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CSJ Journals

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2020, Vol.93, No.5

621-629
Selected Paper

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

Kosuke Hayasaka ,1Tomokazu Shibata ,1Aya Sugahara ,1Atsuya Momotake ,1Toru Matsui ,1Saburo Neya ,2Takumi Ishizuka ,3Yan Xu ,3 and Yasuhiko Yamamoto *1,4,5
1Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
2Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
3Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
4Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
5Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
https://doi.org/10.1246/bcsj.20200013

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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.

figure

Heme bound selectively to the 3′-terminal rG6 G-quartet in the rG6dT7 step of an all parallel G-quadruplex of DNA/RNA chimera d(TTA)r(GGG)d(T) predominantly adopts one of the two possible isomers possessing heme orientations differing by 180° rotation about the pseudo-C2 axis, with respect to the rG6 G-quartet, due to steric contacts between heme side chains and rG6 2′-OH groups.

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