Proton Nuclear Magnetic Resonance Studies on Bulge-Containing DNA Oligonucleotides from a Mutational Hot-Spot Sequence

A series of bulge-containing and normal double-helical synthetic oligodeoxyribonucleotides, of sequence corresponding to a frame-shift mutational hot spot in the X C_Igene, are compared by proton magnetic resonance spectroscopy at 500 MHz. The imino proton resonances of d(GATGGGCAG).d(CTGCCCATC), d(GATGGGCAG)-d(CTGCCCCATC), and d(GATGGGCAG)-d(CTGACCCATC) are assigned by one-dimensional nuclear Overhauser effect spectroscopy. Nonselective T₁ inversion-recovery experiments are used to determine exchangeable proton lifetimes and to compare helix stability and dynamics of the three duplexes. An extra adenosine flanking the internal G*C base pairs has a strongly localized effect on helix stability, but the destabilizing effect of an extra cytidine in a C tract is delocalized over the entire G’C run. These data lead to the conclusion that the position of the bulge migrates along the run in the fast-exchange limit on the NMR time scale. Rapid migration of the bulge defect in homopoiymeric sequences may help rationalize both frame-shift mutagenesis and translational frame shifting. We estimate that the unfavorable free energy of a localized bulge defect is 2.9-3.2 kcal/mol, in good agreement with earlier estimates for RNA helices.