title: Kinetic characterization of small DNA-binding molecules interacting with a DNA strand on a quartz crystal microbalance.
abstract: Quantitative studies of the binding of various DNA-binding antibiotics with dsDNA are useful for drug design, not only for effective antibiotics, but also for antitumor drugs. We studied the binding kinetics, association and dissociation rate constants, and association constants (kon, koff, and Ka, respectively) of intercalators and groove binders, including various antibiotics, to double-stranded DNA (dA30·dT30 and dG30·dC30) immobilized on a highly sensitive 27 MHz quartz-crystal microbalance (QCM) in aqueous solution. Although a simple ethidium bromide intercalator bound to both dA30·dT30 and dG30·dC30, antibiotics that are side-binding intercalators, such as daunomycin, aclacinomycin A, and actinomycin D, with sugar or peptide moieties on the intercalator parts selectively bound to dG30·dC30 with high Ka and small koff values. Nogalamycin, a dumbbell-shaped penetrating intercalator, showed low kon and koff values owing to slow duplex unwinding during the penetration process. Groove binders (Hoechst 33258, distamycin A, and mithramycin) had high Ka values owing to the high kon values. Kinetic parameters depended largely on molecular shapes and DNA-binding molecule binding modes.
authors.affiliation: Innovative Flex Course for Frontier Organic Material Systems (iFront), Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata, Japan; Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan. Electronic address: hfurusaw@yz.yamagata-u.ac.jp.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Furusawa
authors.affiliation: Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan.
authors.forename: Hajime
authors.initials: H
authors.lastname: Nakayama
authors.affiliation: Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan.
authors.forename: Mariko
authors.initials: M
authors.lastname: Funasaki
authors.affiliation: Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan.
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Okahata
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004996:Ethidium / Q000737:chemistry / Q000378:metabolism; D007364:Intercalating Agents / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D058525:Quartz Crystal Microbalance Techniques
chemical_list: D000900:Anti-Bacterial Agents; D007364:Intercalating Agents; D004247:DNA; D004996:Ethidium
keywords: Antibiotics; DNA; Kinetics; Quartz crystal microbalance; Small DNA-Binding molecules