S. Singh et al., CONFORMATIONAL DYNAMISM IN D-(GAATTCCGTTATT) CONTAINING THE COMPLEMENTARY MYB RESPONSIVE ELEMENT D-CCGTTA - NMR AND MD INVESTIGATIONS, Indian Journal of Biochemistry & Biophysics, 32(4), 1995, pp. 189-195
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.