Robust and heritable knockdown of gene expression using a self-cleaving ribozyme in Drosophila.

The current toolkit for genetic manipulation in the model animal Drosophila melanogaster is extensive and versatile but not without its limitations. Here, we report a powerful and heritable method to knockdown gene expression in D. melanogaster using the self-cleaving N79 hammerhead ribozyme, a modification of a naturally occurring ribozyme found in the parasite Schistosoma mansoni. A 111 bp ribozyme cassette, consisting of the N79 ribozyme surrounded by insulating spacer sequences, was inserted into four independent long noncoding RNA genes as well as the male-specific splice variant of doublesex using scarless CRISPR/Cas9-mediated genome editing. Ribozyme-induced RNA cleavage resulted in robust destruction of 3' fragments typically exceeding 90%. Single molecule RNA fluorescence in situ hybridization results suggest that cleavage and destruction can even occur for nascent transcribing RNAs. Knockdown was highly specific to the targeted RNA, with no adverse effects observed in neighboring genes or the other splice variants. To control for potential effects produced by the simple insertion of 111 nucleotides into genes, we tested multiple catalytically inactive ribozyme variants and found that a variant with scrambled N79 sequence best recapitulated natural RNA levels. Thus, self-cleaving ribozymes offer a novel approach for powerful gene knockdown in Drosophila, with potential applications for the study of noncoding RNAs, nuclear-localized RNAs, and specific splice variants of protein-coding genes.

Investigating Steric and Electronic Effects in the Synthesis of Square Planar 6d1 Th(III) Complexes.

The factors affecting the formation and crystal structures of unusual 6d1 Th(III) square planar aryloxide complexes, as exemplified by [Th(OArMe)4]1- (OArMe = OC6H2tBu2-2,6-Me-4), were explored by synthetic and reduction studies of a series of related Th(IV) tetrakis(aryloxide) complexes, Th(OArR)4 (OArR = OC6H2tBu2-2,6-R-4). Specifically, electronic, steric, and countercation effects were explored by varying the aryloxide ligand, the alkali metal reducing agent, and the alkali metal chelating agent. Salt metathesis reactions between ThBr4(DME)2 (DME = 1,2-dimethoxyethane) and 4 equiv of the appropriate potassium aryloxide salt were used to prepare a series of Th(IV) aryloxide complexes in high yields: Th(OArH)4 (OArH = OC6H3tBu2-2,6), Th(OArtBu)4 (OArtBu = OC6H2tBu3-2,4,6), Th(OArOMe)4 (OArOMe = OC6H2tBu2-2,6-OMe-4), and Th(OArPh)4 (OArPh = OC6H2tBu2-2,6-Ph-4). Th(OArH)4 can be reduced by KC8, Na, or Li in the absence or presence of 2.2.2-cryptand (crypt) or 18-crown-6 (crown) to form dark purple solutions that have EPR and UV-visible spectra similar to those of the square planar Th(III) complex, [Th(OArMe)4]1-. Hence, the para position of the aryloxide ligand does not have to be alkylated to obtain the Th(III) complexes. Furthermore, reduction of Th(OArOMe)4, Th(OArtBu)4, and Th(OArPh)4 with KC8 in THF generated purple solutions with EPR and UV-visible spectra that are similar to those of the previously reported Th(III) anion, [Th(OArMe)4]1-. Although many of these reduction reactions did not produce single crystals suitable for study by X-ray diffraction, reduction of Th(OArH)4, Th(OArtBu)4, and Th(OArOMe)4 with Li provided X-ray quality crystals whose structures had square planar coordination geometries. Reduction of Th(OArPh)4 with Li also gave a product with EPR and UV-visible spectra that matched those of [Th(OArMe)4]1-, but X-ray quality crystals of the reduction product were too unstable to provide data. Neither Th(Odipp)4(THF)2 (Odipp = OC6H3iPr2-2,6) nor Th(Odmp)4(THF)2 (Odmp = OC6H3Me2-2,6) could be reduced to Th(III) products under similar conditions. Reduction of U(OArH)3(THF) with KC8 in the presence of 2.2.2-cryptand (crypt) was examined for comparison and formed [K(crypt)][U(OArH)4], which has a tetrahedral arrangement of the aryloxide ligands. Moreover, no further reduction was observed when either [K(crypt)][U(OArH)4] or [K(crown)(THF)2][U(OArH)4] were treated with KC8 or Li.

Cooperative dinitrogen capture by a diboraanthracene/samarocene pair.

The combination of a boron Lewis acid and a decamethylsamarocene, specifically 9,10-Me2-9,10-diboraanthracene with (C5Me5)2SmII(THF)2, in toluene leads to cooperative reductive capture of N2. The product crystallizes as the salt, [(C5Me5)2SmIII(THF)2][(C5Me5)2SmIII(η2-N2B2C14H14)], 1, which formally is comprised of an (NN)2- moiety sandwiched between a [(C5Me5)2SmIII]1+ metallocene cation and the diboraanthracene ditopic Lewis acid.

A pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in Drosophila.

Genome editing via homology-directed repair (HDR) has made possible precise and deliberate modifications to gene sequences. CRISPR/Cas9-mediated HDR is the simplest means to carry this out. However, technical challenges remain to improve efficiency and broaden applicability to any genetic background of Drosophila melanogaster as well as to other Drosophila species. To address these issues, we developed a two-stage marker-assisted strategy in which embryos are injected with RNPs and pre-screened using T7EI. Using sgRNA in complex with recombinant Cas9 protein, we assayed each sgRNA for genome-cutting efficiency. We then conducted HDR using sgRNAs that efficiently cut target genes and the application of a transformation marker that generates RNAi against eyes absent. This allows for screening based on eye morphology rather than colour. These new tools can be used to make a single change or a series of allelic substitutions in a region of interest, or to create additional genetic tools such as balancer chromosomes.

The effector mechanism of siRNA spherical nucleic acids.

Spherical nucleic acids (SNAs) are nanostructures formed by chemically conjugating short linear strands of oligonucleotides to a nanoparticle template. When made with modified small interfering RNA (siRNA) duplexes, SNAs act as single-entity transfection and gene silencing agents and have been used as lead therapeutic constructs in several disease models. However, the manner in which modified siRNA duplex strands that comprise the SNA lead to gene silencing is not understood. Herein, a systematic analysis of siRNA biochemistry involving SNAs shows that Dicer cleaves the modified siRNA duplex from the surface of the nanoparticle, and the liberated siRNA subsequently functions in a way that is dependent on the canonical RNA interference mechanism. By leveraging this understanding, a class of SNAs was chemically designed which increases the siRNA content by an order of magnitude through covalent attachment of each strand of the duplex. As a consequence of increased nucleic acid content, this nanostructure architecture exhibits less cell cytotoxicity than conventional SNAs without a decrease in siRNA activity.