Synthesis of 5-(2-pyrenyl)-2 '-deoxyuridine as a DNA modification for electron-transfer studies: The critical role of the position of the chromophore attachment

5-(2-Pyrenyl)-2'-deoxyuridine (2PydU, 2) has been prepared as a new thymidine analogue in which the 2-position of the pyrene chromophore is connected covalently to the 5-position of uridine through a single C-C bond. The synthesis of 2 starts with the conversion of pyrene (3) into 2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyrene (4) by using an Ir catalyst that was prepared in situ from [IrCl(cod)12 and 4,4'-di-tert-butyl-2,2'-bipyridine (dtbpy) in the presence of NaOMe. The subsequent Suzuki-Miyaura cross-coupling of 4 with 5-iodo-2'-deoxyuridine (5) was performed by using 1,1'-bis[(diphenylphosphanyl)ferrocene]dichloropalladium(11) as the catalyst in a THF/MeOH/H2O mixture as the solvent. The modified nucleoside 2 was characterized by absorption and fluorescence spectroscopy. The results were compared with the strongly electronically coupled 5-(l-pyrenyl)-2'-deoxyuridine (1PydU, 1). Finally, the nucleoside 2 was converted into the corresponding phosphoramidite 7 as a DNA building block. The DNA set 8a-8d was synthesized to explore the optical properties of the 2PydU label in duplex DNA with respect to the counterbase opposite the 2PydX modification site and in comparison with 1PydU-modified DNA. The studies with the 2PydU nucleoside and the 2PydU-modified DNA clearly allow the conclusion to be drawn that the pyrene and the uridine moieties, as the two aromatic groups in this modified nucleoside, are only weakly electronically coupled. Accordingly, the 2PydU label behaves optically like a pyrene derivative, in contrast to the 1PydU label. The chromophore shows the ability for Watson-Crick base-pairing inside the DNA, as revealed by the absorption and fluorescence spectra. 2PydU represents an optical label for DNA that changes its absorption properties upon DNA hybridization and undergoes fluorescence quenching by charge transfer. ((c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008).