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We describe here the preparation of conformationally locked cyclohexane nucleic acids designed as hybrids between locked nucleic acids (LNAs) and cyclohexene nucleic acids (CeNAs), both of which excel in hybridization with complementary RNAs. We have accomplished the synthesis of these adenine derivatives starting from a simple ketoester and installed all four chiral centres by means of total synthesis. The acquired monomers were incorporated into nonamer oligonucleotides.

Taurine (2-aminoethanesulfonic acid) is a representative substructure in biologically active compounds, but can raise difficulties in direct coupling reactions. In this study, the synthesis of taurine-derived sulfonic acids and analogous aromatic sulfonic acids was accomplished by a performic acid promoted oxidation of corresponding symmetrical disulfide precursors. In some of the products, the taurine or sulfanilic acid nitrogen atom is incorporated in a heterocyclic scaffold or part of a peptide bond in dipeptide mimetics. [ABSTRACT FROM AUTHOR]

A new method of the light microscopy detection of BrdU-labeled DNA in situ is described. It is based on the oxidative attack at the deoxyribose moiety by copper(I) in the presence of oxygen, which leads to the abstraction of hydrogen atom from deoxyribose culminating in the elimination of the nucleobase, scission of the nucleic-acid strand and formation of frequent gaps. The gaps allow the reaction of the antibodies with the commonly used markers of replication (e.g. 5-bromo-29- deoxyuridine), which are otherwise masked. The method developed makes it possible to detect nuclear and mitochondrial DNA replication efficiently. In most cases, it does not inhibit effective protein detections and in addition enables simultaneous localization of newly-synthesized RNA. The alternative presently-used methods result in protein denaturation and/or extensive DNA cleavage followed by the DNA-bound proteins peeling off. [ABSTRACT FROM AUTHOR]

5-Bromo-2'-deoxyuridine (BrdU) and 2'-deoxy-5-ethynyluridine (EdU) are widely used as markers of replicated DNA. While BrdU is detected using antibodies, the click reaction typically with fluorescent azido-dyes is used for EdU localisation. We have performed an analysis of ten samples of antibodies against BrdU with respect to their reactivity with EdU. Except for one sample all the others evinced reactivity with EdU. A high level of EdU persists in nuclear DNA even after the reaction of EdU with fluorescent azido-dyes if the common concentration of dye is used. Although a ten-time increase of azido-dye concentration resulted in a decrease of the signal provided by anti-BrdU antibodies, it also resulted in a substantial increase of the non-specific signal. We have shown that this unwanted reactivity is effectively suppressed by non-fluorescent azido molecules. In this respect, we have tested two protocols of the simultaneous localisation of incorporated BrdU and EdU. They differ in the mechanism of the revelation of incorporated BrdU for the reaction with antibodies. The first one was based on the use of hydrochloric acid, the second one on the incubation of samples with copper(I) ions. The use of hydrochloric acid resulted in a significant increase of the non-specific signal. In the case of the second method, no such effect was observed. [ABSTRACT FROM AUTHOR]

Abstract: Two types of DNA oligonucleotide modifications, namely lengthening of the internucleotide linkage by insertion of CH2 methylene group and substitution of deoxyribose by deoxyxylose, were studied with respect to their possible impact on the oligonucleotide binding specificity. Structural effects of the modifications at the mismatched site of DNA/RNA hybrid duplex were monitored via Raman spectroscopy by using a molecular model system consisting of a DNA nonamer (5′-GTG ATA TGC-3′) with the modification at the site of the central thymidine and of RNA counterparts with altered central nucleotide (5′-GCA UNU CAC-3′, N =A or U). A novel approach based on single and double difference Raman spectra allowed extraction and analysis of spectroscopic signatures introduced by chemical modification and mismatched basepairs in NA duplexes. The double difference spectra revealed that substitution of 2′-deoxy-d-deoxyribose by 2′-deoxy-d-deoxyxylose supports bending of the modified dA-dT-dA segment in the mismatched duplex, while lengthening of the internucleotide linkage by insertion of the CH2 methylene group induces irregular distortion of this track. The modifications do not induce a better stacking interaction of the mismatched uracil and thus do not increase the stability of the T·U mismatched duplexes. [Copyright &y& Elsevier]

Abstract: An electrophile-promoted addition of dialkyl-hydroxymethylphosphonate to the protected 4′,5′-didehydronucleosides resulted in an epimeric mixture of 4′-dialkylphosphonomethoxy derivatives of 2′,5′-dideoxynucleosides, novel analogues of 2′-deoxynucleoside 5′-monophosphates. Several types of electrophiles (pyridinium tosylate, NIS, NBS, MCPBA and others) were evaluated in addition reactions with 4′,5′-didehydrothymidine. Out of them, pyridinium tosylate was found to have a practical usefulness in these transformations. Its use has led to the preparation of a series of 4′-phosphonomethoxy derivatives of common 2′-deoxynucleosides. On biological screening, these free phosphonic acids exerted no significant cytostatic or antiviral activity. [Copyright &y& Elsevier]

Abstract: We report here an oxidative cleavage of (5R)- and (5S)-ribofuranosyl-5-C-phosphonate derivatives with periodate anion under both strong acidic and neutral conditions. In both cases, only (5R)-configured compound underwent the expected oxidation reaction and afforded the desired (4R)-erythrofuranosylphosphonate, whereas the second epimer, (5S)-ribofuranosyl-5-C-phosphonate did not provide the corresponding (4S)-erythrofuranosylphosphonate derivative. This different behavior of epimers toward oxidative cleavage is an important phenomenon. The obtained (4R)-erythrofuranosylphosphonate was used for the preparation of phosphonate mimic of adenosine 5′-phosphate via classical nucleosidation reaction. Condensation of the protected shortened AMP analogue with adenosine derivatives, however, provided only the 2′,5′-linked ApA analogue. Study on hybridization of the modified 2′-5′ ApA with polyU revealed its ability to form stable triplex-like complex, similar to natural 2′-5′ r(ApA) and 3′-5′ r(ApA). NMR spectroscopy study showed that the erythrofuranose part of the phosphonate nucleotide unit of modified 2′-5′ ApA was predominantly in the C2′-endo conformation, which is characteristic for B-DNA. [Copyright &y& Elsevier]

The article presents chemical equations related to the article "A New Class of Phosphanucleosides Containing a 3-Hydroxy-hydroxymethylphospholane 1-Oxide Ring" by O. Pav and others in the 2013 issue of the periodical "Tetrahedron."