EFFECT OF ADENINE METHYLATION ON THE STRUCTURE AND DYNAMICS OF TPA STEPS IN DNA - NMR STRUCTURE DETERMINATION OF [D(CGAGGTTTAAACCTCG)](2) AND ITS A9-METHYLATED DERIVATIVE AT 750 MHZ
J. Lingbeck et al., EFFECT OF ADENINE METHYLATION ON THE STRUCTURE AND DYNAMICS OF TPA STEPS IN DNA - NMR STRUCTURE DETERMINATION OF [D(CGAGGTTTAAACCTCG)](2) AND ITS A9-METHYLATED DERIVATIVE AT 750 MHZ, Biochemistry, 35(3), 1996, pp. 719-734
At TpA steps in DNA, the adenine base experiences exceptionally large
amplitude (20 degrees-50 degrees) and slow (10 ms-1 mu s) motion [Kenn
edy et al. (1993) Biochemistry 32, 8022-8035] which has been correlate
d with transitions between multiple conformational states [Lefevre et
al. (1985) FEES Lett. 190, 37-40]. The base dynamics can be detected i
n one-dimensional H-1 NMR spectra as excess line width of the aromatic
proton resonances. The magnitude of the excess line width is temperat
ure dependent and reaches a maximum at some temperature. In order to b
etter understand the origin of the dynamics, we have studied the effec
t of N-6-methylation of the TpA adenine on both the line widths and it
s local structure. Here, solution-state 500 and 750 MHz H-1 NMR data c
ollected on [d(CGAGGTTTAAACCTCG)](2) show that the excess line width o
f the TpA adenine-H2 is diminished when the TpA adenine is N-6-methyla
ted and that the line width no longer experiences a maximum as the tem
perature is varied. The resonances sharpen upon methylation because th
e amplitude of base motion is restricted due to steric effects and due
to other structural changes at the TpA site. Additionally, both the T
pA adenine-H8. and the exchangeable imino resonance of thymine at the
TpA step were also found to have excess line width that is diminished
upon N-6-methylation. In order to elucidate the structural features re
sponsible for TpA base dynamics, solution-state NMR structures of [d(C
GAGGTTTAAACCTCG)](2) and its A9 N-6-methylated derivative were determi
ned at 750 MHz. Comparison of the structures shows that poor base stac
king at the TpA step may contribute to, or be the origin of, its base
dynamics.