Direct decarboxylation of ten-eleven translocation-produced 5-carboxylcytosine in mammalian genomes forms a new mechanism for active DNA demethylation

DNA cytosine methylation (5-methylcytosine, 5mC) is the most important epigenetic mark in higher eukaryotes. 5mC in genomes is dynamically controlled by writers and erasers. DNA (cytosine-5)-methyltransferases (DNMTs) are responsible for the generation and maintenance of 5mC in genomes. Active demethylation of 5-methylcytosine (5mC) is achieved by ten-eleven translocation (TET) dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are further processed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER) to restore unmodified cytosines. The TET-TDG-BER pathway could cause the production of DNA strand breaks and therefore jeopardize the integrity of genomes. Here, we investigated the direct decarboxylation of 5caC in mammalian genomes by using metabolic labeling with 2′-fluorinated 5caC (F-5caC) and mass spectrometry analysis. Our results clearly demonstrated the decarboxylation of 5caC occurring in mammalian genomes, which unveiled that, in addition to the TET-TDG-BER pathway, the direct decarboxylation of TET-produced 5caC constituted a new pathway for active demethylation of 5mC in mammalian genomes.

We demonstrated that the ten-eleven translocation (TET) dioxygenase-mediated oxidation of 5-methylcytosine followed by direct decarboxylation of 5-carboxylcytosine constitutes a novel pathway for active DNA demethylation in mammalian genomes.     

Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase

The discovery of 5-hydroxymethylcytosine (5hmC) in mammalian genomes is a landmark in epigenomics study. Similar to 5-methylcytosine (5mC), 5hmC is viewed as a critical epigenetic modification. Deciphering the functions of 5hmC necessitates the location analysis of 5hmC in genomes. Here, we proposed an engineered deaminase-mediated sequencing (EDM-seq) method for the quantitative detection of 5hmC in DNA at single-nucleotide resolution. This method capitalizes on the engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein to produce differential deamination activity toward cytosine, 5mC, and 5hmC. In EDM-seq, the engineered A3A (eA3A) protein can deaminate C and 5mC but not 5hmC. The original C and 5mC in DNA are deaminated by eA3A to form U and T, both of which are read as T during sequencing, while 5hmC is resistant to deamination by eA3A and is still read as C during sequencing. Therefore, the remaining C in the sequence manifests the original 5hmC. By EDM-seq, we achieved the quantitative detection of 5hmC in genomic DNA of lung cancer tissue. The EDM-seq method is bisulfite-free and does not require DNA glycosylation or chemical treatment, which offers a valuable tool for the straightforward and quantitative detection of 5hmC in DNA at single-nucleotide resolution.

In EDM-seq, the original C and 5mC in DNA are deaminated by eA3A to form U and T, both of which are read as T during sequencing. While the 5hmC is resistant to deamination by eA3A and is still read as C during sequencing.     

Site-specific quantification of 5-carboxylcytosine in DNA by chemical conversion coupled with ligation-based PCR

5-Methylcytosine (5mC) is the most important epigenetic modification in mammals. The active DNA demethylation could be achieved through the ten-eleven translocation (TET) protein-mediated oxidization of 5mC with the generation of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). It has been known that 5mC, 5hmC and 5fC play critical roles in modulating gene expression. However, unlike the 5mC, 5hmC, and 5fC, the functions of 5caC are still underexplored. Investigation of the functions of 5caC relies on the accurate quantification and localization analysis of 5caC in DNA. In the current study, we developed a method by chemical conversion in conjugation with ligation-based real-time quantitative PCR (qPCR) for the site-specific quantification of 5caC in DNA. This method depends on the selective conversion of 5caC to form dihydrouracil (DHU) by pyridine borane treatment. DHU behaves like thymine and pairs with adenine (DHU-A). Thus, the chemical conversion by pyridine borane leads to the transformation of base paring from 5caC-G to DHU-A, which is utilized to achieve the site-specific detection and quantification of 5caC in DNA. As a proof-of-concept, the developed method was successfully applied in the site-specific quantification of 5caC in synthesized DNA spiked in complex biological samples. The method is rapid, straightforward and cost-effective, and shows promising in promoting the investigation of the functional roles of 5caC in future study.     

Online trapping and enrichment ultra performance liquid chromatography–tandem mass spectrometry method for sensitive measurement of “arginine-asymmetric dimethylarginine cycle” biomarkers in human exhaled breath condensate

Background

Exhaled breath condensate (EBC) is a biofluid collected non invasively that, enabling the measurement of several biomarkers, has proven useful in the study of airway inflammatory diseases, including asthma, COPD and cystic fibrosis. To the best of our knowledge, there is no previous report of any analytical method to detect ADMA in EBC.

Objectives

Aim of this work was to develop an online sample trapping and enrichment system, coupled with an UPLC–MS/MS method, for simultaneous quantification of seven metabolites related to “Arginine-ADMA cycle”, using the isotopic dilution.

Methods

Butylated EBC samples were trapped in an online cartridge, washed before and after each injection with cleanup solution to remove matrix components and switched inline into the high pressure analytical column. Multiple reaction monitoring in positive mode was used for analyte quantification by tandem mass spectrometry.

Results

Validation studies were performed in EBC to examine accuracy, precision and robustness of the method. For each compound, the calibration curves showed a coefficient of correlation (r²) greater than 0.992. Accuracy (%Bias) was <3% except for NMMA and H-Arg (<20%), intra- and inter-assay precision (expressed as CV%) were within ±20% and recovery ranged from 97.1 to 102.8% for all analytes.Inter-day variability analysis on 20 EBC of adult subjects did not demonstrate any significant variation of quantitative data for each metabolite. ADMA and SDMA mean concentrations (μmol L⁻¹), measured in EBC samples of asthmatic adolescents are significantly increased (p < 0.0001) than in normal controls (0.0040 ± 0.0021 vs. 0.0012 ± 0.0005 and 0.0020 ± 0.0015 vs. 0.0002 ± 0.0001, respectively), as well the ADMA/Tyr (0.34 ± 0.09 vs. 0.12 ± 0.02, p < 0.0001) and the SDMA/Tyr ratio (0.10 ± 0.04 vs. 0.015 ± 0.004, p < 0.0001).

Conclusions

The proposed method features simple specimen preparation, maintenance of an excellent peak shape of all metabolites and reduced matrix effects as well mass spectrometer noise. Moreover, the possibility to perform different cycles of enrichment, using large injection volumes, compensated for the low concentration of analytes contained in EBC, leading to a good analytical sensitivity. Preliminary data obtained from asthmatic and healthy adolescents, demonstrated that the analytical method applied to EBC seems suitable not only for research purposes, but also for clinical routinely analysis.     

Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine

5-Formylcytosine (fC or (5-CHO)dC) and 5-carboxylcytosine (caC or (5-COOH)dC) have recently been identified as constituents of mammalian DNA. The nucleosides are formed from 5-methylcytosine (mC or (5-Me)dC) via 5-hydroxymethylcytosine (hmC or (5-HOMe)dC) and are possible intermediates of an active DNA demethylation process. Here we show efficient syntheses of phosphoramidites which enable the synthesis of DNA strands containing these cytosine modifications based on Pd(0)-catalyzed functionalization of 5-iododeoxycytidine. The first crystal structure of fC reveals the existence of an intramolecular H-bond between the exocyclic amine and the formyl group, which controls the conformation of the formyl substituent. Using a newly designed in vitro mutagenicity assay we show that fC and caC are only marginally mutagenic, which is a prerequisite for the bases to function as epigenetic control units.     

5-Hydroxymethylcytosine, the sixth base of the genome

5-Hydroxymethylcytosine (hmC) was recently discovered as a new constituent of mammalian DNA. Besides 5-methylcytosine (mC), it is the only other modified base in higher organisms. The discovery is of enormous importance because it shows that the methylation of cytosines to imprint epigenetic information is not a final chemical step that leads to gene silencing but that further chemistry occurs at the methyl group that might have regulatory function. Recent progress in hmC detection--most notably LC-MS and glucosyltransferase assays--helped to decipher the precise distribution of hmC in the body. This led to the surprising finding that, in contrast to constant mC levels, the hmC levels are strongly tissue-specific. The highest values of hmC are found in the central nervous system. It was furthermore discovered that hmC is involved in regulating the pluripotency of stem cells and that it is connected to the processes of cellular development and carcinogenesis. Evidence is currently accumulating that hmC may not exclusively be an intermediate of an active demethylation process, but that it functions instead as an important epigenetic marker.     

A review of recent trends in electrospray ionisation-mass spectrometry for the analysis of metal-organic ligand complexes

Background

Asymmetric dimethylarginine (ADMA), an endogenous nitric oxide (NO) formation inhibitor, has emerged as a promising biomarker of NO-associated endothelial dysfunction in cardiovascular diseases as well in chronic renal failure. The interest in potentially fundamental role of this metabolite, in basic and clinical research, led to the development of numerous analytical methods for the quantitative determination of ADMA and dimethylarginines in biological systems, notably plasma, serum and urine.

Objectives

The aim of this work was to present a simple, fast and accurate UPLC-tandem-MS-based method for the simultaneous determination and quantification of arginine, ADMA, SDMA, NMMA, homo-arginine and citrulline. This method is designed for high sample throughput of only 10 μL of human plasma, serum or urine.

Methods

The analysis time is reduced to 1.9 min by an ultrahigh-performance liquid chromatography run coupled with electrospray ionization (ESI) in the positive mode tandem mass spectrometry detection.

Results

The method was validated in plasma, serum and urine. Correlation coefficients (r²) of the calibration curves in all matrices considered ranged from 0.9810 to 0.9993. Inter- and intra-assay precision, accuracy, recovery and carry-over were evaluated for validation. The LOD was 0.01 μM for all compounds in water, plasma and serum and 0.1 μM in urine. The LOQ was 0.05 μM for ADMA, SDMA, NMMA and H-Arg and 0.5 μM for Arg and Cit in water, plasma and serum; while in urine was 0.1 μM for ADMA, SDMA, NMMA and H-Arg and 0.5 μM for Arg and Cit.The precision was ranged from 1% to 15% expressed as CV% and the accuracy (bias %) was <±7% for all added concentrations with the exception of NMMA (−10%).ADMA mean plasma levels, measured in healthy adults and newborns, were in accord with literature data published: (M ± SD) 0.56 ± 0.10 μM and 0.84 ± 0.21 μM, respectively, showing that ADMA levels in plasma decreased with age. In serum we have similar data (0.54 ± 0.18 μM and 1.14 ± 0.36 μM), while in neonatal urine ADMA was 11.98 ± 7.13 μmol mmol⁻¹ creatinine.

Conclusions

Data from calibration curves and method validation reveal that the method is accurate and precise. The fast run time, the feasibility of high sample throughput and the small amount of sample required make this method very suitable for routine analysis in the clinical setting.     

5-Methylcytosine is Oxidized to the Natural Metabolites of TET Enzymes by a Biomimetic Iron(IV)-Oxo Complex

Ten-eleven-translocation (TET) methyl cytosine dioxygenases play a key role in epigenetics by oxidizing the epigenetic marker 5-methyl cytosine (5mC) to 5-hydroxymethyl cytosine (5hmC), 5-formyl cytosine (5fC), and 5-carboxy cytosine (5cC). Although much of the metabolism of 5mC has been studied closely, certain aspects—such as discrepancies among the observed catalytic activity of TET enzymes and calculated bond dissociation energies of the different cytosine substrates—remain elusive. Here, it is reported that the DNA base 5mC is oxidized to 5hmC, 5fC, and 5cC by a biomimetic iron(IV)-oxo complex, reminiscent of the activity of TET enzymes. Studies show that 5hmC is preferentially turned over compared with 5mC and 5fC and that this is in line with the calculated bond dissociation energies. The optimized syntheses of d₃-5mC and d₂-5hmC are also reported and in the reaction with the biomimetic iron(IV)-oxo complex these deuterated substrates showed large kinetic isotope effects, confirming the hydrogen abstraction as the rate-limiting step. Taken together, these results shed light on the intrinsic reactivity of the C−H bonds of epigenetic markers and the contribution of the second coordination sphere in TET enzymes.     

VOF simulations of the contact angle dynamics during the drop spreading: Standard models and a new wetting force model

Introduction

In this study,a novel numerical implementation for the adhesion of liquid droplets impacting normally on solid dry surfaces is presented. The advantage of this new approach, compared to the majority of existing models, is that the dynamic contact angle forming during the surface wetting process is not inserted as a boundary condition, but is derived implicitly by the induced fluid flow characteristics (interface shape) and the adhesion physics of the gas–liquid-surface interface (triple line), starting only from the advancing and receding equilibrium contact angles. These angles are required in order to define the wetting properties of liquid phases when interacting with a solid surface.

Methodology

The physical model is implemented as a source term in the momentum equation of a Navier-Stokes CFD flow solver as an “adhesion-like” force which acts at the triple-phase contact line as a result of capillary interactions between the liquid drop and the solid substrate. The numerical simulations capture the liquid–air interface movement by considering the volume of fluid (VOF) method and utilizing an automatic local grid refinement technique in order to increase the accuracy of the predictions at the area of interest, and simultaneously minimize numerical diffusion of the interface.

Results

The proposed model is validated against previously reported experimental data of normal impingement of water droplets on dry surfaces at room temperature. A wide range of impact velocities, i.e. Weber numbers from as low as 0.2 up to 117, both for hydrophilic (θ_adv = 10° – 70°) and hydrophobic (θ_adv = 105° – 120°) surfaces, has been examined. Predictions include in addition to droplet spreading dynamics, the estimation of the dynamic contact angle; the latter is found in reasonable agreement against available experimental measurements.

Conclusion

It is thus concluded that theimplementation of this model is an effective approach for overcoming the need of a pre-defined dynamic contact angle law, frequently adopted as an approximate boundary condition for such simulations. Clearly, this model is mostly influential during the spreading phase for the cases of low We number impacts (We < ˜80) since for high impact velocities, inertia dominates significantly over capillary forces in the initial phase of spreading.     

Quantification of DNA methylation and hydroxymethylation in Alzheimer's disease mouse model using LC‐MS/MS

Ambiguous alteration patterns of 5‐methylcytosine (5mC) and 5‐hydroxymethylcytosine (5hmC) involved in Alzheimer's disease (AD) obstructed the mechanism investigation of this neurological disorder from epigenetic view. Here, we applied a fully quantitative and validated LC‐MS/MS method to determine genomic 5mC and 5hmC in the brain cortex of 3 month‐aged (12, 15, and 18 month) AD model mouse and found significant increases of 5mC and 5hmC levels in different months of AD mouse when compared with age‐matched wild‐type control and exhibited rising trend from 12‐month to 18‐month AD mouse, thereby supporting genomic DNA methylation and hydroxymethylation were positively correlated with developing AD.     

Differential scanning calorimetric examination of the tracheal cartilage after primary reconstruction with differential suturing techniques

Objective

Long segmental tracheal defects often lead to life threatening clinical conditions. Treatment of these lesions still represents an unsolved surgical challenge. The aim of the study was to test the effect of continuous and simple interrupted suturing in the replacement of long segment tracheal defects using polytetrafluoroethylene (PTFE) vascular prosthesis in a rabbit model.

Methods

2 cm long segment of the cervical trachea was resected in 20 New Zealand rabbits. The trachea was replaced with reinforced polytetrafluoroethylene vascular graft. The anastomoses were performed telescopically using continuous (group I, n = 10) or simple interrupted sutures (group II, n = 10). Laser Doppler measurements were taken before the resection and following the anastomoses. Length of survivals were noted, the patency and microscopical pattern of the anastomoses were evaluated. Calorimetric examinations were performed to detect possible structural changes in the tracheal cartilage.

Results

Following the resection local microcirculation decreased by 9 ± 4%. The anastomoses caused a significant decrease of 29% in group I (p = 0.02) and 13% in group II. The mean survival was 58 ± 17 and 135 ± 25 days, respectively. Calorimetric results showed no change after the resection, but significant shift in melting temperature and calorimetric enthalpy proved the presence of structural changes of the cartilage in group II.

Conclusions

We saw significant lowering of microcirculation following continuous sutures, while simple interrupted stitches produced only moderate decrease. We found that interrupted suture technique is superior to the continuous technique causing only moderate damage to the tracheal anastomosis.     

Amperometric biosensor for 5-hydroxymethylcytosine based on enzymatic catalysis and using spherical poly(acrylic acid) brushes

5-Hydroxymethylcytosine in DNA (5hmC-DNA) plays an important biological role in sculpting the epigenetic landscape. Its presence is linked to diseases, especially cancers. The authors describe an amperometric biosensor for the determination of 5hmC. It is based on a chemical modification of the hydroxy group of 5hmC in the DNA sequence. Enzymatic signal amplification is accomplished by using DNA methyltransferase (M.HhaI-DNA-cytosine-5-methyltransferase) to achieve chemical modification. A graphene-perylenetetracarboxylic acid nanocomposite was used to modify a glassy carbon electrode (GCE) that acts as a substrate electrode. A composite consisting of horseradish peroxidase on silica/poly(acrylic acid) brushes is employed as the signal amplification unit. Under the optimized conditions, there is a linear response to the logarithm of the 5hmC-DNA concentration in the range from 0.5 to 30 nM, with a 0.23 nM detection limit (at an S/N ratio of 3) in the potential range from ?0.3 V to -0.8 V at 100 mV/s. The bioassay has excellent specificity and can even discriminate the similar base 5mC.

Open image in new window

Graphical abstract An amperometric biosensor is fabricated for 5-hydroxymethylcytosine (5hmC) determination, where DNA methyltransferase was used to achieve chemical modification of 5hmC, and spherical poly(acrylic acid) brushes conjugated horseradish peroxidase was used as the signal amplification unit. The biosensor showed high sensitivity and specificity.

     

Synthesis, crystal structure and thermochemical behaviour of a barium complex [Ba(5-OH-BDC)(H2O)3] [5-OH-H2BDC = 5-hydroxyisophtalic acid]

A novel complex [Ba(5-OH-BDC)(H₂O)₃] [5-OH-H₂BDC = 5-hydroxyisophtalic acid] was synthesized and characterized by X-ray crystallography. The complex is Monoclinic P2₁/c, a = 11.1069(4), b = 14.8192(6), c = 6.5005(2) Å, β = 103.465(3)° and Z = 4, which exhibits a three-dimensional framework formed by linkage of adjacent two-dimensional (6, 3) layers via intermolecular hydrogen bonds. The title complex has been studied by IR spectrum and TG-DTG. The constant-volume combustion energy of the complex, Δ_cU, was determined as being (−3210.45 ± 1.41) kJ mol⁻¹ by a precise rotating-bomb calorimeter at 298.15 K. The standard enthalpy of combustion, , and the standard enthalpy of formation, , were calculated as being (−3207.97 ± 1.41) and (−1922.80 ± 1.76) kJ mol⁻¹, respectively. A calculation model for determining the specific heat capacity of the complex with an improved RD496-III microcalorimeter is also derived. The specific heat capacity of the complex was (6158.387 ± 0.187) J mol⁻¹ K⁻¹.     

Incorporation of methamphetamine and amphetamine in human hair following controlled oral methamphetamine administration

Background

Although hair testing is well established for the assessment of past drug exposure, uncertainties persist about mechanisms of drug incorporation into hair and interpretation of results. The aim of this study was to administer methamphetamine (MAMP) under controlled conditions as a model drug to investigate drug incorporation into human hair.

Material and methods

Seven volunteers with a history of stimulant use received 4 × 10 mg (low) doses of sustained release S-(+)-MAMP HCl within 1 week, with weekly head hair samples collected by shaving. 3 weeks later, 4 of them received 4 × 20 mg (high) doses. After extensive isopropanol/phosphate buffer washing of the hair, MAMP and its metabolite amphetamine (AMP) concentrations were determined in all weekly hair samples by LC–MS–MS in selected reaction monitoring mode with the undeca- and deca-deuterated drugs, respectively, as internal standards (LLOQ, 0.005 ng mg⁻¹).

Results

MAMP T_max occurred from 1 to 2 weeks after both doses, with C_max ranging from 0.6 to 3.5 ng mg⁻¹ after the low and 1.2 to 5.3 ng mg⁻¹ after the high MAMP doses. AMP C_max in hair was 0.1–0.3 ng mg⁻¹ and 0.2–0.5 ng mg⁻¹, respectively, for low and high doses. Highly dose-related concentrations within subjects, but large variability between subjects were observed. MAMP concentrations were above the 0.2 ng mg⁻¹ cut-off for at least 2 weeks following administration of both low and high doses. The overall AMP/MAMP ratio ranged from 0.07 to 0.37 with a mean value of 0.15 ± 0.07, and a median of 0.13. The percentage of MAMP and AMP removed with the washing procedure decreased with time after administration. A strong correlation was found between area under the curve of MAMP (r² = 0.90, p = 0.00) and AMP (r² = 0.94, p = 0.00) concentrations calculated for the 3-week period following administration and the total melanin concentration in hair. Significant correlations were observed also between C_max and melanin.

Conclusions

This study demonstrated that despite large inter-individual differences, the incorporation of MAMP and AMP into hair is dose-related with much of the observed scatter of MAMP and AMP concentrations explained by melanin concentration in hair.     

New 3d–4f supramolecular systems constructed by [Fe(bipy)(CN)4] and partially blocked lanthanide cations

The reaction of acetonitrile (1–5) and mixed acetonitrile/water 1:1 (6–9) solutions containing the cyanide-bearing [Fe(bipy)(CN)₄]⁻ building block (bipy = 2,2′-bipyridine) and the partially blocked [Ln(bpym)]³⁺ cation (Ln = lanthanide trivalent cation and bpym = 2,2′-bipyrimidine) has afforded two new families of 3d–4f supramolecular assemblies of formula [Ln(bpym)(NO₃)₂(H₂O)₃][Fe(bipy)(CN)₄] · H₂O · CH₃CN [Ln = Sm (1), Gd (2), Tb (3), Dy (4) and Ho (5)] and [Ln(bpym)(NO₃)₂(H₂O)₄][Fe(bipy)(CN)₄] [Ln = Pr (6), Nd (7), Sm (8), Gd (9)]. They crystallize in the P2₁/c (1–5) and P2/c (6–9) space groups and their structures are made up of [Fe(bipy)(CN)₄]⁻ anions (1–9) and [Ln(bpym)(NO₃)₂(H₂O)_n]⁺ cations [n = 3 (1–5) and 4 (6–9)] with uncoordinated water and acetonitrile molecules (1–5) which are interlinked through an extensive network of hydrogen bonds and π–π stacking into three-dimensional motifs. Both families have in common the occurrence of the low-spin iron(III) unit [Fe(bipy)(CN)₄]⁻ where two bipy–nitrogen and four cyanide–carbon atoms build a somewhat distorted octahedral surrounding around the iron atom [Fe–N = 1.980(3)–1.988(3) Å (1–5) and 1.988(2)–1.992(2) Å (6–9); Fe–C = 1.904(5)–1.952(4) Å (1–5) and 1.911(2)–1.948(3) Å (6–9)]. The main structural difference between both families concerns the environment of the lanthanide atom which is nine- (1–5)/10-coordinated (6–9) with a chelating bpym, two bidentate nitrate and three (1–5)/four (6–9) water molecules building distorted monocapped (1–5)/bicapped (6–9) square antiprisms. This different lanthanide environment is at the origin of the different hydrogen bonding pattern of the two families of compounds.     

Coordination compounds of N,N′-olefin functionalized imidazolin-2-ylidenes

N-Heterocyclic carbene ligands (NHC) were metalated with Pd(OAc)₂ or [Ni(CH₃CN)₆](BF₄)₂ by in situ deprotonation of imidazolium salts to give the N-olefin functionalized biscarbene complexes [MX₂(NHC)₂] 3-7 (3: M = Pd, X = Br, NHC = 1,3-di(3-butenyl)imidazolin-2-ylidene; 4: M = Pd, X = Br, NHC = 1,3-di(4-pentenyl)imidazolin-2-ylidene; 5: M = Pd, X = I, NHC = 1,3-diallylimidazolin-2-ylidene; 6: M = Ni, X = I, NHC = 1,3-diallylimidazolin-2-ylidene; 7: M = Ni, X = I, NHC = 1-methyl-3-allylimidazolin-2-ylidene). Molecular structure determinations for 4-7 revealed that square-planar complexes with cis (5) or trans (4, 6, 7) coordination geometry at the metal center had been obtained. Reaction of nickelocene with imidazolium bromides afforded the η⁵-cyclopentadienyl (η⁵-Cp) monocarbene nickel complexes [NiBr(η⁵-Cp)(NHC)] 8 and 9 (8: NHC = 1-methyl-3-allylimidazolin-2-ylidene; 9: NHC = 1,3-diallylimidazolin-2-ylidene). The bromine abstraction in complexes 8 and 9 with silver tetrafluoroborate gave complexes [NiBr(η⁵-Cp)(η³-NHC)] 10 and 11. The X-ray structure analysis of 10 and 11 showed a trigonal-pyramidal coordination geometry at the nickel(II) center and coordination of one N-allyl substituent.     

Preferential 5‐Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein

Tet (ten–eleven translocation) family proteins oxidize 5‐methylcytosine (mC) to 5‐hydroxymethylcytosine (hmC), 5‐formylcytosine (fC), and 5‐carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG‐methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.     

Thermochemical studies of 1-hydroxyisoquinoline, 5-hydroxyisoquinoline and 1,5-dihydroxyisoquinoline

The standard (p^° = 0.1 MPa) molar enthalpies of formation, , for crystalline 1-hydroxyisoquinoline, 5-hydroxyisoquinoline and 1,5-diidroxyisoquinoline, were derived from the standard molar enthalpies of combustion, in oxygen, at the temperature 298.15 K, measured by static bomb-combustion calorimetry. The standard molar enthalpies of sublimation, , at T = 298.15 K, were determined by Calvet microcalorimetry. The results were as follows:

1-Hydroxyisoquinoline	4395.1 ± 1.5	113.6 ± 2.2
5-Hydroxyisoquinoline	4455.2 ± 1.9	109.6 ± 2.1
1,5-Dihydroxyisoquinoline	4194.1 ± 2.2	123.6 ± 2.2

Full-size table

     

Rhenium and technetium tricarbonyl complexes anchored by 5-HT1A receptor-binding ligands containing P,O/N donor atom sets

The (2-methoxyphenyl)piperazine pharmacophore, a part of the WAY 100635 structure, has been functionalized with phosphinoarylbenzylamide or phosphinoarylbenzylamine chelator groups using propylene or hexylene alkyl chains as linkers (L2-L4). These heterofunctionalized phosphines bearing an arylpiperazine moiety have been used to stabilize rhenium tricarbonyl complexes of the type [Re(CO)₃Br(κ²-L)] (4, L = L2; 5, L = L3; 6, L = L4), which have been fully characterized, including by X-ray crystallographic analysis in the case of compounds 4 and 5. These monomeric complexes are six-coordinate, displaying a distorted octahedral coordination geometry with a facial arrangement of the carbonyl groups. The other three remaining positions are occupied by a bromide and by the bidentate heterofunctionalized phosphine, which coordinates through the phosphorus and the oxygen atom or through the phosphorus and the nitrogen atom in 4 and 5, respectively. The ^99mTc complexes (3a-6a) were also prepared and their characterization established by comparative HPLC, using the Re complexes as surrogates. The in vitro binding affinity for the 5HT_1A receptor subtype and the selectivity against the 5HT_2A receptors for the rhenium complexes were determined. Compound 3 is the only one which presents a reasonable affinity and selectively towards 5HT_1A (IC₅₀ = 20 nM) and 5HT_2A (IC₅₀ = 4680 nM) receptors, respectively. When the spacer length between the chelate unit and receptor binding domain increased and/or the amide group in the chelator was replaced by a secondary amine unacceptable affinity values for 5HT_1A receptors (IC₅₀ = 200-1100 nM) and lost of selectivity were observed.     

Infinite chains constructed from flexible bis(benzimidazole)-based ligands

Two neutral ligands, L¹ · 2H₂O and L² · H₂O, and seven complexes, [Cu(pmb)₂(L¹)] (1), [Cu(pmb)₂(L²)] (2), [Cu(Ac)₂(L²)] · 4H₂O (3), [Cu(4-aba)₂(L²)] (4), [Ag(4-ts)(L¹)(H₂O)] (5), [Ag₂(epes)₂(L¹)] · 2H₂O (6), [Ag(1,5-nds)_0.5(L²)] · 0.5C₂H₅OH · H₂O (7) [where L¹ = 1,1′-(1,4-butanediyl)bis(2-methylbenzimidazole); L² = 1,1′-(1,4-butanediyl)bis(2-ethylbenzimidazole), pmb = p-methoxybenzoate anion; Ac = acetate anion; 4-aba = 4-aminobenzoate anion; 4-ts = p-toluenesulfonate anion; epes = N-(2-hydroxyethyl)piperazine-N′-(2-ethanesulfonate) anion; 1,5-nds = 1,5-naphthalenedisulfonate anion], have been synthesized and characterized by elemental analysis, IR, and single-crystal X-ray diffraction. The L¹ and L² ligands in compounds 1–7 act as bridging ligands, linking metal ions into chain structures. The chains in compounds 3, 4 and 6 interlace with each other by hydrogen bonds to generate 3D supramolecular structures. In compound 5, π–π interactions between adjacent L¹ ligands hold the chains to a supramolecular layer. In compound 7, the sulfonate anions act as counterions in the framework. The thermal stabilities of 3, 6 and 7, and the luminescent properties for 5–7 in the solid states are also discussed.