We report a series of 2′-deoxyribonucleoside triphosphates bearing dicarba-nido-undecaborategroups prepared either through the Sonogashira cross-coupling or the CuAAC click reaction. The modified dN X TPs were substrates for KOD XL DNA polymerase in enzymatic synthesis of modified DNA through primer extension (PEX). The nido-carborane-and FESAN-modified nucleotides gave analytically useful oxidation signals in square-wave voltammetry and were used for redox labeling of DNA. The redox-modified DNA probes were prepared by PEX using tailed primers and were hybridized to electrode (gold or glassy carbon) containing capture oligonucleotides. The combination of nido-carborane-and FESAN-linked nucleotides with 7-ferrocenylethynyl-7-deaza-dATP and 7-deaza-dGTP allowed polymerase synthesis of DNA fully modified at all four nucleobases, and each of the redox labels gave four differentiable and ratiometric signals in voltammetry. Thus, the combination of these four redox labels constitutes the first fully orthogonal redox coding of all four canonical nucleobases, which can be used for determination of nucleobase composition of short DNA stretches in one simple PEX experiment with electrochemical readout.
We describe the synthesis of novel C5‐triazolyl derived N1‐sulfonylpyrimidines through CuI‐catalyzed alkyne–azide cycloaddition followed by sulfonylation of the formed C5‐triazolyl derivatives with various sulfonyl chlorides under basic conditions. In the latter step, an intriguing difference in the reactivity of the pyrimidine N1 was observed that depended on the nature of the substituent at a distant triazole N1′ site. The N1′‐unsubstituted compounds gave very small amounts of sulfonylation products, whereas N1′‐substituted systems produced high yields of the respective N1‐sulfonyl‐5‐(1,2,3‐triazol‐4‐yl)uracils. Computational analysis revealed a close correlation between the strength of the employed base catalysts and their abilities to increase the nucleophilicity of the uracil N1 atom through subsequent deprotonation, leading to more products. Following this step, the phosphazene tBu–P4 superbase was applied in the sulfonylation, resulting in exclusive formation of the triazole N1′‐unsubstituted N1‐sulfonylpyrimidines.
A phenanthridine-triazolyluracilyl multifunctional ligand, linked by a lysine–glycine peptide, binds to poly rA–poly rU with micromolar affinity and selective fluorescence response.
Unless otherwise stated, all starting materials and solvents required for the synthesis of the DABCO cyanine dyes were purchased from Sigma-Aldrich, Organica Feinchemie GmbH Wolfen, Fluka, Alfa-Aesar, TCI Europe, Deutero GmbH, and used without any further purification. The solvents used for the spectroscopic analyses were purchased form Macron Fine Chemicals TM. All other starting materials and solvents were commercial products of analytical grade and were used without further purification. 2.2 Synthesis and spectroscopic analysis of the dyes 2.3. Analysis methods and equipment All products were characterized using various spectroscopic techniques. The progress of the reactions was monitored employing TLC (Merck F 254 silica gel; chloroform: methanol: acetic acid-80:15:5). Recrystallization from methanol yielded analytical samples of the title cyanines. 1 H-NMR and APT-NMR spectra of the compounds were recorded on a Brucker Avance III 500 MHz instrument in DMSO-d6 at room temperature. Chemical shifts were reported in ppm in δ-values with respect to tetramethylsilane (TMS) as an internal reference, or the corresponding peak of the deuterated solvent. Coupling constants JH-H were expressed in Hz. The structures of all intermediates were also evaluated on the target cyanine dyes. Melting point temperatures were evaluated on a Kofler bench and are uncorrected. Absorption and steady state fluorescence spectra of the unbound dyes were recorded in methanol solutions at room temperature, using 10-mm path-length quartz cuvettes on a Cecil Aurius CE 3021 UV-Vis spectrophotometer and Perkin Elmer LS45 fluorescence spectrometer (fixed slits 10-10 nm) at room temperature. 2.4. Synthetic approach to the DABCO monomethine cyanines and intermediate products 2.4.1. Preparation of intermediates 2a-2c
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