Impact of stereopure chimeric backbone chemistries on the potency and durability of gene silencing by RNA interference.

Herein, we report the systematic investigation of stereopure phosphorothioate (PS) and phosphoryl guanidine (PN) linkages on siRNA-mediated silencing. The incorporation of appropriately positioned and configured stereopure PS and PN linkages to N-acetylgalactosamine (GalNAc)-conjugated siRNAs based on multiple targets (Ttr and HSD17B13) increased potency and durability of mRNA silencing in mouse hepatocytes in vivo compared with reference molecules based on clinically proven formats. The observation that the same modification pattern had beneficial effects on unrelated transcripts suggests that it may be generalizable. The effect of stereopure PN modification on silencing is modulated by 2'-ribose modifications in the vicinity, particularly on the nucleoside 3' to the linkage. These benefits corresponded with both an increase in thermal instability at the 5'-end of the antisense strand and improved Argonaute 2 (Ago2) loading. Application of one of our most effective designs to generate a GalNAc-siRNA targeting human HSD17B13 led to ∼80% silencing that persisted for at least 14 weeks after administration of a single 3 mg/kg subcutaneous dose in transgenic mice. The judicious use of stereopure PN linkages improved the silencing profile of GalNAc-siRNAs without disrupting endogenous RNA interference pathways and without elevating serum biomarkers for liver dysfunction, suggesting they may be suitable for therapeutic application.

Enhanced Thermoelectric Properties of Misfit Bi2Sr2-xCaxCo2Oy: Isovalent Substitutions and Selective Phonon Scattering.

Layered Bi-misfit cobaltates, such as Bi2Sr2Co2Oy, are the natural superlattice of an electrically insulating rocksalt (RS) type Bi2Sr2O4 layer and electrically conducting CoO2 layer, stacked along the crystallographic c-axis. RS and CoO2 layers are related through charge compensation reactions (or charge transfer). Therefore, thermoelectric transport properties are affected when doping or substitution is carried out in the RS layer. In this work, we have shown improved thermoelectric properties of spark plasma sintered Bi2Sr2-xCaxCo2Oy alloys (x = 0, 0.3 and 0.5). The substitution of Ca atoms affects the thermal properties by introducing point-defect phonon scattering, while the electronic conductivity and thermopower remain unaltered.

Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides.

Technologies that recruit and direct the activity of endogenous RNA-editing enzymes to specific cellular RNAs have therapeutic potential, but translating them from cell culture into animal models has been challenging. Here we describe short, chemically modified oligonucleotides called AIMers that direct efficient and specific A-to-I editing of endogenous transcripts by endogenous adenosine deaminases acting on RNA (ADAR) enzymes, including the ubiquitously and constitutively expressed ADAR1 p110 isoform. We show that fully chemically modified AIMers with chimeric backbones containing stereopure phosphorothioate and nitrogen-containing linkages based on phosphoryl guanidine enhanced potency and editing efficiency 100-fold compared with those with uniformly phosphorothioate-modified backbones in vitro. In vivo, AIMers targeted to hepatocytes with N-acetylgalactosamine achieve up to 50% editing with no bystander editing of the endogenous ACTB transcript in non-human primate liver, with editing persisting for at least one month. These results support further investigation of the therapeutic potential of stereopure AIMers.

On the thermoelectric properties of Nb-doped SrTiO3 epitaxial thin films.

The exploration for thermoelectric thin films of complex oxides such as SrTiO3-based oxides is driven by the need for miniaturized harvesting devices for powering the Internet of Things (IoT). However, there is still not a clear consensus in the literature for the underlying influence of film thickness on thermoelectric properties. Here, we report the fabrication of epitaxial thin films of 6% Nb-doped SrTiO3 on (001) (LaAlO3)0.3(Sr2AlTaO6)0.7 (LSAT) single crystal using pulsed laser deposition (PLD) where the film thickness was varied from 2 nm to 68 nm. The thickness dependence shows a subtle increase of tetragonality of the thin film lattice and a gradual drop of the electrical conductivity, the density of charge carriers, and the thermoelectric Seebeck coefficient as the film thickness decreases. DFT-based calculations show that ∼2.8% increase in tetragonality results in an increased splitting between t2g and eg orbitals to ∼42.3 meV. However, experimentally observed tetragonality for films between 68 to 13 nm is only 0.06%. Hence, the effect of thickness on tetragonality is neglected. We have discussed the decrease of conductivity and the Seebeck coefficient based on the decrease of carriers and change in the scattering mechanism, respectively.

A Noncoordinating Acid-Base Catalyst for the Mild and Nonreversible tert-Butylation of Alcohols and Phenols.

A mild and nonreversible tert-butylation of alcohols and phenols can be achieved in high yields using the noncoordinating acid-base catalyst [bis(trifluoromethane)sulfonimide and 2,6-lutidine] with a tert-butylation reagent, tert-butyl 2,2,2-trichloroacetimidate. This method allows the use of substrates containing acid sensitive groups such as ketal, Boc, and boronate esters.

Site-Specific Incorporation of N-(2'-Deoxyguanosine-8-yl)-6-aminochrysene Adduct in DNA and Its Replication in Human Cells.

The environmental pollutant 6-nitrochrysene (6-NC) is a potent mutagen and a mammary carcinogen in rats. 6-NC is the most potent carcinogen ever tested in the newborn mouse assay. In mammalian cells, it is metabolically activated by nitroreduction and a combination of ring oxidation and nitroreduction pathways. The nitroreduction pathway yields two major adducts with 2'-deoxyguanosine (dG), one at the C8-position, N-(dG-8-yl)-6-AC, and the other at the exocyclic N2-position, 5-(dG-N2-yl)-6-AC. Here, we report the total synthesis of a site-specific oligonucleotide containing the 6-NC-derived C8 dG adduct, N-(dG-8-yl)-6-AC. Pd-catalyzed Buchwald-Hartwig cross coupling of 6-aminochrysene with protected C8-bromo-dG derivative served as the key reaction to furnish protected N-(dG-8-yl)-6-AC in 56% yield. The monomer for solid-phase DNA synthesis was prepared by its deprotection followed by conversion to the corresponding 5'-O-dimethoxytrityl 3'-phosphoramidite, which was used to synthesize a site-specifically adducted oligonucleotide. After purification and characterization, the adduct-containing oligonucleotide was incorporated into a plasmid and replicated in human embryonic kidney (HEK) 293T cells, which showed that N-(dG-8-yl)-6-AC stalls DNA replication as evidenced by 77% translesion synthesis (TLS) efficiency relative to the control and that the adduct is mutagenic (mutation frequency (MF) 17.8%) inducing largely G→T transversions. We also investigated the roles of several translesion synthesis DNA polymerases in the bypass of N-(dG-8-yl)-6-AC using siRNA knockdown approach. TLS efficiency was reduced in hPol η-, hPol κ-, hPol ζ-, and hREV1-deficient HEK 293T cells to 66%, 45%, 37%, and 32%, respectively. Notably, TLS efficiency was reduced to 18% in cells with concurrent knockdown of hPol κ, hPol ζ, and REV1, suggesting that these three polymerases play critical roles in bypassing N-(dG-8-yl)-6-AC. MF increased to 23.1% and 32.2% in hPol κ- and hREV1-deficient cells, whereas it decreased to 11.8% in hPol ζ-deficient cells. This suggests that hPol κ and hREV1 are involved in error-free TLS of this lesion, whereas hPol ζ performs error-prone bypass.

Synthesis of Oligodeoxynucleotides Containing a C8-2'-Deoxyguanosine Adduct Formed by the Carcinogen 3-Nitrobenzanthrone.

This unit describes the detailed procedure in five parts for the synthesis of the C8-2'-deoxyguanosine-3-aminobenzanthrone adduct located in a desired site in an oligonucleotide. The synthesis of the protected 2'-deoxyguanosine, O6 -benzyl-N2 -DMTr-3'-5'-bisTBDMS-C8-Br-2'-deoxyguanosine, is described in the first part. The synthesis of the reduced carcinogen 3-aminobenzanthrone is detailed in part two. The third part outlines the key step of the adduct formation between the reduced carcinogen and the protected nucleoside by a palladium-catalyzed cross coupling reaction. The final two parts describe phosphoramidite synthesis from the nucleoside-carcinogen adduct followed by its site-specific incorporation into DNA by solid-phase oligonucleotide synthesis. The adducted oligonucleotides are purified by reversed-phase HPLC and characterized by mass spectrometry. © 2017 by John Wiley & Sons, Inc.

Mechanism of Error-Free Bypass of the Environmental Carcinogen N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone Adduct by Human DNA Polymerase†η.

The environmental pollutant 3-nitrobenzanthrone produces bulky aminobenzanthrone (ABA) DNA adducts with both guanine and adenine nucleobases. A major product occurs at the C8 position of guanine (C8-dG-ABA). These adducts present a strong block to replicative polymerases but, remarkably, can be bypassed in a largely error-free manner by the human Y-family polymerase η (hPol η). Here, we report the crystal structure of a ternary Pol⋅DNA⋅dCTP complex between a C8-dG-ABA-containing template:primer duplex and hPol η. The complex was captured at the insertion stage and provides crucial insight into the mechanism of error-free bypass of this bulky lesion. Specifically, bypass involves accommodation of the ABA moiety inside a hydrophobic cleft to the side of the enzyme active site and formation of an intra-nucleotide hydrogen bond between the phosphate and ABA amino moiety, allowing the adducted guanine to form a standard Watson-Crick pair with the incoming dCTP.

Electronic grade and flexible semiconductor film employing oriented attachment of colloidal ligand-free PbS and PbSe nanocrystals at room temperature.

Electronic grade semiconductor films have been obtained via the sintering of solution processed PbS and PbSe nanocrystals at room temperature. Prior attempts to achieve similar films required the sintering of nanocrystals at higher temperatures (>350 °C), which inhibits the processing of such films on a flexible polymer substrate, and it is also expensive. We reduced the sintering temperature by employing two important strategies: (i) use of ligand-free nanocrystals and (ii) oriented attachment of nanocrystals. Colloidal ligand-free PbS and PbSe nanocrystals were synthesized at 70 °C with high yield (∼70%). However, these nanocrystals start to agglomerate with time in formamide, and upon the removal of the solvation energy, nanocrystals undergo oriented attachment, forming larger elongated crystals. PbS and PbSe nanocrystal films made on both glass and flexible substrates at room temperature exhibit Ohmic behavior with optimum DC conductivities of 0.03 S m(-1) and 0.08 S m(-1), respectively. Mild annealing of the films at 150 °C increases the conductivity values to 1.1 S m(-1) and 137 S m(-1) for PbS and PbSe nanocrystal films, respectively. AC impedance was measured to distinguish the contributions from grain and grain boundaries to the charge transport mechanism. Charge transport properties remain similar after the repeated bending of the film on a flexible polymer substrate. Reasonably high thermoelectric Seebeck coefficients of 600 µV K(-1) and 335 µV K(-1) for PbS and PbSe nanocrystal pellets, respectively, were obtained at room temperature.

Solution-Based Synthesis of Layered Intergrowth Compounds of the Homologous Pbm Bi2n Te3n+m Series as Nanosheets.

Layered intergrowth compounds in the homologous Pbm Bi2n Te3n+m family are interesting because they are examples of natural heterostructures. We present a simple solution-based synthesis of two-dimensional nanosheets of PbBi2 Te4 , Pb2 Bi2 Te5 , and PbBi6 Te10 layered intergrowth compounds, which are members of the Pbm Bi2n Te3n+m [that is, (PbTe)m (Bi2 Te3 )n ] homologous series. Few-layer nanosheets exhibit narrow optical band gaps (0.25-0.7 eV) with semiconducting electronic-transport properties.

Ultrathin septuple layered PbBi2Se4 nanosheets.

Layered lead bismuth selenide, PbBi2Se4, an intergrowth compound of PbSe (rocksalt) and Bi2Se3 (hexagonal), is a topological insulator in the bulk phase. We present a simple solution based synthesis of two dimensional (2D) few seven atomic (septuple) layered PbBi2Se4 nanosheets (4-7 nm thick) for the first time. The excellent electrical transport in ultrathin PbBi2Se4 is attributed to the presence of dominant surface states that offer high electrical mobility (∼153 cm(2) V(-1) s(-1)) and scattering resistant carriers. Ultrathin 3-5 SLs PbBi2Se4 shows an n-type semiconducting behaviour with a band gap of ∼0.6 eV, which is confirmed by optical spectroscopy and thermopower measurements.