Optimized CRISPR-RfxCas13d system for RNA targeting in zebrafish embryos.

CRISPR-Cas systems have been used to induce DNA mutagenesis for gene function discovery. However, the development of tools to eliminate RNAs provides complementary and unique approaches to disrupt gene expression. Here, we present a workflow to perform specific, efficient, and cost-effective mRNA knockdown in zebrafish embryos using our in vivo optimized CRISPR-RfxCas13d (CasRx) system. Although the described protocol focuses on mRNA knockdown in zebrafish embryos, it can also be applied to other vertebrates. For complete details on the use and execution of this protocol, please refer to Kushawah et al. (2020).

Complementary Syntheses Giving Access to a Full Suite of Differentially Substituted Phthalocyanine-Porphyrin Hybrids.

Phthalocyanines and porphyrins are often the scaffolds of choice for use in widespread applications. Synthetic advances allow bespoke derivatives to be made, tailoring their properties. The selective synthesis of unsymmetrical systems, particularly phthalocyanines, has remained a significant unmet challenge. Porphyrin-phthalocyanine hybrids offer the potential to combine the favorable features of both parent structures, but again synthetic strategies are poorly developed. Here we demonstrate strategies that give straightforward, controlled access to differentially substituted meso-aryl-tetrabenzotriazaporphyrins by reaction between an aryl-aminoisoindolene (A) initiator and a complementary phthalonitrile (B). The choice of precursors and reaction conditions allows selective preparation of 1:3 Ar-ABBB and, uniquely, 2:2 Ar-ABBA functionalized hybrids.

CRISPR-Cas13d Induces Efficient mRNA Knockdown in Animal Embryos.

Early embryonic development is driven exclusively by maternal gene products deposited into the oocyte. Although critical in establishing early developmental programs, maternal gene functions have remained elusive due to a paucity of techniques for their systematic disruption and assessment. CRISPR-Cas13 systems have recently been employed to degrade RNA in yeast, plants, and mammalian cell lines. However, no systematic study of the potential of Cas13 has been carried out in an animal system. Here, we show that CRISPR-RfxCas13d (CasRx) is an effective and precise system to deplete specific mRNA transcripts in zebrafish embryos. We demonstrate that zygotically expressed and maternally provided transcripts are efficiently targeted, resulting in a 76% average decrease in transcript levels and recapitulation of well-known embryonic phenotypes. Moreover, we show that this system can be used in medaka, killifish, and mouse embryos. Altogether, our results demonstrate that CRISPR-RfxCas13d is an efficient knockdown platform to interrogate gene function in animal embryos.

Synthesis and Dimerization Studies of a Lipophilic Photoresponsive Aryl-Extended Tetraurea-Calix[4]pyrrole.

We describe the syntheses of the lipophilic aryl-extended α,α,α,α-tetraurea-phenyl-calix[4]pyrrole 1, featuring four appended azo-phenyl groups with two tert-butoxy carbonyl meta-substituents and its photo-inactive counterpart 2. In CD2 Cl2 solutions, both tetraurea-calix[4]pyrroles self-assemble into dimeric capsules by encapsulating one molecule of a suitable bis-N-oxide or two molecules of a mono-N-oxide. The dimeric capsules are mainly stabilized by a cyclic array of sixteen hydrogen bonds established between the eight unidirectionally oriented urea groups. Photoirradiation experiments demonstrated the trans-to-cis isomerization of the azo-phenyl groups and the formation of a plethora of stereo isomeric cis-azo-enriched capsular assemblies. The highly cis-azo enriched capsular assemblies seem to show a reduced stability and their involvement in equilibria with non-capsular counterparts that also bind the N-oxides. The thermally induced cis-to-trans interconversion processes demonstrated the reversibility of the photoisomerization and the photostability of most binding partners. An equimolar mixture of the two tetraureas produced two homodimeric capsules and the heterodimeric counterpart in a ratio close to statistical distribution.

Light-responsive molecular containers.

Encapsulation of small molecules in molecular containers able to release them in a controlled way in order to perform specific tasks (e.g. catalysis or drug delivery) constitutes an idea that has been around for several years. Light is becoming a perfect external stimulus to control the behaviour of molecular capsules. Photocontrol is a clean and reliable technique, allowing reversibility of the processes in many cases. In addition, researchers in this field are moving from mere function description of the capsules to a deeper understanding of the processes governing these systems. We have compiled a selection of reported studies and highlighted the most relevant findings in this rapidly developing field.

Stereoselective Synthesis of Lower and Upper Rim Functionalized Tetra-α Isomers of Calix[4]pyrroles.

Hydroxyaryl alkyl ketones with functionalized alkyl chains often fail to produce the corresponding tetra-α calix[4]pyrroles in Brönsted acid mediated condensations with pyrrole. A remarkable effect exerted by the addition of methyltrialkylammonium chloride during the acid-mediated syntheses of a series of meso-(tetrahydroxyaryl)-meso-tetraalkylcalix[4]pyrroles featuring alkyl terminal chloro or ester groups is reported. The ammonium salt enhances the cyclocondensation reaction and induces the almost exclusive formation of the tetra-α isomers.

Moving systems of polar dimeric capsules out of thermal equilibrium by light irradiation.

Heterodimeric capsules self-assembled from tetraurea calix[4]pyrrole and tetraurea calix[4]arene provide unique molecular containers for the organised inclusion of small polar molecules. By inserting stimuli-responsive groups (azobenzene) in the heterocapsule structure, we are able to modify the equilibrium state of the system or the exchange between different host-guest assemblies in a reversible manner.

Synthesis of meso-substituted subphthalocyanine-subporphyrin hybrids: boron subtribenzodiazaporphyrins.

The first syntheses of hybrid structures that lie between subphthalocyanines and subporphyrins are reported. The versatile single-step synthetic method uses a preformed aminoisoindolene to provide the bridging methine unit and its substituent while trialkoxyborates simultaneously act as Lewis acid, template, and provider of the apical substituent. The selection of each component therefore allows for the controlled formation of diverse, differentially functionalized systems. The new hybrids are isolated as robust, pure materials that display intense absorption and emission in the mid-visible region. The new compounds are further characterized in solution and solid state by variable-temperature NMR spectroscopy and X-ray crystallography, respectively.

Synthesis of a class of core-modified aza-BODIPY derivatives.

The convenient synthesis of a new class of conjugated aza-BODIPY derivatives from readily available precursors has been achieved. The new materials bear close structural similarity to BODIPYs but differ significantly in electronic configuration from known derivatives, leading to markedly different absorption and emission properties.

Efficient transfection of hepatocytes mediated by mRNA complexed to galactosylated cyclodextrins.

In this study, we aimed at specific targeting of polycationic amphiphilic cyclodextrins (paCDs) to HepG2 cells via the asialoglycoprotein receptor (ASGPr). The transfection efficiencies of paCDs modified with galactose moieties were evaluated. In preliminary experiments, attempts to transfect HepG2 cells with pDNA complexed with different modified paCDs resulted in very low transfection levels. In additional series of experiments, we found out that nucleic acid/cyclodextrin complexes (CDplexes) were efficiently taken up by the cells and that photochemical internalization, which facilitates release from endosomes, did not improve transfection. Further experiments showed that pDNA can be readily released from the CDplexes when exposed to negatively charged vesicles. These observations imply that the lack of transfection cannot be attributed to a lack of internalization, release of CDplexes from the endosomal compartment, or release of free pDNA from the CDplexes. This in turn suggests that the nuclear entry of the pDNA represents the main limiting factor in the transfection process. To verify that HepG2 cells were transfected with targeted CDplexes containing mRNA, which does not require entry into the nucleus for being translated. With mRNA encoding the green fluorescent protein, fractions of GFP-positive cells of up to 31% were obtained. The results confirmed that the galactosylated complexes are specifically internalized via the ASGPr.

Mannosyl-coated nanocomplexes from amphiphilic cyclodextrins and pDNA for site-specific gene delivery.

Fully homogeneous facial amphiphiles consisting in a cyclodextrin (CD) platform onto which a polycationic cluster and a multi-tail hydrophobic moiety have been installed (polycationic amphiphilic CDs; paCDs) self-organized in the presence of plasmid DNA to form nanometric complexes (CDplexes) which exhibit broad-range transfection capabilities. We hypothesized that biorecognizable moieties located at the hydrophilic rim in the CD scaffold would be exposed at the surface of the corresponding nanoparticles after DNA-promoted aggregation, endowing the system with molecular recognition abilities towards cell receptors. This concept has been demonstrated by developing an efficient synthetic strategy for the preparation of multivalent polycationic glyco-amphiphilic CDs (pGaCDs). Self-assembled nanoparticles obtained from mannosylated pGaCDs and pDNA (average hydrodynamic diameter 80 nm) have been shown to be specifically recognized by mannose-specific lectins, including concanavalin A (Con A) and the human macrophage mannose receptor (MMR). Further macrophage adhesion studies indicated that unspecific binding, probably due to electrostatic interactions with negatively charged cell membrane components, can also operate. The relative specific versus non-specific internalization is dependent on the pGaCD:pDNA proportion, being optimal at a protonable nitrogen/phosphate (N/P) ratio of 5. The resulting GlycoCDplexes were shown to specifically mediate transfection in Raw 264.7 (murine macrophage) cells expressing the mannose-fucose receptor in vitro. FACS experiments confirmed that transfection using these nanoparticles is mannose-dependent, supporting the potential of the approach towards vectorized gene delivery.

Symmetry complementarity-guided design of anthrax toxin inhibitors based on ß-cyclodextrin: Synthesis and relative activities of face-selective functionalized polycationic clusters.

Three new series of potential anthrax toxin inhibitors based on the ß-cyclodextrin (ßCD) scaffold were developed by exploiting face-selective Cu(I)-catalyzed azide-alkyne 1,3-cycloadditions, amine-isothiocyanate coupling, and allyl group hydroboration-oxidation/hydroxy → amine replacement reactions. The molecular design follows the "symmetry-complementarity" concept between homogeneously functionalized polycationic ßCD derivatives and protective antigen (PA), a component of anthrax toxin known to form C7-symmetric pores on the cell membrane used by lethal and edema factors to gain access to the cytosol. The synthesis and antitoxin activity of a collection of ßCD derivatives differing in the number, arrangement, and face location of the cationic elements are reported herein. These results set the basis for a structure-activity relationship development program of new candidates to combat the anthrax threat.

Insights in cellular uptake mechanisms of pDNA-polycationic amphiphilic cyclodextrin nanoparticles (CDplexes).

It is generally recognized that the major obstacle to efficient gene delivery is cellular internalization and endosomal escape of the DNA. Recently, we have developed a modular strategy for the preparation of well-defined polycationic amphiphilic cyclodextrins (paCDs) capable of complexing and compacting DNA into homogeneous nanoparticles (<70nm). Since paCDs resemble both cationic polymers and cationic lipids, it is conceivable that the corresponding pDNA-paCD nanoparticles (CDplexes) might use the cell internalization and endosomal escape mechanisms described for both lipoplexes and polyplexes. To verify this hypothesis, we have now investigated the uptake and transfection efficiencies of CDplexes in the presence of several inhibitors of endocytosis, namely chlorpromazine, genistein, dynasore and methylated beta-cyclodextrin (MbCD). Our data show that CDplexes obtained from paCD 1, which ranks among the most efficient paCD gene vectors reported up to date, are internalized by both clathrin-dependent (CDE) and clathrin-independent endocytosis (CIE), both processes being cholesterol- and dynamin-dependent. We observed that the largest fraction of gene complexes is taken up via CDE, but this fraction is less relevant for transfection. The smaller fraction that is internalized via the CIE pathway is predominantly responsible for successful transfection.

Polycationic amphiphilic cyclodextrins for gene delivery: synthesis and effect of structural modifications on plasmid DNA complex stability, cytotoxicity, and gene expression.

A molecular-diversity-oriented approach for the preparation of well-defined polycationic amphiphilic cyclodextrins (paCDs) as gene-delivery systems is reported. The synthetic strategy takes advantage of the differential reactivity of primary versus secondary hydroxyl groups on the CD torus to regioselectively decorate each rim with cationic elements and lipophilic tails, respectively. Both the charge density and the hydrophobic-hydrophilic balance can be finely tuned in a highly symmetrical architecture that is reminiscent of both cationic lipids and cationic polymers, the two most prominent types of nonviral gene vectors. The monodisperse nature of paCDs and the modularity of the synthetic scheme are particularly well suited for structure-activity relationship studies. Gel electrophoresis revealed that paCDs self-assemble in the presence of plasmid DNA (pDNA) to provide homogeneous, stable nanoparticles (CDplexes) of 70-150 nm that fully protect pDNA from the environment. The transfection efficiency of the resulting CDplexes has been investigated in vitro on BNL-CL2 and COS-7 cell lines in the absence and presence of serum and found to be intimately dependent on architectural features. Facial amphiphilicity and the presence of a cluster of cationic and hydrogen-bonding centers for cooperative and reversible complexation of the polyanionic DNA chain is crucial to attain high transgene expression levels with very low toxicity profiles. Further enhancement of gene expression, eventually overcoming that of polyplexes from commercial polyethyleneimine (PEI) polymers (22 kDa), is achieved by building up space-oriented dendritic polycationic constructs.

Rational design of cationic cyclooligosaccharides as efficient gene delivery systems.

Self-assembled cyclodextrin (CD)-DNA nanoparticles (CDplexes) exhibiting transfection efficiencies significantly higher than PEI-based polyplexes have been prepared from homogeneous seven-fold symmetric polyaminothiourea amphiphiles constructed on a beta-cyclodextrin scaffold.