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Nature Chemical Biology Aug 20235-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct,...
5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here we present direct methylation sequencing (DM-Seq), a bisulfite-free method for profiling 5mC at single-base resolution using nanogram quantities of DNA. DM-Seq employs two key DNA-modifying enzymes: a neomorphic DNA methyltransferase and a DNA deaminase capable of precise discrimination between cytosine modification states. Coupling these activities with deaminase-resistant adapters enables accurate detection of only 5mC via a C-to-T transition in sequencing. By comparison, we uncover a PCR-related underdetection bias with the hybrid enzymatic-chemical TET-assisted pyridine borane sequencing approach. Importantly, we show that DM-Seq, unlike bisulfite sequencing, unmasks prognostically important CpGs in a clinical tumor sample by not confounding 5mC with 5-hydroxymethylcytosine. DM-Seq thus offers an all-enzymatic, nondestructive, faithful and direct method for the reading of 5mC alone.
Topics: Animals; 5-Methylcytosine; DNA Methylation; Cytosine; DNA; Sequence Analysis, DNA; Mammals
PubMed: 37322153
DOI: 10.1038/s41589-023-01318-1 -
Journal of the American Chemical Society Aug 2023The chemistry and physics of macropolyhedral BH clusters have attracted significant attention due to the interesting photophysical properties of -BH (blue emission,...
The chemistry and physics of macropolyhedral BH clusters have attracted significant attention due to the interesting photophysical properties of -BH (blue emission, laser properties) and related potential applications. We have focused our attention on the "forgotten" -BH isomer, which has received very little attention since its discovery compared to its -BH isomer, presumably because numerous studies have reported this isomer as nonluminescent. In our study, we show that in crystalline form, -BH exhibits blue fluorescence and becomes phosphorescent when substituted at various positions on the cluster, associated with peculiar microstructural-dependent effects. This work is a combined theoretical and experimental investigation that includes the synthesis, separation, structural characterization, and first elucidation of the photophysical properties of three different monothiol-substituted cluster isomers, [1-HS--BH] , [3-HS--BH] , and [4-HS--BH] , of which isomers and have been proved to exist in two different polymorphic forms. All of these newly substituted macropolyhedral cluster derivatives (, , and ) have been fully characterized by NMR spectroscopy, mass spectrometry, single-crystal X-ray diffraction, IR spectroscopy, and luminescence spectroscopy. This study also presents the first report on the mechanochromic shift in the luminescence of a borane cluster and generally enriches the area of rather rare boron-based luminescent materials. In addition, we present the first results proving that they are useful constituents of carbon-free self-assembled monolayers.
PubMed: 37532522
DOI: 10.1021/jacs.3c05530 -
Nanomaterials (Basel, Switzerland) Aug 2023Carbon-doped boron nitride (denoted by BN/C) was prepared through the pyrolysis at 1100 °C of a nanostructured mixture of an alkyl amine borane adduct and ammonia...
Carbon-doped boron nitride (denoted by BN/C) was prepared through the pyrolysis at 1100 °C of a nanostructured mixture of an alkyl amine borane adduct and ammonia borane. The alkyl amine borane adduct acts as a soft template to obtain nanospheres. This bottom-up approach for the synthesis of nanostructured BN/C is relatively simple and compelling. It allows the structure obtained during the emulsion process to be kept. The final BN/C materials are microporous, with interconnected pores in the nanometer range (0.8 nm), a large specific surface area of up to 767 m·g and a pore volume of 0.32 cm·g. The gas sorption studied with CO demonstrated an appealing uptake of 3.43 mmol·g at 0 °C, a high CO/N selectivity (21) and 99% recyclability after up to five adsorption-desorption cycles.
PubMed: 37686897
DOI: 10.3390/nano13172389 -
Chemical Science Feb 2024The carbon dioxide radical anion [CO˙] is a highly reactive species of fundamental and synthetic interest. However, the direct one-electron reduction of CO to generate...
The carbon dioxide radical anion [CO˙] is a highly reactive species of fundamental and synthetic interest. However, the direct one-electron reduction of CO to generate [CO˙] occurs at very negative reduction potentials, which is often a limiting factor for applications. Here, we show that NHC-CO-BR species - generated from the Frustrated Lewis Pair (FLP)-type activation of CO by N-heterocyclic carbenes (NHCs) and boranes (BR) - undergo single electron reduction at a less negative potential than free CO. A net gain of more than one volt was notably measured with a CAAC-CO-B(CF) adduct, which was chemically reduced to afford [CAAC-CO-B(CF)˙]. This room temperature stable radical anion was characterized by EPR spectroscopy and by single-crystal X-ray diffraction analysis. Of particular interest, DFT calculations showed that, thanks to the electron withdrawing properties of the Lewis acid, significant unpaired spin density is localised on the carbon atom of the CO moiety. Finally, these species were shown to exhibit analogous reactivity to the carbon dioxide radical anion [CO˙] toward DMPO. This work demonstrates the advantage provided by FLP systems in the generation and stabilization of [CO˙]-like species.
PubMed: 38425525
DOI: 10.1039/d3sc06325a -
Inorganic Chemistry Oct 2023A series of -substituted acenaphthene-based phosphine selenoether bidentate ligands Acenap(PrP)(SeAr) (-, Acenap = acenaphthene-5,6-diyl, Ar = Ph, mesityl,...
A series of -substituted acenaphthene-based phosphine selenoether bidentate ligands Acenap(PrP)(SeAr) (-, Acenap = acenaphthene-5,6-diyl, Ar = Ph, mesityl, 2,4,6-trisopropylphenyl and supermesityl) were prepared. The rigid acenaphthene framework induces a forced overlap of the phosphine and selenoether lone pairs, resulting in a large magnitude of through-space coupling, ranging from 452 to 545 Hz. These rigid ligands - were used to prepare a series of selected late d-block metals, mercury, and borane complexes, which were characterized, including by multinuclear NMR and single-crystal X-ray diffraction. The Lewis acidic motifs (BH, Mo(CO), Ag, PdCl, PtCl, and HgCl) bridge the two donor atoms (P and Se) in all but one case in the solid-state structures. Where the bridging motif contained NMR-active nuclei (B, Ag, Ag, Pt, and Hg), and couplings are observed directly, in addition to the altered in the respective NMR spectra. The solution NMR data are correlated with single-crystal diffraction data, and in the case of mercury(II) complexes, they are also correlated with the solid-state NMR data and coupling deformation density calculations. The latter indicate that the through-space interaction dominates in free , while in the complex, the main coupling pathway is via the metal atom and not through the carbon framework of the acenaphthene ring system.
PubMed: 37722079
DOI: 10.1021/acs.inorgchem.3c02255 -
Advanced Science (Weinheim,... Jul 2023Ammonia borane (AB), a liquid hydrogen storage material, has attracted increasing attention for hydrogen utilization because of its high hydrogen content. However, the... (Review)
Review
Ammonia borane (AB), a liquid hydrogen storage material, has attracted increasing attention for hydrogen utilization because of its high hydrogen content. However, the slow kinetics of AB hydrolysis and the indefinite catalytic mechanism remain significant problems for its large-scale practical application. Thus, the development of efficient AB hydrolysis catalysts and the determination of their catalytic mechanisms are significant and urgent. A summary of the preparation process and structural characteristics of various supported catalysts is presented in this paper, including graphite, metal-organic frameworks (MOFs), metal oxides, carbon nitride (CN), molybdenum carbide (MoC), carbon nanotubes (CNTs), boron nitride (h-BN), zeolites, carbon dots (CDs), and metal carbide and nitride (MXene). In addition, the relationship between the electronic structure and catalytic performance is discussed to ascertain the actual active sites in the catalytic process. The mechanism of AB hydrolysis catalysis is systematically discussed, and possible catalytic paths are summarized to provide theoretical considerations for the designing of efficient AB hydrolysis catalysts. Furthermore, three methods for stimulating AB from dehydrogenation by-products and the design of possible hydrogen product-regeneration systems are summarized. Finally, the remaining challenges and future research directions for the effective development of AB catalysts are discussed.
PubMed: 37118857
DOI: 10.1002/advs.202300726 -
Molecules (Basel, Switzerland) Sep 2023The octahydridotriborate anion plays a crucial role in the field of polyhedral boron chemistry, facilitating the synthesis of higher boranes and the preparation of...
The octahydridotriborate anion plays a crucial role in the field of polyhedral boron chemistry, facilitating the synthesis of higher boranes and the preparation of diverse transition metal complexes. Among the stable forms of this anion, CsBH (or (n-CH)N)[BH] have been identified. These salts serve as valuable precursors for the synthesis of metallaboranes, wherein the triborate anion acts as a ligand coordinating to the metal center. In this study, we have successfully synthesized a novel rhodatetraborane dihydride, [Rh(-BH)(H)(PPh)] (), which represents a Rh(III) complex featuring a bidentate chelate ligand fasormed by BH. Extensive characterization of this rhodatetraborane complex has been performed using NMR spectroscopy in solution and X-ray diffraction analysis in the solid state. Notably, the complex exhibits intriguing fluxional behavior, which has been investigated using NMR techniques. Moreover, we have explored the reactivity of complex towards pyridine (py) and dimethylphenylphosphine (PMePh). Our findings highlight the labile nature of this four-vertex rhodatetraborane as it undergoes disassembly upon attack from the corresponding Lewis base, resulting in the formation of borane adducts, LBH, where L = py, PMePh. Furthermore, in these reactions, we report the characterization of new cationic hydride complexes, such as [Rh(H)(PPh) (py)] () and [Rh(H)(PMePh)]. Notably, the latter complex has been characterized as the octahydridotriborate salt [Rh(H)(PMePh)][BH] (), which extends the scope of rhodatetraborane derivatives.
PubMed: 37764238
DOI: 10.3390/molecules28186462 -
Molecules (Basel, Switzerland) May 2023Traditionally, drugs were obtained by extraction from medicinal plants, but more recently also by organic synthesis. Today, medicinal chemistry continues to focus on... (Review)
Review
Traditionally, drugs were obtained by extraction from medicinal plants, but more recently also by organic synthesis. Today, medicinal chemistry continues to focus on organic compounds and the majority of commercially available drugs are organic molecules, which can incorporate nitrogen, oxygen, and halogens, as well as carbon and hydrogen. Aromatic organic compounds that play important roles in biochemistry find numerous applications ranging from drug delivery to nanotechnology or biomarkers. We achieved a major accomplishment by demonstrating experimentally/theoretically that boranes, carboranes, as well as metallabis(dicarbollides), exhibit global 3D aromaticity. Based on the stability-aromaticity relationship, as well as on the progress made in the synthesis of derivatized clusters, we have opened up new applications of boron icosahedral clusters as key components in the field of novel healthcare materials. In this brief review, we present the results obtained at the Laboratory of Inorganic Materials and Catalysis (LMI) of the Institut de Ciència de Materials de Barcelona (ICMAB-CSIC) with icosahedral boron clusters. These 3D geometric shape clusters, the semi-metallic nature of boron and the presence of -cluster hydrogen atoms that can interact with biomolecules through non-covalent hydrogen and dihydrogen bonds, play a key role in endowing these compounds with unique properties in largely unexplored (bio)materials.
Topics: Boron; Nanomedicine; Boranes; Pharmaceutical Preparations; Hydrogen
PubMed: 37298925
DOI: 10.3390/molecules28114449 -
Molecules (Basel, Switzerland) Aug 2023The review covers more than a century of decaborane chemistry from the first synthesis by Alfred Stock to the present day. The main attention is paid to the reactions of... (Review)
Review
The review covers more than a century of decaborane chemistry from the first synthesis by Alfred Stock to the present day. The main attention is paid to the reactions of the substitution of hydrogen atoms by various atoms and groups with the formation of -polyhedral boron-halogen, boron-oxygen, boron-sulfur, boron-nitrogen, boron-phosphorus, and boron-carbon bonds. Particular attention is paid to the chemistry of -borane -[BH], whose structure is formed by two decaborane moieties with a common edge, the chemistry of which has been intensively developed in the last decade.
PubMed: 37687117
DOI: 10.3390/molecules28176287 -
Molecules (Basel, Switzerland) Apr 2024Borane-trimethylamine complex (MeN·BH; BTM) is the most stable of the amine-borane complexes that are commercially available, and it is cost-effective. It is a valuable... (Review)
Review
Borane-trimethylamine complex (MeN·BH; BTM) is the most stable of the amine-borane complexes that are commercially available, and it is cost-effective. It is a valuable reagent in organic chemistry with applications in the reduction of carbonyl groups and carbon-nitrogen double bond reduction, with considerable examples in the reduction of oximes, hydrazones and azines. The transfer hydrogenation of aromatic -heterocycles and the selective -monomethylation of primary anilines are further examples of recent applications, whereas the reduction of nitrobenzenes to anilines and the reductive deprotection of -tritylamines are useful tools in the organic synthesis. Moreover, BTM is the main reagent in the regioselective cleavage of cyclic acetals, a reaction of great importance for carbohydrate chemistry. Recent innovative applications of BTM, such as CO utilization as feedstock and radical chemistry by photocatalysis, have extended their usefulness in new reactions. The present review is focused on the applications of borane-trimethylamine complex as a reagent in organic synthesis and has not been covered in previous reviews regarding amine-borane complexes.
PubMed: 38731507
DOI: 10.3390/molecules29092017