title: Nanopore single-molecule analysis of DNA-doxorubicin interactions.
abstract: Anticancer activity and toxicity of doxorubicin (Dox) are associated with its DNA intercalation. To understand the role in gene regulation and the drug mechanism, it is a challenge to detect the DNA-Dox interaction at the single-molecule level without the use of laborious, time-consuming labeling assays and an error-prone amplification method. Here, we utilized the simplest and cheapest, yet highly sensitive, single-molecule nanopore technology to investigate the DNA-Dox interaction and explore in situ the intercalative reaction kinetics. Distinctive electronic signal patterns between DNA and the DNA-Dox complex allow protein nanopore to readily detect the changes in structure and function of DNA. After Dox insertion, nanopore unzipping time of DNA was elevated 10-fold while the blocking current decreased, demonstrating the higher affinity of the DNA-Dox complex (formation constant K(f) = 3.09 × 10(5) M(-1)). Continuous rapid nanopore detection in real time displayed that Dox intercalation in DNA is a two-state dynamic process: fast binding and slow conformational adaption. The nanopore platform provides a powerful tool for studying small molecule-biomacromolecule interactions and paves the way for novel applications aimed at drug screening and functional analysis.
authors.affiliation: Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry and Materials Science, Northwest University , Xi'an 710069, P. R. China.
authors.forename: Fujun
authors.initials: F
authors.lastname: Yao
authors.forename: Jing
authors.initials: J
authors.lastname: Duan
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhang
authors.forename: Yanli
authors.initials: Y
authors.lastname: Guo
authors.forename: Huilin
authors.initials: H
authors.lastname: Guo
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Kang
mesh_terms: D015374:Biosensing Techniques / Q000379:methods*; D018736:DNA Adducts / Q000737:chemistry* / Q000378:metabolism*; D004317:Doxorubicin / Q000737:chemistry* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry; D006460:Hemolysin Proteins / Q000737:chemistry; D006801:Humans; D007364:Intercalating Agents / Q000737:chemistry; D007700:Kinetics; D058608:Nanopores; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation
chemical_list: D018736:DNA Adducts; D029968:Escherichia coli Proteins; D006460:Hemolysin Proteins; C036507:Hlya protein, E coli; D007364:Intercalating Agents; C031902:doxorubicin-DNA; D004317:Doxorubicin