DNA fragment conformations. I—methods for the assignment of DNA fragment proton resonances. ¹H NMR spectra of dApTpGpT and dApCpApTpGpT

Abstract

Abstract A general method for the assignment of DNA fragment proton resonances, especially for the sugar protons, has been presented and used to interpret the 400 MHz proton spectra of dApTpGpT and dApCpApTpGpT in neutral aqueous solution. Only fine splittings of about 3 Hz are observed in the H‐2″ resonances, and the total splitting is larger for the H‐2′ (≈29 Hz) than for the H‐2″ (22–23 Hz) multiplets. The purine and pyrimidine resonances can be distinguished on the basis of the H‐2″ and H‐2″ chemical shifts. The resonances of the H‐2′ and H‐2″ protons (above and below the sugar plane, respectively) of dA and dG exhibit chemical shifts of 2.65—2.80 ppm, while those of dC and dT residues are located at higher fields between 1.95 and 2.40 ppm. At high temperature (≥60°C), δH‐2′>YδH‐2″ for the purine family, while δH‐2′ « δH‐2″ in the case of the pyrimidine family. Except for the terminal residue, the H‐3′ resonances of dA and dG are located at lower fields compared with those of the dC and dT residues. The same is true for the H‐4′ resonances. In general δA 1′ >δG 1′ and in the case of self complementary duplexes the H‐1′ and H‐2′ chemical shift variations versus temperature are found to be larger for the dC than for the dT residues.