3-DIMENSIONAL STRUCTURE OF OLIGODEOXYRIBONUCLEOTIDE D(GGTATACC)(2) INSOLUTION SIMULATED BY DISTANCE RESTRAINED MOLECULAR DYNAMIC CALCULATIONS

The solution - structure of oligodeoxyribonucleotide d(GGTATACC)(2) wa s determined by conventional high - temperature and low - temperature distance restrained Molecular Dynamic (rMD) method. One hundred and ei ghty six NOE constraints from NOESY NMR spectra of 100 ms mixing time and 20 hydrogen bond constraints as well as 32 dihedral angle constrai nts were added to the initial structure of standard B - type DNA. Six superimposed structures with low energy of -302 +/- 5 kJ/mol were obta ined. The root mean square deviations (rmsd) between different structu res were all less than 0.06 nm and the average rmsd was 0.043 nm. The calculated result was illustrated to be reliable also by the back - ca lculated NOESY which was in good agreement with that from experiment.