Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure.
DNA guanine-quadruplexes (G-quadruplexes) complexed with the Fe-containing porphyrin, hemin (iron(III)-protoporphyrin IX), can catalyze oxidation reactions. This so-called DNAzyme has been widely used in the field of DNA nanotechnology. To improve DNAzyme properties, we sought to elucidate the interaction mechanism between G-quadruplex DNA and hemin. Here, we performed volumetric analyses of formation of the complex between an oligonucleotide with the sequence of human telomeric DNA (h-telo) and hemin. The G-quadruplex DNA alone and the G-quadruplex DNA-hemin complex were destabilized with increasing pressure in Na+buffer. The pressure required to destabilize the h-telo-hemin complex was less in K+-containing buffer than in buffer with Na+, which indicates that there was a smaller volumetric change upon h-telo formation in K+buffer than in Na+buffer. The calculated change in h-telo-hemin binding volume (∆Vb) in the Na+buffer was 2.5mLmol-1, whereas it was -41.7 in mLmol-1the K+buffer. The DNAzyme activity in the K+buffer was higher than that in the Na+buffer at atmospheric pressure. Interestingly, the pressure effect on the destabilization of the h-telo-hemin complex in the presence of poly(ethylene glycol)200 (PEG200) was repressed compared to that in the absence of PEG200. These results suggest that differences in volumetric parameters reflect different mechanisms of interaction between hemin and h-telo due to differences in both the fit of hemin into the h-telo structure and hydration. Thus, the pressure-based thermodynamic analysis provided important information about complex formation and could be a useful index to improve function of DNAzymes.
FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
Shuntaro
S
Takahashi
FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan; Dept. of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, University College of Science, 92, A.P.C. Road, Kolkata 700009, India.
Sudipta
S
Bhowmik
FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan; FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan. Electronic address: sugimoto@konan-u.ac.jp.
Naoki
N
Sugimoto
D001274:Atmospheric Pressure; D004247:DNA / Q000737:chemistry*; D021881:DNA, Catalytic / Q000737:chemistry; D054856:G-Quadruplexes; D006427:Hemin / Q000737:chemistry*; D011092:Polyethylene Glycols / Q000737:chemistry; D013816:Thermodynamics
D021881:DNA, Catalytic; D011092:Polyethylene Glycols; D006427:Hemin; D004247:DNA; C000595209:polyethylene glycol 1000
G-quadruplex; Hemin; Molecular crowding; Pressure; Thermodynamics