title: Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA.
abstract: The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change.
authors.affiliation: Institute of Chemical Biology, Henan University, Kaifeng 475004, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Tian
authors.affiliation: Institute of Chemical Biology, Henan University, Kaifeng 475004, China.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Institute of Chemical Biology, Henan University, Kaifeng 475004, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Institute of Chemical Biology, Henan University, Kaifeng 475004, China.
authors.forename: Lina
authors.initials: L
authors.lastname: Song
authors.affiliation: Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; State Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Qiao
authors.affiliation: Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china. Electronic address: 1322078049@qq.com.
authors.forename: Xuejun
authors.initials: X
authors.lastname: Xu
authors.affiliation: The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china. Electronic address: wcjsxq@henu.edu.cn.
authors.forename: Chaojie
authors.initials: C
authors.lastname: Wang
mesh_terms: D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D053644:Naphthalimides / Q000737:chemistry*; D011073:Polyamines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet
chemical_list: D053644:Naphthalimides; D011073:Polyamines; D004247:DNA
keywords: DNA; Model docking; Naphthalimide; Polyamine conjugates; Spectroscopy