Preferential binding and structural distortion by Fe(2+) at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences

Certain DNA sequences are known to be unusually sensitive to nicking via the Fe(2+)-mediated Fenton reaction. Most notable are a purine nucleotide followed by three or more G residues, RGGG, and purine nucleotides flanking a TG combination, RTGR. Our laboratory previously demonstrated that nicking in the RGGG sequences occurs preferentially 5′ to a G residue with the nicking probability decreasing from the 5′ to 3′end of these sequences. Using (1)H NMR to characterize Fe(2+) binding within the duplex CGAGTTAGGGTAGC/GCTACCCTAACTCG and 7-deazaguanine-containing (Z) variants of it, we show that Fe(2+) binds preferentially at the GGG sequence, most strongly towards its 5′ end. Substitutions of individual guanines with Z indicate that the high affinity Fe(2+) binding at AGGG involves two adjacent guanine N7 moieties. Binding is accompanied by large changes in specific imino, aromatic and methyl proton chemical shifts, indicating that a locally distorted structure forms at the binding site that affects the conformation of the two base pairs 3′ to the GGG sequence. The binding of Fe(2+) to RGGG contrasts with that previously observed for the RTGR sequence, which binds Fe(2+) with negligible structural rearrangements.