Analysis of H-1 chemical shifts in DNA: Assessment of the reliability of H-1 chemical shift calculations for use in structure refinement

The reliability of H chemical shift calculations for DNA is assessed by comparing the experimentally and calculated chemical shifts of a reasonably large number of independently determined DNA structures. The calculated chemical shifts are based on semiempirical relations derived by Giessner-Prettre and Pullman [(1987) Q. Rev. Biophys., 20, 113–172]. The standard deviation between calculated and observed chemical shifts is found to be quite small, i.e. 0.17 ppm. This high accuracy, which is achieved without parameter adjustment, makes it possible to analyze the structural dependencies of chemical shifts in a reliable fashion. The conformation-dependent H chemical shift is mainly determined by the ring current effect and the local magnetic anisotropy, while the third possible effect, that of the electric field, is surprisingly small. It was further found that for a double helical environment, the chemical shift of the sugar protons, H2′ to H5′′, is mainly affected by the ring current and magnetic anisotropy of their own base. Consequently, the chemical shift of these sugar protons is determined by two factors, namely the type of base to which the sugar ring is attached, C, T, A, or G, and secondly by the χ-angle. In particular, the H2′ shift varies strongly with the χ-angle, and strong upfield H2′ shifts directly indicate that the χ-angle is in the syn domain. The H1′ shift is not only strongly affected by its own base, but also by its 3′-neighboring base. On the other hand, base protons, in particular H5 of cytosine and methyl protons of thymine, are affected mainly by the 5′-neighboring bases, although some effect (0.2 ppm) stems from the 3′-neighboring base. The H2 protons are mainly affected by the 3′-neighboring base. As a result of these findings a simple scheme is proposed for sequential assignment of resonances from B-helices based on chemical shifts.