Flap Endonuclease 1‑Assisted DNA Walkers for Sensitively and Specifically Sensing ctDNAs
DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base difference...
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| Veröffentlicht in: | Analytical chemistry (Washington) 2021-07, Vol.93 (27), p.9593-9601 |
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| creator | Cheng, Xianyi Bao, Yaofei Liang, Shuo Li, Bo Liu, Yunlong Wu, Haiping Ma, Xueping Chu, Yanan Shao, Yang Meng, Qi Zhou, Guohua Song, Qinxin Zou, Bingjie |
| description | DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. The results of epidermal growth factor receptor (EGFR) L858R mutation detection on cell-free DNA samples from 15 patients with nonsmall cell lung cancer were completely consistent with that of next-generation sequencing, indicating that our DNA walker has potential for liquid biopsy. |
| doi_str_mv | 10.1021/acs.analchem.1c01765 |
| format | Article |
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However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. The results of epidermal growth factor receptor (EGFR) L858R mutation detection on cell-free DNA samples from 15 patients with nonsmall cell lung cancer were completely consistent with that of next-generation sequencing, indicating that our DNA walker has potential for liquid biopsy.</description><identifier>ISSN: 0003-2700</identifier><identifier>EISSN: 1520-6882</identifier><identifier>DOI: 10.1021/acs.analchem.1c01765</identifier><identifier>PMID: 34191475</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Analytical chemistry ; Biopsy ; Biosensing Techniques ; Biosensors ; Carcinoma, Non-Small-Cell Lung ; Chemistry ; Circulating Tumor DNA - analysis ; Deoxyribonucleic acid ; Detection limits ; DNA ; DNA sequencing ; Endonuclease ; Epidermal growth factor ; Flap Endonucleases ; Gold ; Growth factors ; Humans ; Lung cancer ; Lung Neoplasms ; Metal Nanoparticles ; Mutants ; Mutation ; Nanoparticles ; Next-generation sequencing ; Sensitivity enhancement ; Strands ; Target detection ; Walking</subject><ispartof>Analytical chemistry (Washington), 2021-07, Vol.93 (27), p.9593-9601</ispartof><rights>2021 American Chemical Society</rights><rights>Copyright American Chemical Society Jul 13, 2021</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a376t-8e8d7741c92d608c7112c4192a54c71dbd0e5810bccfb22682d9d3d0673679a53</citedby><cites>FETCH-LOGICAL-a376t-8e8d7741c92d608c7112c4192a54c71dbd0e5810bccfb22682d9d3d0673679a53</cites><orcidid>0000-0003-1056-9156</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.1c01765$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.analchem.1c01765$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,780,784,2763,27075,27923,27924,56737,56787</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34191475$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Cheng, Xianyi</creatorcontrib><creatorcontrib>Bao, Yaofei</creatorcontrib><creatorcontrib>Liang, Shuo</creatorcontrib><creatorcontrib>Li, Bo</creatorcontrib><creatorcontrib>Liu, Yunlong</creatorcontrib><creatorcontrib>Wu, Haiping</creatorcontrib><creatorcontrib>Ma, Xueping</creatorcontrib><creatorcontrib>Chu, Yanan</creatorcontrib><creatorcontrib>Shao, Yang</creatorcontrib><creatorcontrib>Meng, Qi</creatorcontrib><creatorcontrib>Zhou, Guohua</creatorcontrib><creatorcontrib>Song, Qinxin</creatorcontrib><creatorcontrib>Zou, Bingjie</creatorcontrib><title>Flap Endonuclease 1‑Assisted DNA Walkers for Sensitively and Specifically Sensing ctDNAs</title><title>Analytical chemistry (Washington)</title><addtitle>Anal. Chem</addtitle><description>DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. 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Chem</addtitle><date>2021-07-13</date><risdate>2021</risdate><volume>93</volume><issue>27</issue><spage>9593</spage><epage>9601</epage><pages>9593-9601</pages><issn>0003-2700</issn><eissn>1520-6882</eissn><abstract>DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. The results of epidermal growth factor receptor (EGFR) L858R mutation detection on cell-free DNA samples from 15 patients with nonsmall cell lung cancer were completely consistent with that of next-generation sequencing, indicating that our DNA walker has potential for liquid biopsy.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>34191475</pmid><doi>10.1021/acs.analchem.1c01765</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0003-1056-9156</orcidid></addata></record> |
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| subjects | Analytical chemistry Biopsy Biosensing Techniques Biosensors Carcinoma, Non-Small-Cell Lung Chemistry Circulating Tumor DNA - analysis Deoxyribonucleic acid Detection limits DNA DNA sequencing Endonuclease Epidermal growth factor Flap Endonucleases Gold Growth factors Humans Lung cancer Lung Neoplasms Metal Nanoparticles Mutants Mutation Nanoparticles Next-generation sequencing Sensitivity enhancement Strands Target detection Walking |
| title | Flap Endonuclease 1‑Assisted DNA Walkers for Sensitively and Specifically Sensing ctDNAs |
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