title: An Exonuclease III-Powered, On-Particle Stochastic DNA Walker.
abstract: DNA-based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)-powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)-based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt-bridge mechanism. The operation of this Exo III-propelled DNA walker was monitored in real time and at the single-particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA-based stochastic DNA walker by exploiting movement-triggered cascade signal amplification.
authors.affiliation: Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
authors.forename: Xiangmeng
authors.initials: X
authors.lastname: Qu
authors.affiliation: Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.|Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhu
authors.affiliation: Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
authors.forename: Guangbao
authors.initials: G
authors.lastname: Yao
authors.affiliation: Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
authors.forename: Shao
authors.initials: S
authors.lastname: Su
authors.affiliation: Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chao
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
authors.forename: Huajie
authors.initials: H
authors.lastname: Liu
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Zuo
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Wang
authors.affiliation: Kellogg College, University of Oxford, Oxford, OX2 6PN, UK.|UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK.
authors.forename: Jiye
authors.initials: J
authors.lastname: Shi
authors.affiliation: Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
authors.forename: Lianhui
authors.initials: L
authors.lastname: Wang
authors.affiliation: Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
authors.affiliation: Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Pei
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
authors.forename: Chunhai
authors.identifier: 0000-0002-7171-7338
authors.initials: C
authors.lastname: Fan
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D005090:Exodeoxyribonucleases / Q000378:metabolism*; D009038:Motion; D053758:Nanoparticles / Q000378:metabolism*; D036103:Nanotechnology / Q000295:instrumentation; D009690:Nucleic Acid Conformation; D013269:Stochastic Processes
chemical_list: D004247:DNA; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III
keywords: Brownian motions; DNA nanotechnology; enzymes; molecular machines; nanoparticles