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Michal Sobkowski

Publications and source records attributed to Michal Sobkowski.

9 recordsLinked to original sources
PubMed2006

A proposal for a convenient notation for P-chiral nucleotide analogues. Part 2. Dinucleoside monophosphate analogues.

A configuration of ligands around a phosphorus atom in P-chiral dinucleoside monophosphate analogues can be described using DP/LP stereochemical notation, which allows immediate correlation between the notation of configuration and the actual spatial arrangement of the phosphorus ligands. The area of applications of this new stereochemical nomenclature covers dinucleoside units bridged by virtually any type of tri-and tetra-coordinated phosphorus moieties, that is, phosphorothioates, phosphoramidates, phosphoramidites, boranephosphates, methanephosphonates, H-phosphonates, and many others.

Chemistry↗
PubMed2006

A proposal for a convenient notation for P-chiral nucleotide analogues. Part 3. Compounds with one nucleoside residue and nonnucleosidic derivatives.

Recently, we have proposed a new DP/LP stereochemical notation for P-chiral dinucleoside monophosphate analogues that permits simple correlation between spatial arrangement of the substituents and the configuration at the phosphorus center. As an extension of this work, we present here applications of the DP/LP notation to derivatives containing only one nucleoside unit (e.g., alkyl nucleoside phosphodiesters, nucleoside phosphomonoesters, cyclic phosphate derivatives, nucleoside di-, and triphosphates) and to nonnucleosidic phosphorus compounds.

Biochemistry↗
PubMed2005

A proposal for a new stereochemical notation for P-chiral nucleotide analogues and related compounds.

A new stereochemical notation for P-chiral nucleotide analogues and related compounds is proposed In this notation, the names of configurations, designated as D(P) and L(P), are derived from a geometrical relationship, rather than from priority rules, of substituents at the phosphorus centre. This new stereochemical description offers clear advantages over the CIP R/S nomenclature, particularly when used for comparing the influence of absolute configuration at the phosphorus centre on physicochemical and biological properties of oligonucleotide analogues or in stereochemical correlation analysis of P-chiral nucleotide derivatives.

Biochemistry↗
PubMed2005

Stereochemistry of internucleotide bond formation by the H-phosphonate method. 1. Synthesis and 31P NMR analysis of 16 diribonulceoside (3'-5')-H-phosphonates and the corresponding phosphorothioates.

Sixteen diribonucleoside (3'-5')-H-phosphonates were synthesized via condensation of the protected ribonucleoside 3'-H-phosphonates with nucleosides, and the influence of a nucleoside sequence on the observed stereoselectivity was analyzed. 31P NMR spectroscopy was used to evaluate a relationship between chemical shift and absolute configuration at the phosphorous center of the H-phosphonate diesters as well as of the corresponding phosphorothioate diesters. Although for the most cases such correlation was found, there was however several exceptions to the rule where the relative positions of resonances arisingfrom Rp and Sp diastereomers were reversed.

Dinucleoside Phosphates↗
PubMed2004

Enzymatic and hybridization properties of oligonucleotide analogs containing novel phosphoramidate internucleotide linkages.

In line with the paradigm, that antisense oligonucleotides should contain minimal structural modifications, in order to minimize the risk of toxicity and antigenicity, we describe here the preparation and the properties of oligonucleotides modified to contain, in addition to phosphodiester bonds, a small number of phosphoramidate internucleotide linkages substituted with aminoethoxyethyl groups in order to convey protection against exo- and endonucleases. Prolonged stability was, in fact, found in model experiments with respective enzymes, as well as in studies done in human blood serum. Regardless of number and position of phosphoramidate linkages, the modified oligonucleotides showed only a slight decrease of Tm in hybridization studies with complementary oligonucleotides.

Amides↗