Characterization of hydrogen bond lengths in Watson-Crick base pairs by cross-correlated relaxation

Abstract

Hydrogen bond lengths in Watson-Crick base pairs can be characterized by cross-correlated relaxation between 1H chemical shift anisotropy and dipole-dipole coupling of 1H and its hydrogen bond acceptor 15N. As a reference, the cross-correlated relaxation between 1H chemical shift anisotropy and dipole-dipole coupling of 1H and its hydrogen bond donor 15N is used. With the two measured cross-correlated relaxation rates, an apparent hydrogen bond length can be determined, which is composed by the hydrogen bond length multiplied by a term representing the amplitude of inter-base motions. Data are presented for the 15N3-1H3...15N1 hydrogen bonds in A=T base pairs of the Antennapedia homeodomain-DNA complex with a correlation time of global rotational diffusion of 20 ns.