A DFT study of the interresidue dependencies of scalar J-coupling and magnetic shielding in the hydrogen-bonding regions of a DNA tripler

Scalar coupling constants and magnetic shieldings in the imino hydrogen-bon ding region of Hoogsteen-Watson-Crick T A-T and Ct G-C triplets have been c alculated as a function of the distance between proton donor and acceptor n itrogen atoms. The Fermi contact contributions to (h2)J(N-15-H . . . N-15), (1)J(N-15-H-1), and (h1)J(H-1 . . . N-15) were computed using density func tional theory/finite perturbation theory (DFT/ FPT) methods for the full ba se triplets at the unrestricted B3PW91/6-311G** level. Chemical shifts B(H- 1) and delta(N-15) were obtained at the same level using the gauge includin g atomic orbital (GIAO) method for magnetic shielding. All three scalar cou plings and all three chemical shifts are strongly interrelated and exhibit monotonic changes with base pair separation. These correlations are in conf ormity with experimental data for a 32-nucleotide DNA tripler. The results suggest that both chemical shifts and coupling constants can be used to gai n information on H-bond donor-acceptor distances in nucleic acids. In addit ion to the DFT/FPT calculations, a simple three-orbital model of the N-H H bond and a sum-over-states analysis is presented. This model reproduces the basic features of the H-bond coupling effect. In accordance with this mode l and the DFT calculations, a positive sign for the (h2)J(NN) coupling is d etermined from an E.COSY experiment.