Marek Sochacki

The synthesis of di- and oligo(deoxyribonucleoside phosphorodithioates) by dithiaphospholane method

Abstract Four dinucleoside phosphorodithioates: T PS2 T ( 1a ), d(C PS2 C) ( 1b ), d{A PS2 A} and d(G PS2 G) ( 1d ) were synthesized by reacting solid support-bound nucleosides with nucleoside 5′-O-DMT-3′-O-(2-thio-1,3,2-dithiaphospholanes) ( 2a-d ) in the presence of DBU. Pyrimidine pentamers, free from phosphorothioate contamination, were obtained by this method.

siRNAs modified with boron cluster and their physicochemical and biological characterization.

RNA interference (RNAi) technology provides a powerful, yet selective, molecular tool to reduce the expression of genes in eukaryotic cells. Despite the success associated with the effective use of siRNA duplexes for gene silencing, there is a need to improve their properties. These properties, related mainly to migration through the cell membranes, stability of siRNA in vivo, and specificity of their silencing activity, can be improved by chemical modifications of siRNA backbone. In this study, we examined the physicochemical and biological properties of siRNA duplexes targeted against BACE1 gene modified at various positions with a lipophilic boron cluster (C2B10H11, CB). The lipophilicity and resistance to enzymatic degradation of the modified oligomers was higher than the unmodified counterparts. As measured in a dual fluorescence assay (BACE1-GFP/RFP), the carboranyl siRNAs (CB-siRNAs) were as active as the parent nonmodified duplexes and their toxicity toward HeLa cells was also similar. The helical structure of CB-siRNAs remained unchanged upon boron cluster introduction, as determined by CD and UV melting experiments.

Complementarity of solvent-free MALDI TOF and solid-state NMR spectroscopy in spectral analysis of polylactides.

We report systematic studies of solvent-free modification of matrix-assisted laser desorption/ionization time-of-flight (SF MALDI-TOF) mass spectrometry in analysis of synthetic polymers employing solid-state NMR spectroscopy as a supporting technique. In the present work oligomeric (M(n) = 4000 g mol(-1)) poly(L-lactide) (PLLA) was employed as a reference sample. The analyte was embedded into four matrixes commonly used in MALDI-TOF analysis of polymers: 1,8-dihydroxy-9-anthracenone (DT), 2,5-dihydroxybenzoic acid (DHB), 2-(4 hydroxyphenylazo)-benzoic acid (HABA), and trans-3-indoleacrylic acid (IAA). Solid-state NMR measurements clearly showed that the initial crystallinity of PLLA had no influence on quality of SF MALDI-TOF spectra since the crystalline structure of the analyte was not preserved during analyte/matrix grinding. Interestingly, the matrix remained crystalline during the samples preparation. It was also found that, on the contrary to the dried droplet (DD) method, the SF approach leads to highly resolved mass spectra for a large variety of matrixes. Finally, problems of polymorphism and mechanochemical processes that can occur during the analyte/matrix grinding are briefly discussed.

Application of ionic liquid matrices in spectral analysis of poly(lactide) - solid state NMR spectroscopy versus matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry

The work presented here shows the complementarity of Solid State NMR (SS NMR) spectroscopy and Matrix-Assisted Laser Desorption/Ionization-time-of-flight (MALDI-TOF) mass spectrometry in spectral analysis of poly(L-lactide) (PLLA) using second-generation ionic liquid matrices (ILM II) prepared from N,N-diisopropylethylamine (DEA) and DHB (2,5-dihydroxybenzoic acid), IAA (3-indoleacrylic acid), and HABA (2-(4-hydroxyphenylazo) benzoic acid). The 13C cross-polarization (CP) magic angle spinning (CP/MAS) SS NMR technique was used to study the structure of ionic liquid matrices, their thermal stability, and the influence of ILM on the morphology of polymer. A comparison of MALDI-TOF spectra for samples prepared employing the dried droplet (DD) and the solvent free (SF) mode showed that the former approach gave better results (signal to noise ratio) very likely due to intimate contact between analyte and matrix domains. This hypothesis was verified by analysis of CP build-up curves for DHB–DEA–PLLA samples prepared employing both methods. We also showed that an alternative method of sample preparation based on the melting of ILM II together with a suspended polymer in the liquid matrix is unsatisfactory, particularly for those matrices which can undergo isomerization at higher temperatures (e.g., HABA–DEA and IAA–DEA).

Deoxyxylothymidine 3′-O-phosphorothioates: Synthesis, stereochemistry and stereocontrolled incorporation into oligothymidylates

Abstract New reagent, 5′-O-DMT-xylothymidine 3′-O-(2-thio-4,4-spiropentamethylene-1,3,2-oxathiaphospholane) and its separated diastereomers can be used for stereocontrolled incorporation of xylothymidine 3′-O-phosphorothioate of predetermined sense of P-chirality into desired oligonucleotide constructs.

Solid-state NMR spectroscopy as a tool supporting optimization of MALDI-TOF MS analysis of polylactides

We report systematic structural studies of poly(l-lactide) (PLLA) employing matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and solid-state NMR spectroscopy. 13C cross polarization magic angle spinning (CP/MAS) NMR data for 1,8-dihydroxy-9-anthracenone (DT), 2,5-dihydroxybenzoic acid (DHB), 2-(4-hydroxyphenylazo)-benzoic acid (HABA), and trans-3-indoleacrylic acid (IAA), four matrices commonly used in MALDI-TOF analysis of polymers, were analyzed to test the influence of crystallization conditions (solvent, inorganic salt) on sample morphology. 13C principal elements of chemical shift tensor (CST) and line-shape analyses were employed to study of the nature of hydrogen bonding and to evaluate the crystallinity and amorphicity of the pure polymer. NMR parameters for PLLA were compared with data for polylactide crystallized with the four matrices under different conditions with the addition of two inorganic salts as cationization agents. This study revealed that the semicrystalline structure of the polymer does not change when it is embedded in the matrix.

A new class of dinucleotide analogues. The synthesis of 3′-O-thymidylyl(5′-deoxy-5′-selene-thymidylyl)-Se-phosphoroselenolate, its O-methyl ester and methanephosphonate derivatives.

Abstract Title compounds 12, 13 and 14 have been prepared via alkylation of 5′-O-protected nucleoside 3′-O-(O-alkylphosphoroselenoates) ( 5, 6 and -3′-O-(methanephosphonoselenoates) ( 7 ). After deprotection, 5′-deoxy-5′-selene dinucleoside Se-phosphates and Se-phosphonates have been obtained with good yields. Their chemical and antiviral (HIV-1) properties have also been examined.

Orthoformates as reagents for derivatization of aminoalkanephosphonic acids for characterization by gas chromatography-mass spectrometry

Studies of the derivatization of aminoalkanephosphonic acids by trialkyl orthoformates are reported. Gas chromatographic retention data and low-resolution electron impact mass spectra for the derivatives are presented.

Analogues of cyclolinopeptide a containing α-hydroxymethyl amino acid residues†

Linear and cyclic cyclolinopeptide A (CLA) analogues containing α‐hydroxymethylleucine (HmL) in positions 1, 4, and 1&4, and α‐hydroxymethylvaline (HmV) in position 5, were synthesized by the solid‐phase peptide strategy and cyclized with the 1‐Ethyl‐3‐(3‐dimethylaminopropyl)‐carbodiimide/1‐hydroxy‐7‐azabenzotriazole (EDC/HOAt) reagent. The peptides were examined for their immunosuppressive activity in the lymphocyte proliferation assays (LPA). Only HmL‐containing peptides demonstrated at about 25% lower immunosuppressive activity, but they are four times more soluble in water solutions than the native CLA. It seems from the LPA results that peptide [(HmL4)CLA] is the most promising for further studies. This peptide was characterized in solution, at room temperature in CDCl3, and the conformation compared with that observed for CLA in the solid state.

Stereochemical effects in fragmentation of diastereoisomers of protected diethyl 1,2‐diamino‐alkylphosphonates

Diastereoisomers of diethyl 5-substituted (2-thioxo-imidazolidin-4-yl)phosphonates, which can be regarded as protected diethyl 1,2-diaminoalkylphosphonates, have been analyzed by electron ionization mass spectrometry. Significant differences in the fragmentation of cis- and trans-diastereoisomers were found. The stereospecificity of the elimination of diethyl phosphonate and the loss of the diethoxyphosphoryl group were studied using specific labeled compounds and collision-induced dissociation. The relative abundances of ions formed via these fragmentation processes can be used for differentiation of both diastereoisomers.