From CPG to hybrid support: Review on the approaches in nucleic acids synthesis in various media.

Solid-phase synthesis is, to date, the preferred method for the manufacture of oligonucleotides, in quantities ranging from a few micrograms for research purposes to several kilograms for therapeutic or commercial use. But for large-scale oligonucleotide manufacture, scaling up and hazardous waste production pose challenges that necessitate the investigation of alternate synthetic techniques. Despite the disadvantages of glass supports, using soluble supports as a substitute presents difficulties because of their high overall yield and complex purification steps. To address these challenges, various independent approaches have been developed; however, other problems such as insufficient cycle efficiency and synthesis of oligonucleotide chains of desired length continue to exist. In this study, we present a review of the current developments, advantages, and difficulties of recently reported alternatives to supports based on controlled pore glass, and discuss the importance of a support choice to resolve issues arising during oligonucleotide synthesis.

Structural and Spectroscopic Properties of Isoconazole and Bifonazole-Experimental and Theoretical Studies.

The paper compares the experimental FT-IR, UV-vis, and 1H NMR spectra of isoconazole and bifonazole with the density functional theory (DFT) calculations using different functionals. The results were compared with previously reported data related to their analogue, posaconazole. The analysis of calculated IR spectra with use of CAM-B3LYP (isoconazole) or B3LYP (bifonazole) functionals shows good accordance with the experimental IR spectrum. The best compatibility between the experimental and theoretical UV spectra was observed with the use of B3LYP or wB97XD functionals for isoconazole or bifonazole, respectively. The reason for the difference in the UV-vis spectra of isoconazole and bifonazole was discussed based on linear response time-dependent DFT and natural bond orbital methods. The calculated 1H NMR spectrum shows that the DFT formalism, particularly the B3LYP functional, give an accurate description of the isoconazole and bifonazole chemical shifts.

Disulfide bridge cross-linking between protein and the RNA backbone as a tool to study RNase H1.

The chemical cross-linking of complexes of proteins with nucleic acids is often used in structural and mechanistic studies of these oftentimes unstable and transient complexes. To date, no method has been reported for the thiol-based conjugation of proteins with an RNA backbone, mainly because of instability of the modified ribonucleic acid that is functionalized at the phosphodiester and its rapid hydrolysis. Here, we report the site-specific synthesis of stable RNA oligonucleotides with a thiol-bearing linker that was attached to the phosphodiester backbone, where the ribonucleotide at the cross-linking site was either replaced with 2'-deoxy- or 2'-fluororibonucleotide. The utility of this approach was validated in cross-linking tests with RNase H1, a model protein for RNA/DNA binding and key effector in DNA-like antisense drug therapy. Furthermore, scale-up cross-linking and purification of the complexes confirmed that the method is useful for obtaining preparations of protein-RNA/DNA complexes with purity and stability that are suitable for further biochemical and structural studies. The present approach broadens the repertoire of disulfide-based cross-linking strategies and is a novel tool for the stabilization of protein-RNA complexes in which the interaction occurs via the RNA backbone. This methodology may be broadly applicable to studies of otherwise unstable or transient complexes of proteins with RNA and RNA/DNA.

Disulfide bridge as a linker in nucleic acids' bioconjugation. Part II: A summary of practical applications.

Disulfide conjugation invariably remains a key tool in research on nucleic acids. This versatile and cost-effective method plays a crucial role in structural studies of DNA and RNA as well as their interactions with other macromolecules in a variety of biological systems. In this article we review applications of disulfide-bridged conjugates of oligonucleotides with other (bio)molecules such as peptides, proteins etc. and present key findings obtained with their help.

Fluorescent 2-(Pyridin-2-yl)vinyl Pyridine Dyes and Their Thermocontrolled Release.

The generation of unique thermosensitive fluorescent dyes via heteroaromatic Heck cross-coupling and N-pyridin-2-yl nucleophilic substitution was described. To demonstrate thermosensitive properties, the precursor was converted into carbonates or phosphates and heated at various temperatures and for various time periods. Significant changes in the fluorescence intensity and emission wavelengths, between carbonates and the cyclic product, were observed, and it was proved that the dyes may serve as removable fluorescent labels with large Stokes shifts (>80 nm). The application of thermosensitive fluorescent dyes in oligonucleotide labeling has been demonstrated.

Disulfide bridge as a linker in nucleic acids' bioconjugation. Part I: An overview of synthetic strategies.

This 2-part article reviews methods of oligonucleotides functionalization with thiol tethers and their consecutive use in conjugation with other (macro)molecules via a disulfide bridge. This relatively inexpensive, robust and reversible method of conjugation of DNAs, RNAs and their analogs holds a prominent position in a modern biochemistry toolbox and therefore there is a wealth of literature on the subject. In part I methods of thiol/disulfide groups introduction into oligonucleotide strands have been systematized and discussed. A digest of conjugation methods is presented as well.

Boron Clusters as a Platform for New Materials: Synthesis of Functionalized o-Carborane (C2 B10 H12 ) Derivatives Incorporating DNA Fragments.

A synthetic strategy for functionalization of the three vertices of o-carborane and the attachment of the obtained triped to the solid support was developed. Further functionalization of the triped with short DNA sequences by automated DNA synthesis was achieved. The proposed methodology is a first example of boron cluster chemistry on a solid support opening new perspectives in boron cluster functionalization.

Modulating the Stability of 2-Pyridinyl Thermolabile Hydroxyl Protecting Groups via the "Chemical Switch" Approach.

A novel and effective method is presented for modulating the stability of 2-Pyridinyl Thermolabile Protecting Groups (2-Py TPGs) in the "chemical switch" approach. The main advantage of the discussed approach is the possibility of changing the nucleophilic character of pyridine nitrogen using different switchable factors, which results in an increase or decrease in the thermal deprotection rate. One of the factors is transformation of a nitro into an amine group via reduction with a low-valent titanium in mild conditions. The usefulness of our approach is corroborated using 3'-O-acetyl nucleosides as model compounds. Their stability in various solvents and temperatures before and after reduction is also examined. Pyridine N-oxide and pH are other factors responsible for the nucleophilicity and stability of 2-Pyridinyl Thermolabile Protecting Groups in thermal deprotection. Protonation of 4-amino 2-Pyridinyl Thermolabile Protecting Groups is demonstrated by (1)H-(15)N HMBC and HSQC NMR analysis.

Investigations on Synperiplanar and Antiperiplanar Isomers of Losartan: Theoretical and Experimental NMR Studies.

Losartan inhibits the renin-angiotensin-aldosterone system by blocking the angiotensin II receptor. It is commonly used in cardiovascular diseases, such as hypertension. Several publications applied the ab initio and density functional theory methods to investigate the molecule of losartan. Only in one of them were the nuclear magnetic resonance spectra calculations carried out, and their results were correlated with the experimental values. The authors focused their attention on calculations of the anion form of losartan, taking into consideration both its synperiplanar and antiperiplanar configurations. Coefficients of determination and mean absolute deviation parameters were calculated for the experimental and calculated chemical shifts for every used basis set. They showed a noticeably stronger correlation for the anti-isomers than for the syn-isomers. Moreover, the solvation model increased the value of this parameter. The results of calculations confirmed that an anti-conformation of the analyte seems to be the preferred one, and such an orientation might be most potent within the receptor cavity, which is in agreement with the results of previous studies.

Microwave-Dependent Thermo-Release Approach for Oligonucleotides 5'-Phosphorylation.

A method for phosphorylating oligonucleotides using a thermosensitive "trigger" is hereby presented. The recovery of the phosphate specifically takes place under neutral conditions when subjected to an elevated temperature. Two identical thermolabile protecting groups are differentially removed with the initial release occurring swiftly and the second at a more gradual pace. The delayed deprotection of the second group led to the development of a method for the purification of 5'-phosphorylated oligonucleotides. Microwave irradiation enables the rapid attainment of complete deprotection, in contrast to conventional heating methods.

Effect of Anisotropy of Reduced Graphene Oxide on Thermal and Electrical Properties in Silicon Carbide Matrix Composites.

Reduced graphene oxide, due to its structure, exhibits anisotropic properties, which are particularly evident in electrical and thermal conductivity. This study focuses on examining the influence of reduced graphene oxide in silicon carbide on these properties in directions perpendicular and parallel to the direction of the aligned rGO flakes in produced composites. Reduced graphene oxide is characterized by very high in-plane thermal and electrical conductivity. It was observed that the addition of rGO increases thermal conductivity from 64 W/mK (reference sample) up to 98 W/mK for a SiC-3 wt.% rGO composite in the direction parallel to the rGO flakes. In the perpendicular direction, the values were slightly lower, reaching up to 84 W/mK. The difference observed in electrical conductivity values is more significant and is 1-2 orders of magnitude higher for the flakes' alignment direction. The measured electrical conductivity increased from 1.2710-8 S/m for the reference SiC sinter up to 1.55 × 10-5 S/m and 1.2410-4 S/m for the composites with 3 wt.% rGO for the perpendicular and parallel directions, respectively. This represents an enhancement of four orders of magnitude, with a clearly visible influence of the anisotropy of the rGO. The composite's enhanced electrical and thermal conductivity make it particularly attractive for electronic devices and high-power applications.

Using the Spark Plasma Sintering System for Fabrication of Advanced Semiconductor Materials.

The interest in the Spark Plasma Sintering (SPS) technique has continuously increased over the last few years. This article shows the possibility of the development of an SPS device used for material processing and synthesis in both scientific and industrial applications and aims to present manufacturing methods and the versatility of an SPS device, presenting examples of processing Arc-Melted- (half-Heusler, cobalt triantimonide) and Self-propagating High-temperature Synthesis (SHS)-synthesized semiconductor (bismuth telluride) materials. The SPS system functionality development is presented, the purpose of which was to broaden the knowledge of the nature of SPS processes. This approach enabled the precise design of material sintering processes and also contributed to increasing the repeatability and accuracy of sintering conditions.

Low bias charge transport in DNA.

The low-bias current-voltage technique was utilized to study charge transport in single-stranded DNA (ssDNA), assessing the method's effectiveness for future studies aimed at estimating the degree of mutation or DNA damage. In the paper, we showed that charge carrier transfer processes in ssDNA can be precisely monitored using low-bias currents. We used negative differential resistance and the Fowler-Nordheim model to differentiate the charge transport mechanisms observed in a device composed of gold electrode-thiol-ssDNA junctions. It was possible to distinguish the processes at the two junctions (Au/thiol and thiol/DNA) due to their distinct current-voltage characteristics. We observed positive charge carrier tunneling, which we attribute to oxidation and reduction processes in the nucleobases of the ssDNA. Our results suggest that even minor changes in DNA chains can be accurately detected using the described methodology.

Effect of Nitrogen Atmosphere Annealing of Alloyed Powders on the Microstructure and Properties of ODS Ferritic Steels.

Oxide Dispersion Strengthened (ODS) ferritic steels are promising materials for the nuclear power sector. This paper presents the results of a study on the sintering process using the Spark Plasma Sintering (SPS) technique, focusing on ODS ferritic steel powders with different contents (0.3 and 0.6 vol.%) of Y2O3. The novelty lies in the analysis of the effect of pre-annealing treatment on powders previously prepared by mechanical alloying on the microstructure, mechanical, and thermal properties of the sinters. Using the SPS method, it was possible to obtain well-densified sinters with a relative density above 98%. Pre-annealing the powders resulted in an increase in the relative density of the sinters and a slight increase in their thermal conductivity. The use of low electron energies during SEM analysis allowed for a fairly good visualization of the reinforcing oxides uniformly dispersed in the matrix. Analysis of the Mössbauer spectroscopy results revealed that pre-annealing induces local atomic rearrangements within the solid solution. In addition, there was an additional spectral component, indicating the formation of a Cr-based paramagnetic phase. The ODS material with a higher Y2O3 content showed increased Vickers hardness values, as well as increased Young's modulus and nanohardness, as determined by nanoindentation tests.

Novel method of synthesis of 5''-phosphate 2'-O-ribosyl-ribonucleosides and their 3'-phosphoramidites.

Synthesis of 5''-phosphate 2'-O-ribosylribonucleosides [Nr(p)] of four common ribonucleosides, and 3'-phosphoramidites of 5''-phosphate 2'-O-ribosyladenosine and 2'-O-ribosylguanosine using the H-phosphonate chemistry is described. An additional ring protected by benzoyl groups was incorporated into the main ribosyl ring in the reaction with 1-O-acetyl-2,3,5-tri-O-benzoyl-ß-D-ribofuranose in the presence of SnCl4. The obtained 2'-O-ribosylribonucleosides (Nr) were applied in the subsequent transformations with selective deprotection. Ethanolamine was applied as a very convenient reagent for selective removal of benzoyl groups. Additionally, the tetraisopropyldisiloxane-1,3-diyl (TIPDSi) group was found to be stable under these deprotection conditions. Thus, the selectively deprotected 5''-hydroxyl group of Nr was transformed into an H-phosphonate monoester which was found to be stable under the following conditions: the removal of the TIPDSi group with triethylammonium fluoride and the dimethoxytritylation of the 5''-hydroxyl function. The 5''-H-phosphonate of Nr precursors was easily transformed to the corresponding dicyanoethyl 5''-O-phosphotriesters before phosphitylation, which gave 3'-phosphoramidite units of Nr(p) in high yield. The derived phosphoramidite units were used in an automated oligonucleotide synthesizer to produce dimer Ar(p)T via the phosphoramidite approach. The obtained products were fully deprotected under standard deprotection conditions giving dimers with a 5''-phosphate monoester function. Application of an alkaline phosphatase to prove the presence of an additional phosphate group was described.

Mechanical and Thermal Properties of W-Ta-B Coatings Deposited by High-Power Impulse Magnetron Sputtering (HiPIMS).

We present the deposition and characterization of tungsten-tantalum diboride (W,Ta)B2 coatings prepared by the high-power impulse magnetron sputtering technique. We evaluated the influence of pulse duration and substrate bias on the properties of (W,Ta)B2 films. A high hardness of up to 35 GPa measured by nanoindentation was simultaneously obtained with good elastic properties. Changing the pulse duration greatly affected the B/(W+Ta) atomic ratio, which influenced the properties of the coatings. The deposited films are thermally stable at up to 1000 °C in vacuum and are able to withstand oxidation at 500 °C.

Cytogenomic features of Richter transformation.

BACKGROUND: Richter transformation (RT) is the development of aggressive lymphoma in patients with chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL). This rare disease is characterised by dismal prognosis. In recent years, there has been a deeper understanding of RT molecular pathogenesis, and disruptions of apoptosis (TP53) and proliferation (CDKN2A, MYC, NOTCH1) has been described as typical aberrations in RT. RESULTS: A single-institution cohort of 33 RT patients were investigated by karyotyping, fluorescence in situ hybridization and single nucleotide polymorphism/copy number (CN) arrays. Most of RTs were typically manifested by diffuse large B-cell lymphoma, not otherwise specified, among the remaining cases one was classified as high-grade B-cell lymphoma with 11q aberrations. The most frequent alterations (40-60% of cases) were represented by MYC rearrangement/gain, deletions of TP53 and CDKN2A, IGH rearrangement and 13q14 deletion. Several other frequent lesions included losses of 14q24.1-q32.33, 7q31.33-q36.3, and gain of 5q35.2. Analysis of 13 CLL/SLL-RT pairs showed that RT arised from the CLL/SLL by acquiring of 10 ~ 12 cytogenetic or CN lesions/case, but without acquisition of loss of heterozygosity regions. Our result affirmed the higher genetic complexity in RT than CLL/SLL and confirmed the linear features of RT clonal evolution as predominant. CONCLUSIONS: Cytogenomic profile was concordant with the literature data, however the role of IGH rearrangement, 14q deletion and 5q35.2 gain need to be explored. We anticipate that further characterization of RT lesions will probably facilitate better understanding of the RT clonal evolution.

Oxidation of H-phosphonates with iodine by intramolecular support of a 2-pyridyl thermolabile protecting group.

Acceleration of H-phosphonate diester oxidation with iodine accompanied by a thermolabile protecting group (TPG) is presented. It is shown that the intermediate product of this reaction is an oxazaphospholidine oxide which forms a phosphate diester only when a 2-pyridyl TPG is applied. The intermediate product is formed with exocyclic nitrogen. The absolute configurations of phosphorothioate diesters, H-phosphonate diesters, and oxazaphospholidine oxides were determined. (31)P NMR spectroscopy was used to evaluate the relationship between chemical shift and absolute configuration at the phosphorus center of H-phosphonate diesters and oxazaphospholidine oxides.

Unexpected Method of High-Viscosity Shear Thickening Fluids Based on Polypropylene Glycols Development via Thermal Treatment.

This study aimed to analyze the influence of the thermal treatment of shear thickening fluids, STFs, on their viscosity. For this purpose, shear thickening fluids based on polypropylene glycols PPG400 and PPG1000 and Aerosil®200 were developed. The shear thickening behavior of obtained fluids was confirmed by using a parallel-plate rheometer. Next, thermogravimetric (TG) analyses were used to characterized thermal stability and weight loss of the STFs at a constant temperature. Finally, the thermal treatment of the STFs obtained was provided using the apparatus developed for this purpose. The received STFs exhibited a very high maximum viscosity up to 15 kPa. The rheology of the STFs measured after thermal treatment indicated that the proposed method allowed the development of STFs with a very high maximum viscosity. The maximum viscosity of the STFs increased twofold when thermal treatment of the STFs at elevated temperature for 210 min was performed. TG confirmed the convergence of the weight loss in the apparatus. Our results show that controlling the thermal treatment of STFs allows STFs to be obtained with high viscosity and a dilatation jump of the STFs by degradation of the liquid matrix.

Microstructure of Rhenium Doped Ni-Cr Deposits Produced by Laser Cladding.

The addition of Rhenium up to 6% to Ni-Cr alloys can dramatically improve the corrosion and oxide resistance of deposited coatings at high operating temperatures. Ni-Cr+Re layers can be successfully produced using conventional powder metallurgy, high rate solidification (HRS), or magnetron sputtering methods. However, in industrial applications, high-performance deposition methods are needed, e.g., laser cladding. Laser cladding has several advantages, e.g., metallurgical bonding, narrow heat-affected zone (HAZ), low dilution, and slight thermal damage to the substrate. In this paper, a powder Ni-Cr composite with 1% (wt.) of Rhenium was produced, then deposited onto a steel substrate (16Mo3) by laser cladding to assess the micro and macrostructural properties of the obtained layers. Besides the macro and microscopic observations, scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) microanalysis of the deposit and HAZ as well as microhardness measurements have been conducted. The microstructure observations revealed four subareas of HAZ gradually changing from the fusion line towards the base material. Maximum hardness occurred in the HAZ, mainly in areas closer to the clad/substrate interface, reaching up to 350-400 HV. No sudden changes in the composition of the deposit and the area of fusion line were observed.