Igor A. Prokhorenko

New Pyrene Derivatives for Fluorescent Labeling of Oligonucleotides

Abstract A series of pyrene-containing reagents have been synthesized and used for the fluorescent labeling of oligonucleotides.

[Synthesis and fluorescent properties of 5-(1-pyrenylethynyl)-2'- deoxyuridine-containing oligodeoxynucleotides].

Novel reagents for the fluorescent labeling of oligo- and polynucleotides have been prepared: 5-(1-pyrenylethynyl)-2′-deoxyuridine 3′-phosphoramidite and a solid support carrying this nucleoside. Oligo-nucleotides containing one or several modified units have been synthesized, and the fluorescence of these probes has been shown to change upon hybridization with the complementary sequence.

Incorporation of a pyrene nucleoside analogue into synthetic oligodeoxynucleotides using a nucleoside-like synthon

Abstract A novel phosphoramidite 4 based on the hydroxyprolinol 1 backbone has been synthesized and used to chemically prepare DNA fragments bearing a pyrene-containing nucleoside analogue.

Reagents for Multiple Non-Radioactive Labelling of Oligonucleotides

Abstract 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.

Two-dye and one- or two-quencher DNA probes for real-time PCR assay: synthesis and comparison with a TaqMan™ probe.

AbstractA typical TaqMan™ real-time PCR probe contains a 5′-fluorescent dye and a 3′-quencher. In the course of the amplification, the probe is degraded starting from the 5′-end, thus releasing fluorescent dye. Some fluorophores (including fluorescein) are known to be prone to self-quenching when located near each other. This work is aimed at studying dye–dye and dye–quencher interactions in multiply modified DNA probes. Twenty-one fluorogenic probes containing one and two fluoresceins (FAM), or a FAM–JOE pair, and one or two BHQ1 quenchers were synthesized using non-nucleoside reagents and “click chemistry” post-modification on solid phase and in solution. The probes were tested in real-time PCR using an ~300-bp-long natural DNA fragment as a template. The structural prerequisites for lowering the probe background fluorescence and increasing the end-plateau fluorescence intensity were evaluated and discussed. FigureFluorogenic TaqMan probes with various modifications for real-time PCR

Oligonucleotide Conjugates of Nile Red

Oligonucleotides containing long chain amine on uridine‐2′‐carbamate have been covalently modified with Nile Red, a hydrophobic long wavelength fluorescent benzophenoxazine dye. The fluorescence of the dye is quenched in oligonucleotide conjugates. Thermal denaturation studies show considerable interactions of Nile Red with DNA–DNA duplexes. †In honor and celebration of the 70th birthday of Professor Leroy B. Townsend.

Simple reagent for the synthesis of oligonucleotides labeled with 3,3,3′,3′-tetramethyl-2,2′-indodicarbocyanine

Synthesis of a phosphoramidite reagent for the preparation of oligonucleotides labeled at the 5′-end with a fluorescent dye, 3,3,3′,3′-tetramethyl-2,2′-indodicarbocyanine, is described. The efficiency of this reagent is confirmed by the synthesis of several labeled oligonucleotides.

Non-nucleoside phosphoramidites of xanthene dyes (FAM, JOE, and TAMRA) for oligonucleotide labeling.

This unit describes the preparation of 5‐ and 6‐carboxy derivatives of the xanthene fluorescent dyes fluorescein (FAM), 4′,5′‐dichloro‐2′,7′‐dimethoxy‐fluorescein (JOE), and tetramethylrhodamine (TAMRA) as individual isomers, and their conversion to non‐nucleoside phosphoramidite reagents suitable for oligonucleotide labeling. The use of a cyclohexylcarbonyl (Chc) protecting group for blocking of phenolic hydroxyls facilitates the chromatographic separation of isomers of carboxy‐FAM and carboxy‐JOE as pentafluorophenyl esters. Acylation of 3‐dimethylaminophenol with 1,2,4‐benzenetricarboxylic anhydride gave a mixture of 4‐dimethylamino‐2‐hydroxy‐2′,4′(5′)‐dicarboxybenzophenones, easily separable into individual compounds upon fractional crystallization. Individual isomeric benzophenones are precursors of 5‐ or 6‐carboxytetramethylrhodamines. The dyes were converted into 6‐aminohexanol‐ (JOE), 4‐trans‐aminocyclohexanol‐ (FAM and JOE), and hydroxyprolinol‐based (TAMRA) phosphoramidite reagents. Curr. Protoc. Nucleic Acid Chem. 52:4.55.1‐4.55.33.

Reagents For The Selective Immobilization Of Oligonucleotides On Solid Supports

New reagents (CPGs and phosphoramidites) for automatic solid phase synthesis of modified oligonucleotides were designed. Three oligonucleotides carrying fluorescent label at the 5′-terminus and an anchor group at the 3′-terminus were prepared and their immobilization in orthogonal conditions on solid supports was studied.

Amicoumacins and Related Compounds: Chemistry and Biology

The review will cover main classes of 3,4-dihydroisocoumarin-derived natural and bioactive compounds with main focus on antibiotics, amicoumacins and xenocoumacins. The 3,4-dihydroisocoumarin natural compounds were reviewed many years ago (Hill, 1986 [2] ; McInerney and Taylor, 1995 [7] ). The recent short account on amicoumacins is in Chinese and does not contain any synthetic data (Han et al., 2013 [23] ).