Detailed structure determination of DNA fragments using complete relaxation matrix analysis of two-dimensional NMR spectra, molecular mechanics calculations and computer graphics

The experimental and theoretical two-dimensional nuclear Overhauser effect spectra, double-quantum-filtered COSY experiments, and molecular mechanics calculations on the self-complementary decamer [d-(5'ATATATATAT3')]2 presented here indicate that the duplex as a time-average assumes a wrinkled D conformation (B DNA family) with a hydration tunnel in the minor groove. Formation of the tunnel is favored by non-bonded and electrostatic interchain sugar-phosphate and ion-DNA interactions in the minor groove. The size of the tunnel in the DNA perfectly accomodates three types of water molecules - one bridging interstrand N3 atoms of adenine, another water molecule bridging interstrand O2 atoms of thymine bases and another water molecule bridging the above mentioned two water molecules. 31 refs.; 3 figs.; 2 tabs