Three-Dimensional DNA Nanomachine Biosensor by Integrating DNA Walker and Rolling Machine Cascade Amplification for Ultrasensitive Detection of Cancer-Related Gene
Stochastic DNA walkers capable of traversing on three-dimensional (3D) tracks have received great deal of attention. However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high proc...
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| Veröffentlicht in: | Analytical chemistry (Washington) 2020-08, Vol.92 (16), p.11111-11118 |
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| creator | Wu, Na Wang, Kun Wang, Yi-Ting Chen, Ming-Li Chen, Xu-Wei Yang, Ting Wang, Jian-Hua |
| description | Stochastic DNA walkers capable of traversing on three-dimensional (3D) tracks have received great deal of attention. However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high processivity of a DNA rolling machine, a sensitive ratiometric DNA nanomachine biosensor is designed. The biosensor is constructed with hairpin-loaded Au nanoparticles (NPs) (hpDNA@AuNPs) as a DNA walker and AgNCs-decorated magnetic NPs (AgNCs@MNPs) as a DNA rolling machine. In the presence of target DNA, exonuclease III (Exo III)-powered DNA walker is activated to accomplish first-stage amplification via a burnt-bridge mechanism, generating a great deal of toehold-loaded AuNPs (Toehold@AuNPs) to hybridize with magnetic nanoparticles loaded with silver-nanoclusters-labeled DNA (AgNCs@MNPs) with the assistance of Exo III. These trigger rapid rolling of AuNPs on the AgNCs@MNPs surface and release free AgNCs, converting the biological signal into a mass spectrometric signal ratio (107Ag/197Au) with detection by ICP-MS. A linear range of 0.5–500 fmol L–1 is achieved with a detection limit of 119 amol L–1 for the p53 gene. The practical applicability of the biosensor has been demonstrated in the accurate assay of the p53 gene in the human blood. |
| doi_str_mv | 10.1021/acs.analchem.0c01074 |
| format | Article |
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However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high processivity of a DNA rolling machine, a sensitive ratiometric DNA nanomachine biosensor is designed. The biosensor is constructed with hairpin-loaded Au nanoparticles (NPs) (hpDNA@AuNPs) as a DNA walker and AgNCs-decorated magnetic NPs (AgNCs@MNPs) as a DNA rolling machine. In the presence of target DNA, exonuclease III (Exo III)-powered DNA walker is activated to accomplish first-stage amplification via a burnt-bridge mechanism, generating a great deal of toehold-loaded AuNPs (Toehold@AuNPs) to hybridize with magnetic nanoparticles loaded with silver-nanoclusters-labeled DNA (AgNCs@MNPs) with the assistance of Exo III. These trigger rapid rolling of AuNPs on the AgNCs@MNPs surface and release free AgNCs, converting the biological signal into a mass spectrometric signal ratio (107Ag/197Au) with detection by ICP-MS. A linear range of 0.5–500 fmol L–1 is achieved with a detection limit of 119 amol L–1 for the p53 gene. The practical applicability of the biosensor has been demonstrated in the accurate assay of the p53 gene in the human blood.</description><identifier>ISSN: 0003-2700</identifier><identifier>EISSN: 1520-6882</identifier><identifier>DOI: 10.1021/acs.analchem.0c01074</identifier><identifier>PMID: 32646212</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Amplification ; Analytical chemistry ; Biosensing Techniques - methods ; Biosensors ; Chemistry ; Deoxyribonucleic acid ; DNA ; DNA - blood ; DNA - chemistry ; DNA - genetics ; Exonuclease ; Genes, p53 ; Gold ; Gold - chemistry ; Humans ; Inverted Repeat Sequences ; Limit of Detection ; Magnetic Phenomena ; Metal Nanoparticles - chemistry ; Nanoclusters ; Nanoparticles ; Nucleic Acid Amplification Techniques - methods ; Nucleic Acid Hybridization ; p53 Protein ; Silver ; Silver - chemistry ; Spectrometry ; Tumor Suppressor Protein p53 - genetics ; Walking</subject><ispartof>Analytical chemistry (Washington), 2020-08, Vol.92 (16), p.11111-11118</ispartof><rights>Copyright American Chemical Society Aug 18, 2020</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a442t-ff14e1cfb15519e65c41852b6ed08df52d11b75ac014de8c964b546a802bc0e73</citedby><cites>FETCH-LOGICAL-a442t-ff14e1cfb15519e65c41852b6ed08df52d11b75ac014de8c964b546a802bc0e73</cites><orcidid>0000-0001-8536-8864 ; 0000-0001-5517-5658 ; 0000-0003-2175-3610 ; 0000-0001-7189-5022</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/acs.analchem.0c01074$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.analchem.0c01074$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,776,780,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32646212$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wu, Na</creatorcontrib><creatorcontrib>Wang, Kun</creatorcontrib><creatorcontrib>Wang, Yi-Ting</creatorcontrib><creatorcontrib>Chen, Ming-Li</creatorcontrib><creatorcontrib>Chen, Xu-Wei</creatorcontrib><creatorcontrib>Yang, Ting</creatorcontrib><creatorcontrib>Wang, Jian-Hua</creatorcontrib><title>Three-Dimensional DNA Nanomachine Biosensor by Integrating DNA Walker and Rolling Machine Cascade Amplification for Ultrasensitive Detection of Cancer-Related Gene</title><title>Analytical chemistry (Washington)</title><addtitle>Anal. Chem</addtitle><description>Stochastic DNA walkers capable of traversing on three-dimensional (3D) tracks have received great deal of attention. However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high processivity of a DNA rolling machine, a sensitive ratiometric DNA nanomachine biosensor is designed. The biosensor is constructed with hairpin-loaded Au nanoparticles (NPs) (hpDNA@AuNPs) as a DNA walker and AgNCs-decorated magnetic NPs (AgNCs@MNPs) as a DNA rolling machine. In the presence of target DNA, exonuclease III (Exo III)-powered DNA walker is activated to accomplish first-stage amplification via a burnt-bridge mechanism, generating a great deal of toehold-loaded AuNPs (Toehold@AuNPs) to hybridize with magnetic nanoparticles loaded with silver-nanoclusters-labeled DNA (AgNCs@MNPs) with the assistance of Exo III. These trigger rapid rolling of AuNPs on the AgNCs@MNPs surface and release free AgNCs, converting the biological signal into a mass spectrometric signal ratio (107Ag/197Au) with detection by ICP-MS. A linear range of 0.5–500 fmol L–1 is achieved with a detection limit of 119 amol L–1 for the p53 gene. 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Wang, Kun ; Wang, Yi-Ting ; Chen, Ming-Li ; Chen, Xu-Wei ; Yang, Ting ; Wang, Jian-Hua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a442t-ff14e1cfb15519e65c41852b6ed08df52d11b75ac014de8c964b546a802bc0e73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Amplification</topic><topic>Analytical chemistry</topic><topic>Biosensing Techniques - methods</topic><topic>Biosensors</topic><topic>Chemistry</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - blood</topic><topic>DNA - chemistry</topic><topic>DNA - genetics</topic><topic>Exonuclease</topic><topic>Genes, p53</topic><topic>Gold</topic><topic>Gold - chemistry</topic><topic>Humans</topic><topic>Inverted Repeat Sequences</topic><topic>Limit of Detection</topic><topic>Magnetic Phenomena</topic><topic>Metal Nanoparticles - chemistry</topic><topic>Nanoclusters</topic><topic>Nanoparticles</topic><topic>Nucleic Acid Amplification Techniques - methods</topic><topic>Nucleic Acid Hybridization</topic><topic>p53 Protein</topic><topic>Silver</topic><topic>Silver - chemistry</topic><topic>Spectrometry</topic><topic>Tumor Suppressor Protein p53 - genetics</topic><topic>Walking</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wu, Na</creatorcontrib><creatorcontrib>Wang, Kun</creatorcontrib><creatorcontrib>Wang, Yi-Ting</creatorcontrib><creatorcontrib>Chen, Ming-Li</creatorcontrib><creatorcontrib>Chen, Xu-Wei</creatorcontrib><creatorcontrib>Yang, Ting</creatorcontrib><creatorcontrib>Wang, Jian-Hua</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><jtitle>Analytical chemistry (Washington)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Na</au><au>Wang, Kun</au><au>Wang, Yi-Ting</au><au>Chen, Ming-Li</au><au>Chen, Xu-Wei</au><au>Yang, Ting</au><au>Wang, Jian-Hua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Three-Dimensional DNA Nanomachine Biosensor by Integrating DNA Walker and Rolling Machine Cascade Amplification for Ultrasensitive Detection of Cancer-Related Gene</atitle><jtitle>Analytical chemistry (Washington)</jtitle><addtitle>Anal. Chem</addtitle><date>2020-08-18</date><risdate>2020</risdate><volume>92</volume><issue>16</issue><spage>11111</spage><epage>11118</epage><pages>11111-11118</pages><issn>0003-2700</issn><eissn>1520-6882</eissn><abstract>Stochastic DNA walkers capable of traversing on three-dimensional (3D) tracks have received great deal of attention. However, DNA walker-based biosensors exhibit limited amplification efficiency because of their slow walking kinetics and low processivity. Herein, by taking advantage of the high processivity of a DNA rolling machine, a sensitive ratiometric DNA nanomachine biosensor is designed. The biosensor is constructed with hairpin-loaded Au nanoparticles (NPs) (hpDNA@AuNPs) as a DNA walker and AgNCs-decorated magnetic NPs (AgNCs@MNPs) as a DNA rolling machine. In the presence of target DNA, exonuclease III (Exo III)-powered DNA walker is activated to accomplish first-stage amplification via a burnt-bridge mechanism, generating a great deal of toehold-loaded AuNPs (Toehold@AuNPs) to hybridize with magnetic nanoparticles loaded with silver-nanoclusters-labeled DNA (AgNCs@MNPs) with the assistance of Exo III. These trigger rapid rolling of AuNPs on the AgNCs@MNPs surface and release free AgNCs, converting the biological signal into a mass spectrometric signal ratio (107Ag/197Au) with detection by ICP-MS. A linear range of 0.5–500 fmol L–1 is achieved with a detection limit of 119 amol L–1 for the p53 gene. 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| subjects | Amplification Analytical chemistry Biosensing Techniques - methods Biosensors Chemistry Deoxyribonucleic acid DNA DNA - blood DNA - chemistry DNA - genetics Exonuclease Genes, p53 Gold Gold - chemistry Humans Inverted Repeat Sequences Limit of Detection Magnetic Phenomena Metal Nanoparticles - chemistry Nanoclusters Nanoparticles Nucleic Acid Amplification Techniques - methods Nucleic Acid Hybridization p53 Protein Silver Silver - chemistry Spectrometry Tumor Suppressor Protein p53 - genetics Walking |
| title | Three-Dimensional DNA Nanomachine Biosensor by Integrating DNA Walker and Rolling Machine Cascade Amplification for Ultrasensitive Detection of Cancer-Related Gene |
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