title: Electrochemical properties of interstrand cross-linked DNA duplexes labeled with Nile blue.
abstract: DNA molecules have attracted considerable attention as functional materials in various fields such as electrochemical sensors with redox-labeled DNA. However, the recently developed interstrand cross-link (ICL) technique for double-stranded DNA can adequately modify the electronic properties inside the duplex. Hence, the electrochemical investigation of ICL-DNA helps us to understand the electron transfer of redox-labeled DNA at an electrode surface, which would develop useful sensors. In this study, the first insight into this matter is presented. We prepared 17-mer DNA duplexes incorporating Nile blue (NB-DNA) at one end as a redox marker and a disulfide tether at the other end for immobilization onto an electrode. The duplexes were covalently cross-linked by bifunctional cross-linkers that utilize either a propyl or naphthalene residue to replace a base pair. Their electrochemical responses at the electrode surface were compared to evaluate the effect of the ICL on the electron-transfer reactions of the redox-labeled DNA duplexes. A direct transfer of electrons between NB and the electrode was observed for a standard DNA, as previously reported, whereas interstrand cross-linked DNA (CL-DNA) strands showed a decrease in the direct electron-transfer pathway. This is expected to result from constraining the elastic bending/flexibility of the duplex caused by the covalent cross-links. Interestingly, the CL-DNA incorporating naphthalene residues exhibited additional voltammetric peaks derived from DNA-mediated electron transfer (through base π stacking), which was not observed in the mismatched CL-DNA. The present results indicate that the ICL significantly affects electron transfer in the redox-labeled DNA at the electrode and can be an important determinant for electrochemical signaling in addition to its role in stabilizing the duplex structure.
authors.affiliation: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo 062-8517, Japan.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Mie
authors.forename: Keiko
authors.initials: K
authors.lastname: Kowata
authors.forename: Naoshi
authors.initials: N
authors.lastname: Kojima
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Komatsu
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003432:Cross-Linking Reagents / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004220:Disulfides / Q000737:chemistry; D055664:Electrochemical Techniques; D004566:Electrodes; D004579:Electron Transport; D004583:Electrons; D005456:Fluorescent Dyes / Q000737:chemistry*; D008969:Molecular Sequence Data; D009281:Naphthalenes / Q000737:chemistry; D009690:Nucleic Acid Conformation; D010078:Oxazines / Q000737:chemistry*; D010084:Oxidation-Reduction; D020005:Propanols / Q000737:chemistry; D055672:Static Electricity
chemical_list: D003432:Cross-Linking Reagents; D004220:Disulfides; D005456:Fluorescent Dyes; D009281:Naphthalenes; D010078:Oxazines; D020005:Propanols; C008619:Nile Blue; D004247:DNA