¹⁵N NMR Studies of a Nitrile-Modified Nucleoside

Abstract

Nitrile-modified molecules have proven to be excellent probes of local environments in biomolecules via both vibrational and fluorescence spectroscopy. The utility of the nitrile group as a spectroscopic probe has been expanded here to (15)N NMR spectroscopy by selective (15)N incorporation. The (15)N NMR chemical shift (δ((15)N)) of the (15)N-labeled 5-cyano-2'-deoxyuridine (C(15)NdU, 1a) was found to change from 153.47 to 143.80 ppm in going from THF-d(8) to D(2)O. A 0.81 ppm downfield shift was measured upon formation of a hydrogen-bond-mediated heterodimer between 2,6-diheptanamidopyridine and a silyl ether analogue of 1a in chloroform, and the small intrinsic temperature dependence of δ((15)N) of C(15)NdU was measured as a 0.38 ppm downfield shift from 298 to 338 K. The experiments were complemented with density functional theory calculations exploring the effect of solvation on the (15)N NMR chemical shift.

Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside

“…21, 24 Further studies have extended the application of these probes in nucleosides to infrared, 2D IR, and NMR experiments. 28, 29 The sensitivity of these reporters to the local environment 1, 2, 8, 28 and hydrogen bonding 2, 5 provides an avenue to track these dynamics by 2D IR methods using chemical exchange 30, 31 and spectral diffusion. 11–13, 17 …”

“…3, 28, 29, 42, 46 With these synthetic approaches, N 3 and CN probes can be placed virtually anywhere providing a useful monitor of site-specific dynamics in environments such as the major groove, minor groove, and phosphate-sugar region. Herein, we demonstrate the effectiveness of a pair of vibrational reporters as tools to investigate structural and dynamic aspects of different regions of DNA and RNA aptamers using 2D IR.…”

“…Specifically, the aliphatic azide substitutions are stable under most conditions and often avoid accidental Fermi resonances, allowing the azide reporter to more effectively detect local environment in peptides, proteins, and nucleosides. ,,− Both the N 3 transition and the CN transition have many similar spectral properties and a direct comparison of these probes has been documented using 2′-azido-5-cyano-2′-deoxyuridine (N 3 CNdU) . The changes in vibrational frequency resulting from hydrogen bonding and sensitivity to local electric field changes of both localized infrared transitions offer many advantages to studies of structural dynamics. , Further studies have extended the application of these probes in nucleosides to infrared, 2D IR, and NMR experiments. , The sensitivity of these reporters to the local environment ,,, and hydrogen bonding , provides an avenue to track these dynamics by 2D IR methods using chemical exchange , and spectral diffusion. − , …”

“…Although difficulties have been encountered for incorporating azide reporters into nucleic acids using standard methods, − several approaches for the incorporation of stable azide and nitrile groups into DNA and RNA have been successful recently. ,,,, With these synthetic approaches, N 3 and CN probes can be placed virtually anywhere providing a useful monitor of site-specific dynamics in environments such as the major groove, minor groove, and phosphate–sugar region. Herein, we demonstrate the effectiveness of a pair of vibrational reporters as tools to investigate structural and dynamic aspects of different regions of DNA and RNA aptamers using 2D IR.…”

“…21,24 Further studies have extended the application of these probes in nucleosides to infrared, 2D IR, and NMR experiments. 28,29 The sensitivity of these reporters to the local environment 1,2,8,28 and hydrogen bonding 2,5 provides an avenue to track these dynamics by 2D IR methods using chemical exchange 30,31 and spectral diffusion. [11][12][13]17 Two-dimensional infrared (2D IR) photon echo spectroscopy has shown utility in both observing and understanding vibrational properties including spectral diffusion, intermode coupling, conformational analysis, chemical exchange, and many others.…”