Alan M Szalai, Giovanni Ferrari, Lars Richter, Jakob Hartmann, Merve-Zeynep Kesici, Bosong Ji, Kush Coshic, Martin R J Dagleish, Annika Jaeger, Aleksei Aksimentiev, Ingrid Tessmer, Izabela Kamińska, Andrés M Vera, Philip Tinnefeld
{"title":"Single-molecule dynamic structural biology with vertically arranged DNA on a fluorescence microscope.","authors":"Alan M Szalai, Giovanni Ferrari, Lars Richter, Jakob Hartmann, Merve-Zeynep Kesici, Bosong Ji, Kush Coshic, Martin R J Dagleish, Annika Jaeger, Aleksei Aksimentiev, Ingrid Tessmer, Izabela Kamińska, Andrés M Vera, Philip Tinnefeld","doi":"10.1038/s41592-024-02498-x","DOIUrl":null,"url":null,"abstract":"<p><p>The intricate interplay between DNA and proteins is key for biological functions such as DNA replication, transcription and repair. Dynamic nanoscale observations of DNA structural features are necessary for understanding these interactions. Here we introduce graphene energy transfer with vertical nucleic acids (GETvNA), a method to investigate DNA-protein interactions that exploits the vertical orientation adopted by double-stranded DNA on graphene. This approach enables the dynamic study of DNA conformational changes via energy transfer from a probe dye to graphene, achieving spatial resolution down to the Ångström scale at subsecond temporal resolution. We measured DNA bending induced by adenine tracts, bulges, abasic sites and the binding of endonuclease IV. In addition, we observed the translocation of the O<sup>6</sup>-alkylguanine DNA alkyltransferase on DNA, reaching single base-pair resolution and detecting preferential binding to adenine tracts. This method promises widespread use for dynamical studies of nucleic acids and nucleic acid-protein interactions with resolution so far reserved for traditional structural biology techniques.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1000,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nature Methods","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1038/s41592-024-02498-x","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
The intricate interplay between DNA and proteins is key for biological functions such as DNA replication, transcription and repair. Dynamic nanoscale observations of DNA structural features are necessary for understanding these interactions. Here we introduce graphene energy transfer with vertical nucleic acids (GETvNA), a method to investigate DNA-protein interactions that exploits the vertical orientation adopted by double-stranded DNA on graphene. This approach enables the dynamic study of DNA conformational changes via energy transfer from a probe dye to graphene, achieving spatial resolution down to the Ångström scale at subsecond temporal resolution. We measured DNA bending induced by adenine tracts, bulges, abasic sites and the binding of endonuclease IV. In addition, we observed the translocation of the O6-alkylguanine DNA alkyltransferase on DNA, reaching single base-pair resolution and detecting preferential binding to adenine tracts. This method promises widespread use for dynamical studies of nucleic acids and nucleic acid-protein interactions with resolution so far reserved for traditional structural biology techniques.
DNA 与蛋白质之间错综复杂的相互作用是 DNA 复制、转录和修复等生物功能的关键。要了解这些相互作用,就必须对 DNA 结构特征进行纳米级动态观测。在这里,我们介绍了垂直核酸的石墨烯能量转移(GETvNA),这是一种研究 DNA 蛋白相互作用的方法,它利用了双链 DNA 在石墨烯上的垂直取向。这种方法能够通过探针染料到石墨烯的能量转移动态研究 DNA 的构象变化,在亚秒级的时间分辨率下实现低至 Ångström 级的空间分辨率。我们测量了腺嘌呤束、隆起、消旋位点和内切酶 IV 结合引起的 DNA 弯曲。此外,我们还观察了 DNA 上 O6-烷基鸟嘌呤 DNA 烷基转移酶的转移,达到了单碱基对分辨率,并检测到了与腺嘌呤束的优先结合。这种方法有望广泛应用于核酸动态研究和核酸与蛋白质相互作用的研究,其分辨率迄今为止只能用于传统的结构生物学技术。
期刊介绍:
Nature Methods is a monthly journal that focuses on publishing innovative methods and substantial enhancements to fundamental life sciences research techniques. Geared towards a diverse, interdisciplinary readership of researchers in academia and industry engaged in laboratory work, the journal offers new tools for research and emphasizes the immediate practical significance of the featured work. It publishes primary research papers and reviews recent technical and methodological advancements, with a particular interest in primary methods papers relevant to the biological and biomedical sciences. This includes methods rooted in chemistry with practical applications for studying biological problems.