title: Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers.
abstract: DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s-1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.
authors.affiliation: School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Pan
authors.affiliation: School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Tae-Gon
authors.initials: TG
authors.lastname: Cha
authors.affiliation: School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Feiran
authors.initials: F
authors.lastname: Li
authors.affiliation: School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Haorong
authors.identifier: 0000-0002-8218-9817
authors.initials: H
authors.lastname: Chen
authors.affiliation: School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Nina A
authors.initials: NA
authors.lastname: Bragg
authors.affiliation: School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Jong Hyun
authors.initials: JH
authors.lastname: Choi
mesh_terms: D004247:DNA / Q000737:chemistry*; D007259:Infrared Rays; D008856:Microscopy, Fluorescence; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D004247:DNA
keywords: DNA nanotechnology; DNA walker; single molecule kinetics; subdiffraction imaging