Toward a dynamical structure of DNA: comparison of theoretical and experimental NOE intensities

Comparisons of experimental and calculated interproton nuclear Overhauser effect (NOE) buildup curves for duplex d(CGCGAATTCGCG)2 have been made. The calculated NOEs are based on molecular dynamics simulations including counterions and water and on the single-structure canonical A, B, and crystal forms. The calculated NOE effects include consideration of the motions of individual interproton vectors and the anisotropic tumbling of the DNA. The effects due to inclusion of anisotropic tumbling are much larger than those due to the local motion, and both improve the agreement between calculated and experimental results. The predictions based on the dynamical models agree significantly better with experiment than those based on either of the canonical forms or the crystal structure.