title: Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments.
abstract: Removal of a damaged base in DNA produces an abasic site (AP site) nanocavity. If left un-repaired in vivo by the specific enzyme, this nanocavity will result in nucleotide mutation in the following DNA replication. Therefore, selective recognition of AP site nanocavity by small molecules is important for identification of such DNA damage and development of genetic drugs. In this work, we investigate the fluorescence behavior of isoquinoline alkaloids including palmatine (PAL), berberine (BER), epiberberine (EPI), jatrorrhizine (JAT), coptisine (COP), coralyne (COR), worenine (WOR), berberrubine (BEU), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT) upon binding with the AP nanocavity. PAL is screened out as the most efficient fluorophore-switched probe to recognize the AP nanocavity over the fully matched DNA. Its fluorescence enhancement occurs for all of the AP nanocavity sequence environments, which has not been achieved by the previously used probes. The bridged π conjugation effect should partially contribute to the AP nanocavity-specific fluorescence, as opposed to the solvent effect. Due to the strong binding with the AP nanocavity, PAL will find wide applications in the DNA damage recognition and sensor development.
authors.affiliation: Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
authors.forename: Yuehua
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.affiliation: Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
authors.forename: Hua
authors.initials: H
authors.lastname: Liu
authors.affiliation: Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
authors.forename: Xiaoshun
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China. Electronic address: yshao@zjnu.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Shao
mesh_terms: D000470:Alkaloids / Q000737:chemistry; D001483:Base Sequence; D001600:Berberine Alkaloids / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D007700:Kinetics; D015335:Molecular Probes / Q000737:chemistry*; D053758:Nanoparticles / Q000737:chemistry*; D012996:Solutions; D013050:Spectrometry, Fluorescence; D044366:Transition Temperature
chemical_list: D000470:Alkaloids; D001600:Berberine Alkaloids; D005456:Fluorescent Dyes; D015335:Molecular Probes; D012996:Solutions; C000666:coralyne; D004247:DNA; C005413:palmatine
keywords: Abasic site; Fluorescence enhancement; Isoquinoline alkaloids; Molecular recognition; Nucleic acid; Palmatine