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
    Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571 , Japan
  • Tomokazu Shibata
    Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571 , Japan
  • Aya Sugahara
    Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571 , Japan
  • Atsuya Momotake
    Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571 , Japan
  • Toru Matsui
    Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571 , Japan
  • Saburo Neya
    Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675 , Japan
  • Takumi Ishizuka
    Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692 , Japan
  • Yan Xu
    Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692 , Japan
  • Yasuhiko Yamamoto
    Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571 , Japan

Abstract

<jats:title>Abstract</jats:title> <jats:p>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.</jats:p>

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