title: Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation.
abstract: Dynamic DNA enzyme-based walkers complete their stepwise movements along the prescribed track through a series of reactions, including hybridization, enzymatic cleavage, and strand displacement; however, their overall translocation kinetics is not well understood. Here, we perform mechanistic studies to elucidate several key parameters that govern the kinetics and processivity of DNA enzyme-based walkers. These parameters include DNA enzyme core type and structure, upper and lower recognition arm lengths, and divalent metal cation species and concentration. A theoretical model is developed within the framework of single-molecule kinetics to describe overall translocation kinetics as well as each reaction step. A better understanding of kinetics and design parameters enables us to demonstrate a walker movement near 5 μm at an average speed of ∼1 nm s(-1). We also show that the translocation kinetics of DNA walkers can be effectively controlled by external light stimuli using photoisomerizable azobenzene moieties. A 2-fold increase in the cleavage reaction is observed when the hairpin stems of enzyme catalytic cores are open under UV irradiation. This study provides general design guidelines to construct highly processive, autonomous DNA walker systems and to regulate their translocation kinetics, which would facilitate the development of functional DNA walkers.
authors.affiliation: †School of Mechanical Engineering, ‡Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: Tae-Gon
authors.initials: TG
authors.lastname: Cha
authors.affiliation: †School of Mechanical Engineering, ‡Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: Jing
authors.initials: J
authors.lastname: Pan
authors.affiliation: †School of Mechanical Engineering, ‡Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: Haorong
authors.initials: H
authors.lastname: Chen
authors.affiliation: †School of Mechanical Engineering, ‡Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: Heather N
authors.initials: HN
authors.lastname: Robinson
authors.affiliation: †School of Mechanical Engineering, ‡Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: Xiang
authors.initials: X
authors.lastname: Li
authors.affiliation: †School of Mechanical Engineering, ‡Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: Chengde
authors.initials: C
authors.lastname: Mao
authors.affiliation: †School of Mechanical Engineering, ‡Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: Jong Hyun
authors.initials: JH
authors.lastname: Choi
mesh_terms: D001391:Azo Compounds / Q000737:chemistry; D001483:Base Sequence; D055162:Biocatalysis; D021881:DNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015195:Drug Design; D007536:Isomerism; D007700:Kinetics; D008027:Light; D009068:Movement; D036103:Nanotechnology / Q000379:methods*
chemical_list: D001391:Azo Compounds; D021881:DNA, Catalytic; C009850:azobenzene