title: Characterization of the binding of neomycin/paromomycin sulfate with DNA using acridine orange as fluorescence probe and molecular docking technique.
abstract: The binding of neomycin sulfate (NS)/paromomycin sulfate (PS) with DNA was investigated by fluorescence quenching using acridine orange (AO) as a fluorescence probe. Fluorescence lifetime, FT-IR, circular dichroism (CD), relative viscosity, ionic strength, DNA melting temperature, and molecular docking were performed to explore the binding mechanism. The binding constant of NS/PS and DNA was 6.70 × 103/1.44 × 103L mol-1at 291 K. The values of ΔHθ, ΔSθ, and ΔGθsuggested that van der Waals force or hydrogen bond might be the main binding force between NS/PS and DNA. The results of Stern-Volmer plots and fluorescence lifetime measurements all revealed that NS/PS quenching the fluorescence of DNA-AO was static in nature. FT-IR indicated that the interaction between DNA and NS/PS did occur. The relative viscosity and melting temperature of DNA were almost unchanged when NS/PS was introduced to the solution. The fluorescence intensity of NS/PS-DNA-AO was decreased with the increase in the ionic strength. For CD spectra of DNA, the intensity of positive band at nearly 275 nm was decreased and that of negative band at nearly 245 nm was increased with the increase in the concentration of NS/PS. The binding constant of NS/PS with double-stranded DNA (dsDNA) was larger than that of NS/PS with single-stranded DNA (ssDNA). From these studies, the binding mode of NS/PS with DNA was evaluated to be groove binding. The results of molecular docking further indicated that NS/PS could enter into the minor groove in the A-T rich region of DNA.
authors.affiliation: a College of Chemistry , Changchun Normal University , Changchun 130032 , P.R. China.
authors.forename: Huifeng
authors.initials: H
authors.lastname: Zhou
authors.affiliation: a College of Chemistry , Changchun Normal University , Changchun 130032 , P.R. China.
authors.forename: Shuyun
authors.initials: S
authors.lastname: Bi
authors.affiliation: a College of Chemistry , Changchun Normal University , Changchun 130032 , P.R. China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: a College of Chemistry , Changchun Normal University , Changchun 130032 , P.R. China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
mesh_terms: D000165:Acridine Orange / Q000737:chemistry*; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D062105:Molecular Docking Simulation; D009355:Neomycin / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009994:Osmolar Concentration; D010303:Paromomycin / Q000737:chemistry*; D012996:Solutions; D013696:Temperature; D013816:Thermodynamics; D014783:Viscosity
chemical_list: D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D012996:Solutions; D010303:Paromomycin; D004247:DNA; C427203:calf thymus DNA; D000165:Acridine Orange; D009355:Neomycin
keywords: DNA; acridine orange; groove binding; neomycin sulfate; paromomycin sulfates