4',5'-Dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE): synthesis and spectral properties of oligonucleotide conjugates

A convenient procedure for the preparation of the fluorescent dye 4',5'-dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE) is reported; the overall yield achieved starting from isovanillin is 10 times higher (40% vs 4%) compared to the known procedure. Isomers (5- and 6-) are easily chromatographically separable as pentafluorophenyl esters of 3',6'-O-bis(cyclohexylcarbonyl) derivatives. Four non-nucleoside JOE phosphoramidites based on 5- and 6-isomers and flexible 6-aminohexanol (AH) or rigid 4-trans-aminocyclohexanol (ACH) linkers have been prepared and used for oligonucleotide labeling. Spectral and photophysical properties of 5'-JOE-modified oligonucleotides have been studied. Fluorescence quantum yield of the dye correlates with the nature of the linker (rigid vs flexible) and with the presence of dG nucleosides in close proximity to a JOE residue.     

Novel interstrand communication systems within DNA duplexes based on 1-, 2- and 4-(phenylethynyl)pyrenes attached to 2'-amino-LNA: high-affinity hybridization and fluorescence sensing

Functionalisation of 2'-amino-LNA oligonucleotides with 1-, 2- and 4-(phenylethynyl)pyrene fluorophores via a carbonyl linker (PEPyc) resulted in efficient interstrand communication systems in nucleic acid duplexes, providing effective tools for stabilization of nanostructures and fluorescence monitoring of DNA self-assembly.     

Naphthoquinone-derived polyol macrolides from natural sources

Russian Chemical Bulletin - New biologically active substances isolated from natural sources provide valuable information on structural motifs that are important for a specific type of activity and...     

5-Arylethynyl-2'-deoxyuridines, compounds active against HSV-1

Three new 5-arylethynyl-2'-deoxyuridines containing bulky aryls have been prepared and tested against HSV-1 in Vero cells. The introduction of a substituent in the phenyl group of an inactive compound, 5-phenylethynyl-2'-deoxyuridine, leads to the appearance of anti-HSV properties. The most active compounds are those containing a polycyclic aromatic hydrocarbon residue attached to the 5 position of 2'-deoxyuridine through a rigid triple bond.     

(R)-2,4-Dihydroxybutyramide seco-pseudonucleosides: new versatile homochiral synthons for synthesis of modified oligonucleotides

[reaction: see text] Two series of seco-pseudonucleoside synthons were synthesized from (R)-(+)-alpha-hydroxy-gamma-butyrolactone and (R)-(-)-pantolactone by aminolysis, side-chain protection, dimethoxytritylation, and phosphitylation or solid-phase attachment. The phosphoramidites and solid supports were used in automated DNA synthesis to prepare oligonucleotides modified with one or more 2,4-dihydroxybutyramide units bearing side-chain reporter groups. These new oligonucleotide modification reagents allow the introduction of a label into any desired position within an oligonucleotide chain during solid-phase assembly.     

Astolides A and B,antifungal and cytotoxic naphthoquinone-derived polyol macrolactones from Streptomyces hygroscopicus

Two new natural compounds, astolides A,B, were isolated from Streptomyces hygroscopicus collected from the alkaline soil obtained from Saratov region, Russia. The structures were elucidated by interpretation of UV spectroscopic, MS, 1D and 2D NMR data. The relative configurations were determined by analysis of NOESY/ROESY spectra and coupling constants. The isolated compounds were evaluated for their inhibitory activity against bacteria, fungi and yeasts and showed pronounced antifungal activity. Both compounds are noticeably cytotoxic, being active against doxorubicin-resistant human leukemia cell line.     

Branched Linkers for Site-Specific Fluorescent Labeling of Antibodies

Fluorescent antibodies have proved to be an invaluable tool for molecular biology and diagnostics. They are routinely produced by modification of lysine residues, which leads to high heterogeneity. As such, their affinity may be compromised if the antigen-binding site is affected, the probability of which increases along with the degree of labeling. In this work, we propose a methodology for the synthesis of site-specific antibody-dye conjugates with a high degree of labeling. To this end, we synthesized two oxyamine-based branched triazide linkers and coupled them with a periodate-oxidized anti-PRAME antibody 6H8; two oxyamine-based linear monoazide linkers of similar structure were used as controls. The azide-labeled antibodies were subsequently conjugated with fluorescent dyes via SPAAC, a copper-free click reaction. Compared to their counterparts made with linear linkers, the branched conjugates possessed a higher degree of labeling. The utility of the methodology was demonstrated in the detection of the PRAME protein on the surface of the cell by flow cytometry.     

Reagents for Multiple Non-Radioactive Labelling of Oligonucleotides

Novel phosphoramidite reagents for nonradioactive polylabelling of oligonucleotides have been developed, including two branching reagents, 4 and 8, and a biotin-containing phosphoramidite 19 which can be used to incorporate a biotin moiety into any position of the oligonucleotide.     

Structure-activity studies of irumamycin type macrolides from Streptomyces sp. INA-Ac-5812

Three natural glycosylated macrolide compounds, known irumamycin 1 and X-14952B 2, as well as new isoirumamycin 3, were isolated from ethyl acetate mycelium extract of Streptomyces sp. INA-Ac-5812. Structures of the compounds were elucidated using 1D and 2D NMR. Isoirumamycin 3 was found to be an isomer of irumamycin with an 18-membered macrolactone ring instead of 20-membered macrolide in irumamycin. A previously unknown stereo configuration of irumamycin epoxide (C23, C24) and hemiketal (C3, C7) fragments was deduced from NMR data (ROESY/NOESY and HSQMBC). Cytotoxic, antifungal and antibacterial activities were studied for all isolated compounds. Comparison of the collected data showed crucial importance of 20-membered macrolactone ring for antimicrobial properties of this antibiotic family.     

S(O)-pixyl protecting group as efficient mass-tag

We report herein the design, preparation and first applications of novel trityl tags with adjustable stability, efficient as protecting groups or MS analytes.