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A Sensitive Multispectroscopic Probe for Nucleic Acids

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journal contribution
posted on 17.06.2010, 00:00 by Xin Sonia Gai, Edward E. Fenlon, Scott H. Brewer
Azides have recently been used as vibrational probes of proteins, but their incorporation into nucleic acids has been limited to photo-cross-linking or click chemistry applications. The utility of 2′-azido-2′-deoxyuridine (N3-dU, 1) as an IR and 15N NMR spectroscopic probe of the sugar phosphate backbone region of nucleic acids was investigated by measuring the effects of solvent, heterodimer formation, and temperature on peak frequencies and IR bandwidth. The azide IR asymmetric stretching band (ν̃N3) of N3-dU was sensitive to its environment, undergoing a blue shift of 13.5 cm−1 when changing the solvent from THF to water. The solvent effects on 15N chemical shifts (δ15N) of each of the nitrogen atoms in the azido group was studied, and the terminal nitrogen atom was the most sensitive to solvent, shifting downfield by 3.8 ppm when changing the solvent from THF-d8 to D2O. Formation of a base-pair-like heterodimer between 3 (a silyl ether analogue of 1) and 2,6-diheptanamidopyridine (4) in chloroform resulted in minimal changes in the IR and 15N NMR spectral frequency and chemical shift, respectively, as expected given the location of the azido moiety. The intrinsic temperature dependence of ν̃N3 and δ15N were found to be minimal over the temperature range studied especially compared to the solvent dependence of these spectral observables. The analysis of the experimental studies was complemented by density functional theory (DFT) calculations on model systems.