two types of liposomes used as well as the isomeric forms of the spiropyran photoswitch.

Switchable gene expression in Escherichia coli using a miniaturized photobioreactor

We present a light-switchable gene expression system for both inducible and switchable control of gene expression at a single cell level in Escherichia coli using a previously constructed light-sensing system. The λ cI repressor gene with an LVA degradation tag was expressed under the control of the ompC promoter on the chromosome. The green fluorescent protein (GFP) gene fused to a λ repressor-repressible promoter was used as a reporter. This light-switchable system allows rapid and reversible induction or repression of expression of the target gene at any desired time. This system also ensures homogenous expression across the entire cell population. We also report the design of a miniaturized photobioreactor to be used in combination with the light-switchable gene expression system. The miniaturized photobioreactor helps to reduce unintended induction of the light receptor due to environmental disturbances and allows precise control over the duration of induction. This system would be a good tool for switchable, homogenous, strong, and highly regulatable expression of target genes over a wide range of induction times. Hence, it could be applied to study gene function, optimize metabolic pathways, and control biological systems both spatially and temporally.

Characterization of one- and two-photon photochemical uncaging efficiency

The idea of using light to unleash biologically active compounds from inert precursors (uncaging) was introduced over 30 years ago. Recent efforts prompted the development of photoremovable protecting groups that have increased photochemical efficiencies for one- and two-photon excitation to allow more sophisticated applications. This requires characterization of one- and two-photon photochemical efficiencies of the uncaging processes.The present chapter focuses on the characterization of one-photon quantum yields and two-photon cross-sections.

o-Fluoroazobenzenes as readily synthesized photoswitches offering nearly quantitative two-way isomerization with visible light

Azobenzene functionalized with ortho-fluorine atoms has a lower energy of the n-orbital of the Z-isomer, resulting in a separation of the E and Z isomers' n→π* absorption bands. Introducing para-substituents allows for further tuning of the absorption spectra of o-fluoroazobenzenes. In particular, electron-withdrawing ester groups give rise to a 50 nm separation of the n→π* transitions. Green and blue light can therefore be used to induce E→Z and Z→E isomerizations, respectively. The o-fluoroazobenzene scaffold is readily synthesized and can be inserted into larger structures via its aryl termini. These new azobenzene derivatives can be switched in both ways with high photoconversions, and their Z-isomers display a remarkably long thermal half-life.

Substitution effect on the one- and two-photon sensitivity of DMAQ "caging" groups

The systematic SAR study of a "caging" group showed a strong influence of the position of the donor dimethylamino group on the efficiency of photolysis of the DMAQ (2-hydroxymethylene-(N,N-dimethylamino)quinoline) caged acetate under one-photon near-UV or two-photon near-IR excitation. Photorelease of l-glutamate by the most efficient 8-DMAQ derivative strongly and efficiently activated glutamate receptors, generating large, fast rising responses similar to those elicited by glutamate photoreleased from the widely used MNI-caged glutamate.