CONFORMATIONAL DYNAMISM IN D-(GAATTCCGTTATT) CONTAINING THE COMPLEMENTARY MYB RESPONSIVE ELEMENT D-CCGTTA - NMR AND MD INVESTIGATIONS

Conformational features of the DNA segment d-(GAATTCCGTTATT) containin g the complementary Myb responsive element CCGTTA has been studied by NMR and molecular dynamics calculations with a view to see the role of 3D structure in specific DNA recognition. From the low field imino pr oton NMR spectra, the DNA sequence is seen to exist as a duplex with p yrimidine mismatches in the centre. The 2D NMR spectra however show th at the molecule exhibits substantial dynamism even at 1 degrees C. Sev eral extra cross peaks, more than the expected number, ape seen in par ticular regions in all the spectra. These observations indicate that t he duplex undergoes slow transitions between base-paired and unbase-pa ired states due to mismatches in the centre. Hence, to characterise th ose transitions a restrained verlet dynamics has been performed for 50 ps using X-PLOR force field. Structural intermediates at regular inter vals have been analysed, and we see that the dynamism in the molecule results in substantial fluctuations in the different torsion angles. T he mismatch sites are seen to exhibit the highest degree of fluctuatio ns, with the bases stacking in and looping out of the duplex. The suga r geometry is seen to be fairly steady around the S domain for mast of the residues.