Single-Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides.

Argonaute proteins repress gene expression and defend against foreign nucleic acids using short RNAs or DNAs to specify the correct target RNA or DNA sequence. We have developed single-molecule methods to analyze target binding and cleavage mediated by the Argonaute:guide complex, RISC. We find that both eukaryotic and prokaryotic Argonaute proteins reshape the fundamental properties of RNA:RNA, RNA:DNA, and DNA:DNA hybridization­a small RNA or DNA bound to Argonaute as a guide no longer follows the well-established rules by which oligonucleotides find, bind, and dissociate from complementary nucleic acid sequences. Argonautes distinguish substrates from targets with similar complementarity. Mouse AGO2, for example, binds tighter to miRNA targets than its RNAi cleavage product, even though the cleaved product contains more base pairs. By re-writing the rules for nucleic acid hybridization, Argonautes allow oligonucleotides to serve as specificity determinants with thermodynamic and kinetic properties more typical of RNA-binding proteins than of RNA or DNA.

Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties.

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) guide Argonaute proteins to silence mRNA expression. Argonaute binding alters the properties of an RNA guide, creating functional domains. We show that the domains established by Argonaute-the anchor, seed, central, 3' supplementary, and tail regions-have distinct biochemical properties that explain the differences between how animal miRNAs and siRNAs bind their targets. Extensive complementarity between an siRNA and its target slows the rate at which fly Argonaute2 (Ago2) binds to and dissociates from the target. Highlighting its role in antiviral defense, fly Ago2 dissociates so slowly from extensively complementary target RNAs that essentially every fully paired target is cleaved. Conversely, mouse AGO2, which mainly mediates miRNA-directed repression, dissociates rapidly and with similar rates for fully paired and seed-matched targets. Our data narrow the range of biochemically reasonable models for how Argonaute-bound siRNAs and miRNAs find, bind, and regulate their targets.

Sleeping Beauty mRNA-LNP enables stable rAAV transgene expression in mouse and NHP hepatocytes and improves vector potency.

Recombinant adeno-associated virus (rAAV) vector gene delivery systems have demonstrated great promise in clinical trials but continue to face durability and dose-related challenges. Unlike rAAV gene therapy, integrating gene addition approaches can provide curative expression in mitotically active cells and pediatric populations. We explored a novel in vivo delivery approach based on an engineered transposase, Sleeping Beauty (SB100X), delivered as an mRNA within a lipid nanoparticle (LNP), in combination with an rAAV-delivered transposable transgene. This combinatorial approach achieved correction of ornithine transcarbamylase deficiency in the neonatal Spfash mouse model following a single delivery to dividing hepatocytes in the newborn liver. Correction remained stable into adulthood, while a conventional rAAV approach resulted in a return to the disease state. In non-human primates, integration by transposition, mediated by this technology, improved gene expression 10-fold over conventional rAAV-mediated gene transfer while requiring 5-fold less vector. Additionally, integration site analysis confirmed a random profile while specifically targeting TA dinucleotides across the genome. Together, these findings demonstrate that transposable elements can improve rAAV-delivered therapies by lowering the vector dose requirement and associated toxicity while expanding target cell types.

Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivo.

Small interfering RNA (siRNA)-based drugs require chemical modifications or formulation to promote stability, minimize innate immunity, and enable delivery to target tissues. Partially modified siRNAs (up to 70% of the nucleotides) provide significant stabilization in vitro and are commercially available; thus are commonly used to evaluate efficacy of bio-conjugates for in vivo delivery. In contrast, most clinically-advanced non-formulated compounds, using conjugation as a delivery strategy, are fully chemically modified (100% of nucleotides). Here, we compare partially and fully chemically modified siRNAs in conjugate mediated delivery. We show that fully modified siRNAs are retained at 100x greater levels in various tissues, independently of the nature of the conjugate or siRNA sequence, and support productive mRNA silencing. Thus, fully chemically stabilized siRNAs may provide a better platform to identify novel moieties (peptides, aptamers, small molecules) for targeted RNAi delivery.

Single-Molecule Magnet Behavior of Individual Polyoxometalate Molecules Incorporated within Biopolymer or Metal-Organic Framework Matrices.

The chemically and structurally highly stable polyoxometalate (POM) single-molecule magnet (SMM) [(FeW9 O34 )2 Fe4 (H2 O)2 ](10-) (Fe6 W18 ) has been incorporated by direct or post-synthetic approaches into a biopolymer gelatin (Gel) matrix and two crystalline metal-organic frameworks (MOFs), including one diamagnetic (UiO-67) and one magnetic (MIL-101(Cr)). Integrity of the POM in the Fe6 W18 @Gel, Fe6 W18 @UiO-67 and Fe6 W18 @MIL-101(Cr) composites was confirmed by a set of complementary techniques. Magnetic studies indicate that the POMs are magnetically well isolated. Remarkably, in Fe6 W18 @Gel, the SMM properties of the embedded molecules are close to those of the crystals, with clear quantum tunneling steps in the hysteresis loops. For the Fe6 W18 @UiO-67 composite, the molecules retain their SMM properties, the energy barrier being slightly reduced in comparison to the crystalline material and the molecules exhibiting a tunneling rate of magnetization significantly faster than for Fe6 W18 @Gel. When Fe6 W18 is introduced into MIL-101(Cr), the width of the hysteresis loops is drastically reduced and the quantum tunneling steps are smeared out because of the magnetic interactions between the antiferromagnetic matrix and the SMM guest molecules.

Heteroanionic Materials Based on Copper Clusters, Bisphosphonates, and Polyoxometalates: Magnetic Properties and Comparative Electrocatalytic NO(x) Reduction Studies.

Three compounds associating for the first time polyoxotungstates, bisphosphonates, and copper ions were structurally characterized. They consist in heteropolyanionic monodimensional materials where [Cu6(Ale)4(H2O)4](4-) (Ale = alendronate = [O3PC(O)(C3H6NH3)PO3](4-)) complexes alternate with polyoxometalate (POM) units. In Na12[{SiW9O34Cu3(Ale)(H2O)}{Cu6(Ale)4(H2O)4}]·50H2O (SiW9CuAle), the polyoxometalate core consists in a {SiW9Cu3} monomer capped by a pentacoordinated Ale ligand, while sandwich-type Keggin {(SbW9O33)2Cu3(H2O)(2.5)Cl(0.5)} and Dawson {(P2W15O56)2Cu4(H2O)2} complexes are found in Na8Li29[{(SbW9O33)2Cu3(H2O)(2.5)Cl(0.5)}2{Cu6(Ale)4(H2O)4}3]·163H2O (SbW9CuAle) and Na20[{(P2W15O56)2Cu4(H2O)2}{Cu6(Ale)4(H2O)4}]·50H2O (P2W15CuAle), respectively. A comparative magnetic study of the SiW9CuAle and SbW9CuAle compounds enabled full quantification of the Cu(II) superexchange interactions both for the POM and non-POM subunits, evidencing that, while the paramagnetic centers are anti-ferromagnetically coupled in the polyoxometalate units, both anti-ferromagnetic and ferromagnetic interactions coexist in the {Cu6(Ale)4(H2O)4} cluster. All the studied compounds present a good efficiency upon the reduction of HNO2 or NO2(-), the POM acting as a catalyst. However, it has been found that SbW9CuAle is inactive toward the reduction of nitrates, highlighting that both the {(SbW9O33)2Cu3} unit and the {Cu6(Ale)4(H2O)4} cluster do not act as electrocatalysts for this reaction. In contrast, SiW9CuAle and P2W15CuAle have shown a significant activity upon the reduction of NO3(-) and thus both at pH 1 and pH 5, evidencing that the chemical nature of the polyoxometalate is a crucial parameter even if it acts as precatalyst. Moreover, comparison of the activities of P2W15CuAle and [(P2W15O56)2Cu4(H2O)2](16-) evidenced that if the [Cu6(Ale)4(H2O)4](4-) cluster does not act as electrocatalyst, it acts as a cofactor, significantly enhancing the catalytic efficiency of the active POM.

Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates.

Small interfering RNAs (siRNAs) direct Argonaute proteins, the core components of the RNA-induced silencing complex (RISC), to cleave complementary target RNAs. Here, we describe a method to purify active RISC containing a single, unique small RNA guide sequence. We begin by capturing RISC using a complementary 2'-O-methyl oligonucleotide tethered to beads. Unlike other methods that capture RISC but do not allow its recovery, our strategy purifies active, soluble RISC in good yield. The method takes advantage of the finding that RISC partially paired to a target through its siRNA guide dissociates more than 300 times faster than a fully paired siRNA in RISC. We use this strategy to purify fly Ago1- and Ago2-RISC, as well as mouse AGO2-RISC. The method can discriminate among RISCs programmed with different guide strands, making it possible to deplete and recover specific RISC populations. Endogenous microRNA:Argonaute complexes can also be purified from cell lysates. Our method scales readily and takes less than a day to complete.

Synthesis, characterization, and tuning of the liquid crystal properties of ionic materials based on the cyclic polyoxothiometalate [{Mo4O4S4(H2O)3(OH)2}2(P8W48O184)](36-).

A series of compounds resulting from the ionic association of a nanoscopic inorganic cluster of formula [K2NaxLiy{Mo4O4S4(OH)2(H2O)3}2(HzP8W48O184)]((34-x-y-z)-), 1, with several organic cations such as dimethyldioctadecylammonium DODA(+), trimethylhexadecylammonium TMAC16(+), alkylmethylimidazoliums mimCn(+) (n = 12-20) and alkyl-dimethylimidazoliums dmimCn(+) (n = 12 and 16) was prepared and characterized in the solid state by FT-IR, EDX, Elemental analysis, TGA and solid state NMR. The solid state NMR experiments performed on (1)H, (13)C and (31)P nuclei evidenced the interactions between the cations and 1 as well as the organization of the alkyl chains of the cations within the solid. Polarized optical microscopy, DSC and SA-XRD experiments implicated mesomorphic phases for DODA(+) and mimCn(+) salts of 1. The crystallographic parameters were determined and demonstrated that the inter-lamellar spacing could be controlled upon changing the length of the alkyl chain, a very interesting result if we consider the huge size of the inorganic cluster 1 and the simple nature of the cations.

Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing.

Small RNAs loaded into Argonaute proteins direct silencing of complementary target mRNAs. It has been proposed that multiple, imperfectly complementary small interfering RNAs or microRNAs, when bound to the 3' untranslated region of a target mRNA, function cooperatively to silence target expression. We report that, in cultured human HeLa cells and mouse embryonic fibroblasts, Argonaute1 (Ago1), Ago3, and Ago4 act cooperatively to silence both perfectly and partially complementary target RNAs bearing multiple small RNA-binding sites. Our data suggest that for Ago1, Ago3, and Ago4, multiple, adjacent small RNA-binding sites facilitate cooperative interactions that stabilize Argonaute binding. In contrast, small RNAs bound to Ago2 and pairing perfectly to an mRNA target act independently to silence expression. Noncooperative silencing by Ago2 does not require the endoribonuclease activity of the protein: A mutant Ago2 that cannot cleave its mRNA target also silences noncooperatively. We propose that Ago2 binds its targets by a mechanism fundamentally distinct from that used by the three other mammalian Argonaute proteins.

Potent and systematic RNAi mediated silencing with single oligonucleotide compounds.

RNA interference (RNAi) has been established as an important tool for functional genomics studies and has great promise as a therapeutic intervention for human diseases. In mammalian cells, RNAi is conventionally induced by 19-27-bp RNA duplexes generated by hybridization of two complementary oligonucleotide strands (oligos). Here we describe a novel class of RNAi molecules composed of a single 25-28-nucleotide (nt) oligo. The oligo has a 16-nt mRNA targeting region, followed by an additional 8-10 nt to enable self-dimerization into a partially complementary duplex. Analysis of numerous diverse structures demonstrates that molecules composed of two short helices separated by a loop can efficiently enter and activate the RNA-induced silencing complex (RISC). This finding enables the design of highly effective single-oligo compounds for any mRNA target.

Glucan particles for selective delivery of siRNA to phagocytic cells in mice.

Phagocytic macrophages and dendritic cells are desirable targets for potential RNAi (RNA interference) therapeutics because they often mediate pathogenic inflammation and autoimmune responses. We recently engineered a complex 5 component glucan-based encapsulation system for siRNA (small interfering RNA) delivery to phagocytes. In experiments designed to simplify this original formulation, we discovered that the amphipathic peptide Endo-Porter forms stable nanocomplexes with siRNA that can mediate potent gene silencing in multiple cell types. In order to restrict such gene silencing to phagocytes, a method was developed to entrap siRNA-Endo-Porter complexes in glucan shells of 2-4 µm diameter in the absence of other components. The resulting glucan particles containing fluorescently labelled siRNA were readily internalized by macrophages, but not other cell types, and released the labelled siRNA into the macrophage cytoplasm. Intraperitoneal administration of such glucan particles containing siRNA-Endo-Porter complexes to mice caused gene silencing specifically in macrophages that internalized the particles. These results from the present study indicate that specific targeting to phagocytes is mediated by the glucan, whereas Endo-Porter peptide serves both to anchor siRNA within glucan particles and to catalyse escape of siRNA from phagosomes. Thus we have developed a simplified siRNA delivery system that effectively and specifically targets phagocytes in culture or in intact mice.

Modified dsRNAs that are not processed by Dicer maintain potency and are incorporated into the RISC.

Chemical modification of RNA duplexes can provide practical advantages for RNA interference (RNAi) triggering molecules including increased stability, safety and specificity. The impact of nucleotide modifications on Dicer processing, RISC loading and RNAi-mediated mRNA cleavage was investigated with duplexes >or=25 bp in length. It is known that dsRNAs >or=25 bp are processed by Dicer to create classic 19-bp siRNAs with 3'-end overhangs. We demonstrate that the presence of minimal modification configurations on longer RNA duplexes can block Dicer processing and result in the loading of the full-length guide strand into RISC with resultant mRNA cleavage at a defined site. These longer, modified duplexes can be highly potent gene silencers, with EC50s in the picomolar concentration range, demonstrating that Dicer processing is not required for incorporation into RISC or potent target silencing.

A bootstrapping algorithm to improve cohort identification using structured data.

Cohort identification is an important step in conducting clinical research studies. Use of ICD-9 codes to identify disease cohorts is a common approach that can yield satisfactory results in certain conditions; however, for many use-cases more accurate methods are required. In this study, we propose a bootstrapping method that supplements ICD-9 codes with lab results, medications, etc. to build classification models that can be used to identify cohorts more accurately. The proposed method does not require prior information about the true class of the patients. We used the method to identify Diabetes Mellitus (DM) and Hyperlipidemia (HL) patient cohorts from a database of 800 thousand patients. Evaluation results show that the method identified 11,000 patients who did not have DM related ICD-9 codes as positive for DM and 52,000 patients without HL codes as positive for HL. A review of 400 patient charts (200 patients for each condition) by two clinicians shows that in both the conditions studied, the labeling assigned by the proposed approach is more consistent with that of the clinicians compared to labeling through ICD-9 codes. The method is reasonably automated and, we believe, holds potential for inexpensive, more accurate cohort identification.

A Multifunctional Dual-Luminescent Polyoxometalate@Metal-Organic Framework EuW10@UiO-67 Composite as Chemical Probe and Temperature Sensor.

The luminescent [EuW10O36]9- polyoxometalate has been introduced into the cavities of the highly porous zirconium luminescent metal-organic framework UiO-67 via a direct synthesis approach, affording the EuW10@UiO-67 hybrid. Using a combination of techniques (TGA, BET, elemental analysis, EDX mapping,…) this new material has been fully characterized, evidencing that it contains only 0.25% in europium and that the polyoxometalate units are located inside the octahedral cavities and not at the surface of the UiO-67 crystallites. Despite the low amount of europium, it is shown that EuW10@UiO-67 acts as a solid-state luminescent sensor for the detection of amino-acids, the growth of the emission intensity globally following the growth of the amino-acid pKa. In addition, EuW10@UiO-67 acts as a sensor for the detection of metallic cations, with a high sensitivity for Fe3+. Noticeably, the recyclability of the reported material has been established. Finally, it is shown that the dual-luminescent EuW10@UiO-67 material behave as a self-calibrated-ratiometric thermometer in the physiological range.

Bicapped Keggin polyoxomolybdates: discrete species and experimental and theoretical investigations on the electronic delocalization in a chain compound.

Three monomeric polyoxometalates [M(C10H8N2)3][α-PMoMoO40Zn2(C10H8N2)2]·2H2O (M-PMo12Zn2, M = Fe, Co, Ru) with {Zn(bpy)2}2+ units capped on reduced α-Keggin polyanions and [M(bpy)3]2+ counter-ions were synthesized under hydrothermal conditions. The 1D polymer [N(C4H9)4][Ru(C10H8N2)3][α-PMoMoO43] (Ru-PMo14) was prepared by a similar strategy, in the absence of 2,2'-bpy ligands. In this chain capped reduced Keggin anions are linked via Mo-O-Mo bridges and are surrounded by both tetrabutylammonium cations and [Ru(bpy)3]2+ counter-ions. The compounds were characterized in the solid state by single crystal and powder X-ray diffraction and IR spectroscopy and in solution by 31P NMR spectroscopy. 31P diffusion ordered NMR spectroscopy (DOSY) indicates that the diffusion coefficient of the dissolved species of Ru-PMo14 corresponds to a dimeric structure. Magnetic susceptibility measurements performed on Ru-PMo14 show the existence of antiferromagnetic interactions between the d1 electrons of the six MoV centers, with a singlet spin ground state. However, attempts to fit the data in the 2-300 K temperature range with Heisenberg Hamiltonians adapted for 0 or 1D systems suggest that these electrons are delocalized. Density Functional Theory (DFT) and Wave Function Theory (WFT) calculations indicate a migration of the electrons of the capping MoV centers into the PMo12 units at high temperature, allowing the rationalization of the experimental observations.

A Single Administration of CRISPR/Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing.

The development of clinically viable delivery methods presents one of the greatest challenges in the therapeutic application of CRISPR/Cas9 mediated genome editing. Here, we report the development of a lipid nanoparticle (LNP)-mediated delivery system that, with a single administration, enabled significant editing of the mouse transthyretin (Ttr) gene in the liver, with a >97% reduction in serum protein levels that persisted for at least 12 months. These results were achieved with an LNP delivery system that was biodegradable and well tolerated. The LNP delivery system was combined with a sgRNA having a chemical modification pattern that was important for high levels of in vivo activity. The formulation was similarly effective in a rat model. Our work demonstrates that this LNP system can deliver CRISPR/Cas9 components to achieve clinically relevant levels of in vivo genome editing with a concomitant reduction of TTR serum protein, highlighting the potential of this system as an effective genome editing platform.

Immobilization of polyoxometalates in the Zr-based metal organic framework UiO-67.

The encapsulation of polyoxometalates within the large pores of the Zr(iv) biphenyldicarboxylate UiO-67 metal-organic framework has been achieved, for the first time, by direct solvothermal synthesis. The resulting POM@UiO-67 composite materials were fully characterized by XRPD, IR, MAS NMR, N2 porosimetry measurements and cyclic voltammetry.

Immobilization of Co-containing polyoxometalates in MIL-101(Cr): structural integrity versus chemical transformation.

The encapsulation of three different cobalt substituted polyoxometalates (POMs) within the mesoporous chromium(iii) terephthalate MIL-101(Cr) metal-organic framework (MOF) was studied by a simple and green impregnation method using water. The POM@MIL composite materials were fully characterized by EDX, XRPD, IR, MAS NMR and N2 porosimetry measurements. The encapsulated POMs were then extracted by an exchange procedure using a LiCl solution. (31)P NMR spectroscopy is the key experiment which indicates that the monosubstituted Keggin anion [PW11CoO39(H2O)](5-) (PW11Co) and the sandwich-type anion [(PW9O34)2Co4(H2O)2](10-) (P2W18Co4) can be encapsulated and extracted without degradation, neither of the POM nor of the MOF, while the hybrid sandwich-type POM [(PW9O34)2Co7(OH)2(H2O)4(O3PC(O)(C3H6NH3)PO3)2](14-) (Co7-Ale) evolves into P2W18Co4 inside the cavities of the mesoporous material. The PW11Co Keggin anion is the most quantitatively uploaded and the most easily extracted anion. (31)P MAS-NMR spectroscopy further suggests that this anion is more mobile inside the cavities of the MOF than the P2W18Co4 POM.