{"title":"通过扩展悬臂控制杂交链反应深度及其分析应用","authors":"Hongzheng Zheng, Xuesi Li, Xiuqian Liu, Xiaowen Xu","doi":"10.1021/acs.analchem.4c03841","DOIUrl":null,"url":null,"abstract":"Hybridization chain reaction (HCR) is a powerful enzyme-free nucleic acid amplification strategy. Triggered by an initiator strand, it yields nicked double helices analogous to alternating copolymers. However, there is no effective way to regulate the HCR reaction, and the most apparent phenomenon is the uncontrollable polymerization of product after introducing an initiator. Here we explore controlling the depth of the HCR reaction by extended dangling ends on hairpin monomers and report that sequence length, nucleotide composition, and secondary structure can alter HCR polymerization and can be utilized for the desired regulation. Interaction dynamics between initiator and hairpin monomers simulated by oxDNA are in good accordance with experimental results. Such a controlling effect can be utilized for new analytical applications that HCR cannot previously achieve, such as analyzing strand-extension enzymes and identifying short-sequence structures. The finding provides a concise but effective way for controlling the depth of HCR reaction and opens the application scope of HCR to more fields.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.7000,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Controlling the Depth of Hybridization Chain Reaction by Extended Dangling Ends and Its Analytical Applications\",\"authors\":\"Hongzheng Zheng, Xuesi Li, Xiuqian Liu, Xiaowen Xu\",\"doi\":\"10.1021/acs.analchem.4c03841\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Hybridization chain reaction (HCR) is a powerful enzyme-free nucleic acid amplification strategy. Triggered by an initiator strand, it yields nicked double helices analogous to alternating copolymers. However, there is no effective way to regulate the HCR reaction, and the most apparent phenomenon is the uncontrollable polymerization of product after introducing an initiator. Here we explore controlling the depth of the HCR reaction by extended dangling ends on hairpin monomers and report that sequence length, nucleotide composition, and secondary structure can alter HCR polymerization and can be utilized for the desired regulation. Interaction dynamics between initiator and hairpin monomers simulated by oxDNA are in good accordance with experimental results. Such a controlling effect can be utilized for new analytical applications that HCR cannot previously achieve, such as analyzing strand-extension enzymes and identifying short-sequence structures. The finding provides a concise but effective way for controlling the depth of HCR reaction and opens the application scope of HCR to more fields.\",\"PeriodicalId\":27,\"journal\":{\"name\":\"Analytical Chemistry\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":6.7000,\"publicationDate\":\"2024-10-15\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Analytical Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.analchem.4c03841\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, ANALYTICAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Analytical Chemistry","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.analchem.4c03841","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, ANALYTICAL","Score":null,"Total":0}
Controlling the Depth of Hybridization Chain Reaction by Extended Dangling Ends and Its Analytical Applications
Hybridization chain reaction (HCR) is a powerful enzyme-free nucleic acid amplification strategy. Triggered by an initiator strand, it yields nicked double helices analogous to alternating copolymers. However, there is no effective way to regulate the HCR reaction, and the most apparent phenomenon is the uncontrollable polymerization of product after introducing an initiator. Here we explore controlling the depth of the HCR reaction by extended dangling ends on hairpin monomers and report that sequence length, nucleotide composition, and secondary structure can alter HCR polymerization and can be utilized for the desired regulation. Interaction dynamics between initiator and hairpin monomers simulated by oxDNA are in good accordance with experimental results. Such a controlling effect can be utilized for new analytical applications that HCR cannot previously achieve, such as analyzing strand-extension enzymes and identifying short-sequence structures. The finding provides a concise but effective way for controlling the depth of HCR reaction and opens the application scope of HCR to more fields.
期刊介绍:
Analytical Chemistry, a peer-reviewed research journal, focuses on disseminating new and original knowledge across all branches of analytical chemistry. Fundamental articles may explore general principles of chemical measurement science and need not directly address existing or potential analytical methodology. They can be entirely theoretical or report experimental results. Contributions may cover various phases of analytical operations, including sampling, bioanalysis, electrochemistry, mass spectrometry, microscale and nanoscale systems, environmental analysis, separations, spectroscopy, chemical reactions and selectivity, instrumentation, imaging, surface analysis, and data processing. Papers discussing known analytical methods should present a significant, original application of the method, a notable improvement, or results on an important analyte.