Structure refinement of oligonucleotides by molecular dynamics with nuclear overhauser effect interproton distance restraints: Application to 5′ d(C-G-T-A-C-G) 2

Abstract

The solution structure of the self-complementary DNA hexamer 5′ d(C-G-T-A-C-G) 2 is refined by restrained molecular dynamics in which 192 interproton distances, determined from pre-steady-state nuclear Overhauser enhancement measurements, are incorporated into the total energy of the system in the form of effective potentials. First the method is tested by applying an idealized set of distance restraints taken from classical B-DNA to a simulation starting off from A-DNA and vice versa. It is shown that in both cases the expected transition between A- and B-DNA occurs. Second, a set of restrained molecular dynamics calculations is carried out starting from both A- and B-DNA with the experimental interproton distances for 5′ d(C-G-T-A-C-G) 2 as restraints. Convergence to the same B-type structure is achieved with the interproton distances equal to the measured values within experimental error. The root-mean-square atomic difference between the two average restrained dynamics structures (<1 Å) is approximately the same as the root-mean-square fluctuations of the atoms.