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<p>We present a tour de force of atomistic molecular dynamics simulations involving the coordinated effort of 14 research groups of the Ascona B-DNA Consortium (ABC). This initiative provides a complete characterization of the 2080 DNA hexamers embedded in 190 carefully selected 20-mer duplexes, each simulated in replicate for at least 10 microseconds in explicit solvent. The consortium generates 0.25 petabytes of data, capturing millisecond-scale ensembles at the oligomer level and dynamics up to 10<sup>−1 </sup>seconds at the base-pair level. Analysis yields a comprehensive description of sequence-dependent DNA properties, including rare events such as backbone transitions, reversible base-pair changes, and partial unfolding. Processing these atomistic ensembles reveals a hidden physical code of DNA, helping explain rules of genome composition and evolution beyond coding regions. This community effort delivers unprecedented, validated FAIR data to support coarse-grained and AI models of DNA at cellular scale.</p>

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hexABC seeking the physical code of DNA

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年6月24日

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  • Federica Battistini,
  • Miłosz Wieczór,
  • Adam Hospital,
  • Marco Pasi,
  • Juan Pablo Arcón,
  • Israel Serrano-Chacón,
  • Alba Sala,
  • Subhamoy Deb,
  • Agustín García-Doñate,
  • Matthew Burman,
  • Elliot W. Chan,
  • Liwei Chang,
  • Gabriela da Rosa,
  • Jorge R. Espinosa,
  • Gia Linh Hoang,
  • Kazi A. Hossain,
  • Michał Jurkowski,
  • Romain Poupon,
  • Rahul Sharma,
  • Ran Sun,
  • Thomas C. Bishop,
  • Paolo Carloni,
  • Thomas E. Cheatham III,
  • Rosana Collepardo-Guevara,
  • Jacek Czub,
  • Pablo D. Dans,
  • Sarah A. Harris,
  • Charles Laughton,
  • Rodrigo Galindo-Murillo,
  • John H. Maddocks,
  • Agnes Noy,
  • Alberto Pérez,
  • Daiva Petkevičiūtė-Gerlach,
  • Modesto Orozco

摘要

We present a tour de force of atomistic molecular dynamics simulations involving the coordinated effort of 14 research groups of the Ascona B-DNA Consortium (ABC). This initiative provides a complete characterization of the 2080 DNA hexamers embedded in 190 carefully selected 20-mer duplexes, each simulated in replicate for at least 10 microseconds in explicit solvent. The consortium generates 0.25 petabytes of data, capturing millisecond-scale ensembles at the oligomer level and dynamics up to 10−1 seconds at the base-pair level. Analysis yields a comprehensive description of sequence-dependent DNA properties, including rare events such as backbone transitions, reversible base-pair changes, and partial unfolding. Processing these atomistic ensembles reveals a hidden physical code of DNA, helping explain rules of genome composition and evolution beyond coding regions. This community effort delivers unprecedented, validated FAIR data to support coarse-grained and AI models of DNA at cellular scale.