title: Photo-cross-linked oligonucleotide duplex as a decoy-DNA for inhibition of restriction endonuclease activity.
abstract: As a novel type of regulator molecule for DNA-recognizing proteins, a photo-cross-linked oligonucleotide duplex was designed and synthesized. The molecule regulated the activity of a restriction endonuclease by being recognized as a substrate. This type of regulating molecule is regarded as a decoy-DNA. 4,5',8-[4-Aminoethylaminomethyl]-trioxalen (aeAMT) was conjugated with an oligodeoxyribonucleotide (ODN) at the 5'-end and the aeAMT was cross-linked with the thymine residue of the complementary oligonucleotide upon UVA irradiation. The terminally cross-linked oligonucleotides, singly clipped (SC) decoy-DNA, acquired thermal stability. An oligonucleoside phosphorothioate (OPT) was also introduced as one or both components, yielding three types of decoy-DNAs, SC-ODN-ODN (SC.DD), SC-OPT-ODN (SC.SD), and SC-OPT-OPT (SC.SS). The SC decoy-DNAs inhibited the function of the restriction endonuclease, AatII, in a sequence-specific and concentration-dependent manner with an appreciable IC50 value (1.3 microM for SC.DD, 0.016 microM for SC.SD, 0.002 microM for SC.SS). The SC decoy-DNAs were found to be effective for regulating the DNA recognizing proteins.
authors.affiliation: Department of Polymer Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan. akiram@ipc.kit.ac.jp
authors.forename: A
authors.initials: A
authors.lastname: Murakami
authors.forename: Y
authors.initials: Y
authors.lastname: Yamamoto
authors.forename: M
authors.initials: M
authors.lastname: Namba
authors.forename: R
authors.initials: R
authors.lastname: Iwase
authors.forename: T
authors.initials: T
authors.lastname: Yamaoka
mesh_terms: D004247:DNA / Q000737:chemistry / Q000494:pharmacology* / Q000528:radiation effects*; D004720:Endonucleases / Q000037:antagonists & inhibitors* / Q000737:chemistry; D006576:Heterocyclic Compounds, 4 or More Rings / Q000737:chemistry / Q000494:pharmacology* / Q000528:radiation effects*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000494:pharmacology* / Q000528:radiation effects*; D010777:Photochemistry; D013696:Temperature; D014466:Ultraviolet Rays
chemical_list: C506010:4,5',8-(4-Aminoethylaminomethyl)-trioxalen; D006576:Heterocyclic Compounds, 4 or More Rings; D009838:Oligodeoxyribonucleotides; D004247:DNA; D004720:Endonucleases