Nucleoside, pyrene-modified

Mayer, E., Valis, L., Huber, R., Amann, N. and Wagenknecht, H. A. (2003). Preparation of pyrene-modified purine and pyrimidine nucleosides via Suzuki-Miyaura cross-couplings and characterization of their fluorescent properties. Synthesis 2335-2340. 

This conformation would place the chromophore residue into a stacked situation within the adjacent DNA bases while replacing the counterbase of the complementary strand. To obtain more structural information, NOESY experiments were performed on the pyrene-modified nucleosides. The spectra of the modified pyrimidines Py-dU and Py-C clearly showed a significant NOESY cross peak between H-6 of the dU part or the C part, respectively and H-2 of the corresponding 2 -deoxyribose moiety. The NOESY cross peak was comparably as strong as the cross peaks between H-2 and H-l or H-3, respectively. These NMR results can only be explained with the preferred anti conformation of these nucleosides. 

By use of the nucleoside Py-dU we prepared a range of pyrene-modified duplexes by phosphoramidite chemistry [29]. The covalently attached pyrene group is located outside the DNA base stack. On excitation intramolecular ET in the Py-dU group represents injection of an excess electron into the DNA base stack. The differences between the prepared DNA duplexes are the bases located next to the Py-dU group. 

Kumar et reported the synthesis of pyrene-modified nucleotides and their effects in secondary nucleic acid structures. Pyrene was attached to the 5 -position of thymidine (26a) or to the 2 -position of 2 -deojgairidine via a triazolomethylene linker (26b), or via a triazole linker (26c). These nucleosides were converted into their phosphoramidites and then incorporated into oligonucleotides, and analysed by thermal stability and fluorescence studies. These experiments indicated that these oligonucleotides can act as specific recognition probes. 

A critical structural issue with the subsequent incorporation of this type of chromophore-modified nucleosides into DNA duplexes is the assumption that it forms Watson-Crick base pairs with A as the counterbase. Our concern was that the large pyrene moiety may force the nucleosides into a syn conformation. 

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