title: A DNA nanomachine based on rolling circle amplification-bridged two-stage exonuclease III-assisted recycling strategy for label-free multi-amplified biosensing of nucleic acid.
abstract: An autonomous DNA nanomachine based on rolling circle amplification (RCA)-bridged two-stage exonuclease III (Exo III)-induced recycling amplification (Exo III-RCA-Exo III) was developed for label-free and highly sensitive homogeneous multi-amplified detection of DNA combined with sensitive fluorescence detection technique. According to the configuration, the analysis of DNA is accomplished by recognizing the target to a unlabeled molecular beacon (UMB) that integrates target-binding and signal transducer within one multifunctional design, followed by the target-binding of UMB in duplex DNA removed stepwise by Exo III accompanied by the releasing of target DNA for the successive hybridization and cleavage process and autonomous generation of the primer that initiate RCA process with a rational designed padlock DNA. The RCA products containing thousands of repeated catalytic sequences catalytically hybridize with a hairpin reporter probe that includes a "caged" inactive G-quadruplex sequence (HGP) and were then detected by Exo III-assisted recycling amplification, liberating the active G-quadruplex and generating remarkable ZnPPIX/G-quadruplex fluorescence signals with the help of zinc(II)-protoporphyrin IX (ZnPPIX). The proposed strategy showed a wide dynamic range over 7 orders of magnitude with a low limit of detection of 0.51 aM. In addition, this designed protocol can discriminate mismatched DNA from perfectly matched target DNA, and holds a great potential for early diagnosis in gene-related diseases.
authors.affiliation: Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China. Electronic address: xueqingwang1983@163.com.
authors.forename: Qingwang
authors.initials: Q
authors.lastname: Xue
authors.affiliation: Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China.
authors.forename: Yanqin
authors.initials: Y
authors.lastname: Lv
authors.affiliation: Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Cui
authors.affiliation: Shandong Provincial Key Lab of Test Technology on Food Quality and Safety, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Gu
authors.affiliation: Shandong Provincial Key Lab of Test Technology on Food Quality and Safety, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
authors.forename: Shuqiu
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Chemistry, Liaocheng University, Liaocheng 252059, Shandong, China; Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China. Electronic address: liujifeng111@gmail.com.
authors.forename: Jifeng
authors.initials: J
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D015374:Biosensing Techniques / Q000379:methods*; D004247:DNA / Q000032:analysis* / Q000235:genetics*; D005090:Exodeoxyribonucleases / Q000378:metabolism*; D057230:Limit of Detection; D036103:Nanotechnology / Q000379:methods*; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*
chemical_list: D004247:DNA; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III
keywords: Exonuclease III-assisted amplification; Fluorescence detection; G-quadruplex; Hairpin DNA probe; Rolling circle amplification