Scholarlink

<p>DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Microscopy (AFM) with a new high-throughput automated pipeline, we can quantify the length, conformation, and topology of individual complex DNA molecules with sub-molecular resolution. Our pipeline uses deep-learning methods to trace the backbone of individual DNA molecules and identify crossing points, efficiently determining which segment passes over which. We use this pipeline to determine the structure of stalled replication intermediates from <i>Xenopus</i> egg extracts, including theta structures and late replication products, and the topology of plasmids, knots and catenanes from the <i>E. coli</i> Xer recombination system. We use coarse-grained simulations to quantify the effect of surface immobilisation on twist-writhe partitioning. Our pipeline opens avenues for understanding how fundamental biological processes are regulated by DNA topology.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年7月1日

查看全文
  • Elizabeth P. Holmes,
  • Max C. Gamill,
  • James I. Provan,
  • Laura Wiggins,
  • Renáta Rusková,
  • Sylvia Whittle,
  • Thomas E. Catley,
  • Kavit H. S. Main,
  • Neil Shephard,
  • Helen. E. Bryant,
  • Neville S. Gilhooly,
  • Agnieszka Gambus,
  • Dušan Račko,
  • Sean D. Colloms,
  • Alice L. B. Pyne

摘要

DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Microscopy (AFM) with a new high-throughput automated pipeline, we can quantify the length, conformation, and topology of individual complex DNA molecules with sub-molecular resolution. Our pipeline uses deep-learning methods to trace the backbone of individual DNA molecules and identify crossing points, efficiently determining which segment passes over which. We use this pipeline to determine the structure of stalled replication intermediates from Xenopus egg extracts, including theta structures and late replication products, and the topology of plasmids, knots and catenanes from the E. coli Xer recombination system. We use coarse-grained simulations to quantify the effect of surface immobilisation on twist-writhe partitioning. Our pipeline opens avenues for understanding how fundamental biological processes are regulated by DNA topology.