Characterization of Structure and Catalytic Activity of a Complex between Heme and an All Parallel-Stranded Tetrameric G-Quadruplex Formed from DNA/RNA Chimera Sequence d(TTA)r(GGG)dT

Abstract

An all-parallel tetrameric G-quadruplex formed from a DNA/RNA chimera sequence, d(TTA)r(GGG)d(T) ([Chimera(7mer)]₄), and its interaction with heme have been characterized. [Chimera(7mer)]₄ was found to be remarkably more stable compared with a G-quadruplex formed from its DNA counterpart d(TTAGGGT), ([DNA(7mer)]₄), despite the structural similarity between them, and the increased stability of [Chimera(7mer)]₄ is likely to be due to the formation of interstrand hydrogen bonds between the rG5 2′-OH and rG6 amino NH₂ groups. Heme bound selectively to the 3′-terminal G-quartet (rG6 G-quartet) in the rG6dT7 step of [Chimera(7mer)]₄ did not exhibit the heme orientational disorder resulting from the formation of two isomers possessing heme orientations differing by 180° rotation about the pseudo-C₂ axis, with respect to the interacting G-quartet, although it is a general feature of heme-DNA complexes. In a complex between heme and [Chimera(7mer)]₄, the predominance of one isomer in the heme orientational disorder over the other one is possibly due to contacts between the rG6 2′-OH group of the G-quartet and heme side chain ones. Peroxidase activity of heme bound to a G-quartet was found to be independent of the presence of the 2′-OH group in the ribose of the constituent units of the G-quartet.

DNA/RNA chimera, All-parallel G-quadruplex, Heme