High resolution proton nuclear magnetic resonance investigation of the structural and dynamic properties of d(C15A15)·d(T15G15)

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Abstract
The high resolution proton NMR spectra of the synthetic DNA block polymer d(C15A15) .cntdot. d(T15G15) were studied in order to more completely understand telestability in DNA, and to provide fundamental NMR data on DNA helices and random coils. Spectra were measured in the spectral region from 0-15 ppm downfield from the usual standard, sodium 4,4-dimethyl-4-silapentane-1-sulfonate (DSS), at various temperatures (24-98.degree. C) in solutions containing moderate or high ionic strength. The effect of actinomycin binding to the block polymer also was studied. The majority of base pairs in the AT helix of the block polymer have the same conformation as in d(A)n .cntdot. d(T)25 and d(A)21 .cntdot. d(T)21. The conformation of the GC helix in the block polymer is different from the AT helix and this perturbs the conformation of 3 or 4 A.cntdot.T base pairs at the junction of the AT-GC helix. The conformation of the AT helix is unaffected by salt over the range examined (.apprx. 0.04-.apprx. 2 M), but the conformation of the GC helix changes. These are subtle changes in the conformation of the AT helix as the temperature is increased and resonances characteristic of the random coil and the double-helical state can be simultaneously observed. Binding of actinomycin, which is specific for the GC helix, induces quite large (over 1 ppm) upfield shifts of the resonances from the GC base pairs. This is consistent with an intercalation model in which actionmycin D (Am) is assymetrically sandwiched between 2 GC base pairs in such a manner that overlap with the guanosine residues is greater than with the neighboring cytidines. The presence of the drug may also perturb A.cntdot.T base pairs located near the AT-GC junction, but it has no effect on the majority of the AT pairs. Am elevated the Tm [melting temperature] of the AT helix, even though it binds to the other end of the DNA.

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