Structures and Catalytic Activities of Complexes between Heme and All Parallel-Stranded Monomeric G-Quadruplex DNAs
- Yasuhiko Yamamoto*Yasuhiko Yamamoto*Phone and fax: +81-29-853-6521. E-mail: [email protected]Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanTsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, JapanLife Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, JapanMore by Yasuhiko Yamamoto,
- Haruka ArakiHaruka ArakiDepartment of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanMore by Haruka Araki,
- Ryosuke ShinomiyaRyosuke ShinomiyaDepartment of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanMore by Ryosuke Shinomiya,
- Kosuke HayasakaKosuke HayasakaDepartment of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanMore by Kosuke Hayasaka,
- Yusaku NakayamaYusaku NakayamaDepartment of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanMore by Yusaku Nakayama,
- Kentaro OchiKentaro OchiDepartment of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanMore by Kentaro Ochi,
- Tomokazu ShibataTomokazu ShibataDepartment of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanMore by Tomokazu Shibata,
- Atsuya MomotakeAtsuya MomotakeDepartment of Chemistry, University of Tsukuba, Tsukuba 305-8571, JapanMore by Atsuya Momotake,
- Takako OhyamaTakako OhyamaNMR Division, RIKEN SPring-8 Center, RIKEN, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, JapanMore by Takako Ohyama,
- Masaki HagiharaMasaki HagiharaGraduate School of Science and Technology, Hirosaki University, Hirosaki 036-8561, JapanMore by Masaki Hagihara, and
- Hikaru Hemmi
Abstract
Heme in its ferrous and ferric states [heme(Fe2+) and heme(Fe3+), respectively] binds selectively to the 3′-terminal G-quartet of all parallel-stranded monomeric G-quadruplex DNAs formed from inosine(I)-containing sequences, i.e., d(TAGGGTGGGTTGGGTGIG) DNA(18mer) and d(TAGGGTGGGTTGGGTGIGA) DNA(18mer/A), through a π–π stacking interaction between the porphyrin moiety of the heme and the G-quartet, to form 1:1 complexes [heme–DNA(18mer) and heme–DNA(18mer/A) complexes, respectively]. These complexes exhibited enhanced peroxidase activities, compared with that of heme(Fe3+) alone, and the activity of the heme(Fe3+)–DNA(18mer/A) complex was greater than that of the heme(Fe3+)–DNA(18mer) one, indicating that the 3′-terminal A of the DNA sequence acts as an acid–base catalyst that promotes the catalytic reaction. In the complexes, a water molecule (H2O) at the interface between the heme and G-quartet is coordinated to the heme Fe atom as an axial ligand and possibly acts as an electron-donating ligand that promotes heterolytic peroxide bond cleavage of hydrogen peroxide bound to the heme Fe atom, trans to the H2O, for the generation of an active species. The intermolecular nuclear Overhauser effects observed among heme, DNA, and Fe-bound H2O indicated that the H2O rotates about the H2O–Fe coordination bond with respect to both the heme and DNA in the complex. Thus, the H2O in the complex is unique in terms of not only its electronic properties but also its dynamic ones. These findings provide novel insights into the design of heme–deoxyribozymes and −ribozymes.
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