Article ; Online: In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq).
2024 Volume 695, Page(s) 159–191
Abstract: DNA secondary structures are essential elements of the genomic landscape, playing a critical role in regulating various cellular processes. These structures refer to G-quadruplexes, cruciforms, Z-DNA or H-DNA structures, amongst others (collectively ... ...
| Abstract | DNA secondary structures are essential elements of the genomic landscape, playing a critical role in regulating various cellular processes. These structures refer to G-quadruplexes, cruciforms, Z-DNA or H-DNA structures, amongst others (collectively called 'non-B DNA'), which DNA molecules can adopt beyond the B conformation. DNA secondary structures have significant biological roles, and their landscape is dynamic and can rearrange due to various factors, including changes in cellular conditions, temperature, and DNA-binding proteins. Understanding this dynamic nature is crucial for unraveling their functions in cellular processes. Detecting DNA secondary structures remains a challenge. Conventional methods, such as gel electrophoresis and chemical probing, have limitations in terms of sensitivity and specificity. Emerging techniques, including next-generation sequencing and single-molecule approaches, offer promise but face challenges since these techniques are mostly limited to only one type of secondary structure. Here we describe an updated version of a technique permanganate/S1 nuclease footprinting, which uses potassium permanganate to trap single-stranded DNA regions as found in many non-B structures, in combination with S1 nuclease digest and adapter ligation to detect genome-wide non-B formation. To overcome technical hurdles, we combined this method with direct adapter ligation and sequencing (PDAL-Seq). Furthermore, we established a user-friendly pipeline available on Galaxy to standardize PDAL-Seq data analysis. This optimized method allows the analysis of many types of DNA secondary structures that form in a living cell and will advance our knowledge of their roles in health and disease. |
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| MeSH term(s) | DNA/chemistry ; G-Quadruplexes ; Oxides ; Manganese Compounds ; Oligonucleotides |
| Chemical Substances | permanganic acid (14333-13-2) ; DNA (9007-49-2) ; Oxides ; Manganese Compounds ; Oligonucleotides |
| Language | English |
| Publishing date | 2024-01-23 |
| Publishing country | United States |
| Document type | Journal Article |
| ISSN | 1557-7988 |
| ISSN (online) | 1557-7988 |
| DOI | 10.1016/bs.mie.2023.12.003 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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