Engineering TALE-linked deaminases to facilitate precision adenine base editing in mitochondrial DNA.

DddA-derived cytosine base editors (DdCBEs) and transcription activator-like effector (TALE)-linked deaminases (TALEDs) catalyze targeted base editing of mitochondrial DNA (mtDNA) in eukaryotic cells, a method useful for modeling of mitochondrial genetic disorders and developing novel therapeutic modalities. Here, we report that A-to-G-editing TALEDs but not C-to-T-editing DdCBEs induce tens of thousands of transcriptome-wide off-target edits in human cells. To avoid these unwanted RNA edits, we engineered the substrate-binding site in TadA8e, the deoxy-adenine deaminase in TALEDs, and created TALED variants with fine-tuned deaminase activity. Our engineered TALED variants not only reduced RNA off-target edits by >99% but also minimized off-target mtDNA mutations and bystander edits at a target site. Unlike wild-type versions, our TALED variants were not cytotoxic and did not cause developmental arrest of mouse embryos. As a result, we obtained mice with pathogenic mtDNA mutations, associated with Leigh syndrome, which showed reduced heart rates.

Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases.

Mitochondrial DNA (mtDNA) editing paves the way for disease modeling of mitochondrial genetic disorders in cell lines and animals and also for the treatment of these diseases in the future. Bacterial cytidine deaminase DddA-derived cytosine base editors (DdCBEs) enabling mtDNA editing, however, are largely limited to C-to-T conversions in the 5'-TC context (e.g., TC-to-TT conversions), suitable for generating merely 1/8 of all possible transition (purine-to-purine and pyrimidine-to-pyrimidine) mutations. Here, we present transcription-activator-like effector (TALE)-linked deaminases (TALEDs), composed of custom-designed TALE DNA-binding arrays, a catalytically impaired, full-length DddA variant or split DddA originated from Burkholderia cenocepacia, and an engineered deoxyadenosine deaminase derived from the E. coli TadA protein, which induce targeted A-to-G editing in human mitochondria. Custom-designed TALEDs were highly efficient in human cells, catalyzing A-to-G conversions at a total of 17 target sites in various mitochondrial genes with editing frequencies of up to 49%.

BMP4 signaling plays critical roles in self-renewal of R2i mouse embryonic stem cells.

Mouse embryonic stem cells (mESCs) can be maintained in a pluripotent state under R2i culture conditions that inhibit the TGF-ß and ERK signaling pathways. BMP4 is another member of the TGF-ß family that plays a crucial role in maintaining the pluripotency state of mESCs. It has been reported that inhibition of BMP4 caused the death of R2i-grown cells. In this study, we used the loss-of-function approach to investigate the role of BMP4 signaling in mESC self-renewal. Inhibition of this pathway with Noggin and dorsomorphin, two bone morphogenetic protein (BMP) antagonists, elicited a quick death of the R2i-grown cells. We showed that the canonical pathway of BMP4 (BMP/SMAD) was dispensable for self-renewal and maintaining pluripotency of these cells. Transcriptome analysis of the BMPi-treated cells revealed that the p53 signaling and two adhesion (AD) and apoptotic mitochondrial change (MT) pathways could be involved in the cell death of the BMPi-treated cells. According to our results, inhibition of BMP4 signaling caused a decrease in cell adhesion and ECM detachment, which triggered anoikis in the R2i-grown cells. Altogether, these findings demonstrate that endogenous BMP signaling is required for the survival of mESCs under the R2i condition.

Synthesis of Alternating Polyisocyanate Copolymers by Anionic Polymerization for Mimicking Amphiphilic Helical Peptides.

The amphiphilic conformation of α-helical peptides has important biological functions, such as ion transport, antifreeze, and innate immunity, which can be mimicked by alternating polyisocyanate copolymers. We synthesized poly(allyl isocyanate-alt-(S)-(-)-α-methylbenzyl isocyanate (P(AIC-alt-SMBIC)) and ammonium-containing P(AIC-alt-SMBIC) (N-P(AIC-alt-SMBIC)), ensuring the amphiphilic helical conformation. The benzyl group of SMBIC plays an important role in alternating copolymerization with its steric and electron-withdrawing effects, while AIC provides an alkene group capable of introducing a customized functional group. The P(AIC-alt-SMBIC) with predominantly alternating sequence was acquired at fSMBIC /fAIC =8 with a controlled molecular weight and narrow dispersity. N-P(AIC-alt-SMBIC)s were synthesized from thiol-ene radical addition with P(AIC-alt-SMBIC).

Clathrate Hydrate Inhibition by Polyisocyanate with Diethylammonium Group.

Polymers containing amide groups have been used as kinetic hydrate inhibitors (KHIs). The amide group has good performance for hydrate nucleus adsorption, resulting in inhibition of hydrate growth. Polyisocyanates composed of an amide backbone can be KHI candidates; however, the use of polyisocyanates as KHIs has not yet been reported. Herein, we prepared water-soluble poly[3-[[2-(diethylamino)ethyl]thio]-1-propyl isocyanate-ran-hexyl isocyanate] (P(DETPIC-ran-HIC)) to investigate the ability of polyisocyanates to inhibit hydrate formation. In the tetrahydrofuran (THF) clathrate hydrate crystal growth inhibition tests, P(DETPIC-ran-HIC) showed better performance than the polyamide, poly(N-vinylpyrrolidone) (PVP).

Solution-State Long-Range Molecular Ordering in Poly(3-hexylthiophene).

A blend of poly(3-hexylthiophene) (P3HT) and poly(n-hexyl isocyanate-block-2-vinylpyridine) (PHIC-b-P2VP) in a common solvent shows the formation of long-range (micrometer-scale) nanowires of P3HT through hydrophobic interactions between the hexyl arms of P3HT and PHIC in a parallel way, which increase the planarity that leads to the generation of vibration bands with a lower free exciton bandwidth (W = 67 meV) in the solution state, which is further decreased to 9 meV after 48 h annealing of the blend film. The resulting nanowires of the P3HT show a 100-fold increase in current in comparison to pristine P3HT.

Discovery of Novel Cell Surface Markers for Purification of Embryonic Dopamine Progenitors for Transplantation in Parkinson's Disease Animal Models.

Despite the progress in safety and efficacy of cell replacement therapy with pluripotent stem cells (PSCs), the presence of residual undifferentiated stem cells or proliferating neural progenitor cells with rostral identity remains a major challenge. Here we report the generation of a LIM homeobox transcription factor 1 alpha (LMX1A) knock-in GFP reporter human embryonic stem cell (hESC) line that marks the early dopaminergic progenitors during neural differentiation to find reliable membrane protein markers for isolation of midbrain dopaminergic neurons. Purified GFP positive cells in vitro exhibited expression of mRNA and proteins that characterized and matched the midbrain dopaminergic identity. Further quantitative proteomics analysis of enriched LMX1A+ cells identified several membrane-associated proteins including a polysialylated embryonic form of neural cell adhesion molecule (PSA-NCAM) and contactin 2 (CNTN2), enabling prospective isolation of LMX1A+ progenitor cells. Transplantation of human-PSC-derived purified CNTN2+ progenitors enhanced dopamine release from transplanted cells in the host brain and alleviated Parkinson's disease-related phenotypes in animal models. This study establishes an efficient approach for purification of large numbers of human-PSC-derived dopaminergic progenitors for therapeutic applications.

Determination of complex dielectric function of CH3NH3PbBr3 perovskite cubic colloidal quantum dots by modified iterative matrix inversion method.

Recent advances in lead halide perovskite quantum dots appeal with their potential in various optoelectronic devices such as photovoltaics, photodetectors, light-emitting diodes (LEDs) and lasers. However, lack of information on the intrinsic optical properties of lead halide perovskite quantum dots (QDs) lags the progress in device performances and further development in various applications. In this letter, the complex dielectric function of CH3NH3PbBr3 perovskite cubic colloidal QDs was determined from the UV-Vis absorption by using a modified iterative matrix inversion (IMI) method. The modified IMI method takes into account the dilute solution with cubic inclusions, while the conventional method only considers spherical or elliptical inclusions by Maxwell-Garnett (MG) effective medium theory. In addition, singly subtractive Kramer Kronig (SSKK) relations have also been considered to compensate for possible errors arising from the finite wavelength range of the experimental absorption data.

Surface markers of human embryonic stem cells: a meta analysis of membrane proteomics reports.

INTRODUCTION: Human embryonic stem cells (hESCs) have unique biological features and attributes that make them attractive in various areas of biomedical research. With heightened applications, there is an ever increasing need for advancement of proteome analysis. Membrane proteins are one of the most important subset of hESC proteins as they can be used as surface markers. Areas covered: This review discusses commonly used surface markers of hESCs, and provides in-depth analysis of available hESC membrane proteome reports and the existence of these markers in many other cell types, especially cancer cells. Appreciating, existing ambiguity in the definition of a membrane protein, we have attempted a meta analysis of the published membrane protein reports of hESCs by using a combination of protein databases and prediction tools to find the most confident plasma membrane proteins in hESCs. Furthermore, responsiveness of plasma membrane proteins to differentiation has been discussed based on available transcriptome profiling data bank. Expert commentary: Combined transcriptome and membrane proteome analysis highlighted additional proteins that may eventually find utility as new cell surface markers.

Dual function of a living polymerization initiator through the formation of a chain-end-protecting cluster: density functional theory calculation.

Sodium benzanilide (Na(+)BA(-)) initiators have opened a new route to living anionic polymerization of n-hexylisocyanate (HIC) with 100% yield and controlled molecular weight. The NaBA initiators not only provide initiation points for polymerization by attacking HIC monomers but also successfully prevent back-biting side reactions without any help from additives. Our hypothesis on this dual function of the NaBA initiators is that they self-assemble to form protection shields around the chain ends. Indeed, our density functional theory calculations performed under experimental conditions on the free energy of formation of (NaBA)n clusters of various sizes and conformations searched by Monte Carlo simulations show that the BA(-) moiety forms a stable complex with Na(+) in a fan-like circular-sector shape owing to its double binding sites (N(-)-C=O ↔ N=C-O(-)) and that the tightly-bound NaBA units spontaneously self-assemble to form small (NaBA)n clusters (n = 2 and 4). The growing end of the polymer chain [(BA)(HIC)n(-)], which resembles BA(-), would also assemble with n - 1 NaBA units to form an n-mer cluster. We expect that the chain end in this cluster would be more available to attack small HIC monomers coming into the cluster (leading to chain growth) rather than folding back to attack the middle of the chain (leading to cyclotrimerization to isocyanurates and depolymerization).

Isoindigo-based small molecules for high-performance solution-processed organic photovoltaic devices: the electron donating effect of the donor group on photo-physical properties and device performance.

Five solution processable isoindigo-based donor-acceptor-donor (D-A-D) small molecules with different electron donating strengths have been designed and synthesized. The variation in the electron donating strength of the donor group strongly affected the optical, thermal, electrochemical and photovoltaic device performances of the isoindigo organic materials. The highest power conversion efficiency of ~3.2% was achieved in the bulk heterojunction photovoltaic device consisting of ID3T as the donor and PC70BM as the acceptor. This work demonstrates the potential of isoindigo moieties as electron-deficient units and presents guidelines for the synthesis of D-A-D small molecules for producing highly efficient, solution-processed organic photovoltaic devices.

Prime editing with genuine Cas9 nickases minimizes unwanted indels.

Unlike CRISPR-Cas9 nucleases, which yield DNA double-strand breaks (DSBs), Cas9 nickases (nCas9s), which are created by replacing key catalytic amino-acid residues in one of the two nuclease domains of S. pyogenesis Cas9 (SpCas9), produce nicks or single-strand breaks. Two SpCas9 variants, namely, nCas9 (D10A) and nCas9 (H840A), which cleave target (guide RNA-pairing) and non-target DNA strands, respectively, are widely used for various purposes, including paired nicking, homology-directed repair, base editing, and prime editing. In an effort to define the off-target nicks caused by these nickases, we perform Digenome-seq, a method based on whole genome sequencing of genomic DNA treated with a nuclease or nickase of interest, and find that nCas9 (H840A) but not nCas9 (D10A) can cleave both strands, producing unwanted DSBs, albeit less efficiently than wild-type Cas9. To inactivate the HNH nuclease domain further, we incorporate additional mutations into nCas9 (H840A). Double-mutant nCas9 (H840A + N863A) does not exhibit the DSB-inducing behavior in vitro and, either alone or in fusion with the M-MLV reverse transcriptase (prime editor, PE2 or PE3), induces a lower frequency of unwanted indels, compared to nCas9 (H840A), caused by error-prone repair of DSBs. When incorporated into prime editor and used with engineered pegRNAs (ePE3), we find that the nCas9 variant (H840A + N854A) dramatically increases the frequency of correct edits, but not unwanted indels, yielding the highest purity of editing outcomes compared to nCas9 (H840A).

Uni-molecular hollow micelles from amphiphilic homopolymer poly(2-(4-vinylphenyl)pyridine).

Amphiphilic homopolymer poly(2-(4-vinylphenyl)pyridine) (PVPPy) forms hollow micelles with uni-molecular thickness in a tetrahydrofuran/water (95/5 v/v) azeotropic solvent. Depending on the pH of the media, the micelles may be transformed to vesicles.

Arrangement of C60 via the self-assembly of post-functionalizable polyisocyanate block copolymer.

Poly(furfuryl isocyanate) (PFIC), which includes the reactive furan group, was synthesized by anionic polymerization using a sodium benzhydroxide (Na-BH), self-assembly initiator. We determined the optimum polymerization conditions by varying both the reaction time and the molar ratio of the monomer to the initiator. Block copolymer, poly(furfuryl isocyanate)-b-poly(n-hexyl isocyanate), was synthesized under optimized polymerization conditions. The PFIC was modified by Diels-Alder reactions with C60 for functionalization. Transmission electron microscopy (TEM) was used to study the self-assembly of block copolymers and modified block copolymer with C60. C60 formed highly ordered aggregates on the PFIC domains via self-assembly of the block copolymer.

Intermolecular interactions of an isoindigo-based organic semiconductor with various crosslinkers through hydrogen bonding.

Three crosslinkers (1,4-diaminobutane, 1,8-diaminooctane, and 1,6-hexanediol) were selected to produce hydrogen-bonded networks using a simple and effective method. The effects of these crosslinkers on the arrangement of crystalline structures were successfully studied using X-ray diffraction and high-voltage electron microscopy. The hydrogen-bonded isoindigo-based small molecules with 1,4-diaminobutane showed the best performance, with a crystal structure showing long-range order, due to the more suitable length of the 1,4-diaminobutane chain. The hole mobility estimated from hole-only devices based on isoindigo was enhanced from 1.24 × 10-6 cm2 V-1 s-1 to 7.28 × 10-4 cm2 V-1 s-1 as a result of the inclusion of this crosslinker, due to the formation of stronger interactions between the molecules.

Synthesis and photophysical properties of N-alkyl dithieno[3,2-b:2',3'-d]pyrrole based donor/acceptor-π-conjugated copolymers for solar-cell application.

Two kinds of donor-acceptor π-conjugated copolymer based on poly{[N-hexyl-dithieno(3,2-b:2',3'-d)pyrrole-2,6-diyl]alt-[isoindigo]} (PDTP-IID) and poly{[N-hexyl-dithieno(3,2-b:2',3'-d)pyrrole-2,6-diyl]alt-[thiazol-2,5-diyl]} (PDTP-Thz) were investigated. These copolymers were synthesized via a Stille coupling reaction. The results showed the structure-property relationships of different donor-acceptor (D-A) combinations. The polymer structures and photophysical properties were characterized by 1H NMR, TGA, DSC, UV-vis absorption spectroscopy, AFM, CV, and XRD measurement. Through UV-vis absorption and cyclic voltammetry (CV) measurements, it showed that the copolymers exhibit not only a low bandgap of 1.29 eV and 1.51 eV but also a deep highest occupied molecular orbital (HOMO) of -5.49 and -5.11 eV. Moreover, photovoltaic properties in combination with the fullerene derivatives were investigated. The device based on the copolymers with PC71BM exhibited higher maximum power conversion efficiency and higher maximum short-circuit current density of 0.23% with 1.64 mA cm-2 of PDTP-IID:PC71BM and 0.13% with 1.11 mA cm-2 of PDTP-Thz:PC71BM than those of the copolymers with PC61BM. Measurements performed for N-hexyl-dithieno(3,2-b:2',3'-d)pyrrole-based copolymers proved the potential of these polymers to be applied in optoelectronic applications.

Polymers based on thieno[3,4-c]pyrrole-4,6-dione and pyromellitic diimide by CH-CH arylation reaction for high-performance thin-film transistors.

Three homopolymers were successfully synthesized by direct CH-CH arylation polymerization of thieno[3,4-c]pyrrole-4,6-dione or pyromellitic diimide derivatives affording highly purified polymers with high molecular weights (43.0-174.7 K). Thieno[3,4-c]pyrrole-4,6-dione and pyromellitic diimide derivatives are considered as electron-withdrawing units. The synthesized homopolymers P1, P2, and P3 showed band gaps in the range of 2.13-2.08 eV, respectively. The electron mobilities of the three homopolymers have been investigated. The thin film transistor for P1 prepared by the eutectic-melt-assisted nanoimprinting method achieved an electron mobility of 2.11 × 10-3 cm2 s-1 V-1. Based on the obtained results, the synthesized polymers can be used as potential electron acceptors in solar cell applications.

Base editing in human cells with monomeric DddA-TALE fusion deaminases.

Inter-bacterial toxin DddA-derived cytosine base editors (DdCBEs) enable targeted C-to-T conversions in nuclear and organellar DNA. DddAtox, the deaminase catalytic domain derived from Burkholderia cenocepacia, is split into two inactive halves to avoid its cytotoxicity in eukaryotic cells, when fused to transcription activator-like effector (TALE) DNA-binding proteins to make DdCBEs. As a result, DdCBEs function as pairs, which hampers gene delivery via viral vectors with a small cargo size. Here, we present non-toxic, full-length DddAtox variants to make monomeric DdCBEs (mDdCBEs), enabling mitochondrial DNA editing with high efficiencies of up to 50%, when transiently expressed in human cells. We demonstrate that mDdCBEs expressed via AAV in cultured human cells can achieve nearly homoplasmic C-to-T editing in mitochondrial DNA. Interestingly, mDdCBEs often produce mutation patterns different from those obtained with conventional dimeric DdCBEs. Furthermore, mDdCBEs allow base editing at sites for which only one TALE protein can be designed. We also show that transfection of mDdCBE-encoding mRNA, rather than plasmid, can reduce off-target editing in human mitochondrial DNA.

Self-assembly of POSS-Polystyrene Bottlebrush Block Copolymers on an Angle-Robust Selective Absorber for Enhancing the Purity of Reflective Structural Color.

A facile approach for improving color purity is explored by the introduction of an angle-robust selective absorber (ARSA) into bottlebrush block copolymer (BBCP)-based one-dimensional (1D) photonic crystals (PCs). The BBCPs of poly[(3-(12-(cis-5-norbornene-exo-2,3-dicarboximido)dodecanoylamino)propyl POSS)-block-(norbornene-graft-styrene)], Px (x = 1-4), with ultrahigh molecular weights (Mn ∼ 2260 kDa) and low dispersities (D̵ ∼ 1.07) are synthesized by ring-opening metathesis polymerization. The 1D PCs of the lamellar structure are fabricated by self-assembly of the BBCP with different periodicities for full color-generation (blue, green, and red). The optically tailored substrate (i.e., ARSA) is used to modulate the spectral line shape with selective absorption in the near-infrared range. Optical simulation proposes the optimized 1D PC structures on the ARSA, and it provides the reproducibility of the predictable color. The simulated structures are well matched with the experimental results, verifying the enhancement of color saturation even at various incident angles (0-70°).

Synthesis of Well-defined Amphiphilic Block Copolymers by Organotellurium-Mediated Living Radical Polymerization (TERP).

Low-molecular weight amphiphilic diblock copolymers, polystyrene-block-poly (2-vinylpyridine) (PS-b-P2VP), and (P2VP-b-PS) with different block ratios were synthesized for the first time via organotellurium-mediated living radical polymerization (TERP). For both the homo- and block copolymerizations, good agreement between the theoretical, and experimental molecular weights was found with nearly 100% yield in every case. The molecular weight distribution for all the samples ranged between 1.10 and 1.24, which is well below the theoretical lower limit of 1.50 for a conventional free radical polymerization. Furthermore, a very simple approach to producing highly dense arrays of titania nanoparticles (TiO2 ) is presented using a site-selective reaction of titanium tetraisopropoxide within the P2VP domains of micellar film of P2VP-b-PS in toluene through the sol-gel method.