hexABC seeking the physical code of DNA
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. DNA’s physical properties are key to gene regulation and protein binding. Here, authors use massive simulations to map all 2,080 unique DNA hexamers, revealing a “physical code” that explains how sequence mechanics shape genome evolution.
Authors
- Thomas Connor Bishop (ORCID: https://orcid.org/0000-0003-4264-4261)
- Modesto Orozco (ORCID: https://orcid.org/0000-0002-8608-3278)
- Alba Sala (ORCID: https://orcid.org/0000-0003-1046-7432)
- Daiva Petkevičiūtė-Gerlach (ORCID: https://orcid.org/0000-0002-7646-2442)
- Agnes Noy (ORCID: https://orcid.org/0000-0003-0673-8949)
- Israel Serrano‐Chacón (ORCID: https://orcid.org/0000-0002-4303-9349)
- Juan Pablo Arcon (ORCID: https://orcid.org/0000-0003-3350-1576)
- Jorge R. Espinosa (ORCID: https://orcid.org/0000-0001-9530-2658)
- Paolo Carloni (ORCID: https://orcid.org/0000-0002-9010-0149)
- Rodrigo Galindo‐Murillo (ORCID: https://orcid.org/0000-0001-5847-4143)
- Marco Pasi (ORCID: https://orcid.org/0000-0001-9804-7322)
- Jacek Czub (ORCID: https://orcid.org/0000-0003-3639-6935)
- Pablo D. Dans (ORCID: https://orcid.org/0000-0002-5927-372X)
- Sarah Anne Harris (ORCID: https://orcid.org/0000-0002-2812-1651)
- Alberto Pérez (ORCID: https://orcid.org/0000-0002-5054-5338)
- Charles A. Laughton (ORCID: https://orcid.org/0000-0003-4090-3960)
- John H. Maddocks (ORCID: https://orcid.org/0000-0003-1127-8481)
- Liwei Chang (ORCID: https://orcid.org/0000-0001-5847-0820)
- Matthew Burman
- Rosana Collepardo‐Guevara (ORCID: https://orcid.org/0000-0003-1781-7351)
- Kazi Amirul Hossain (ORCID: https://orcid.org/0000-0002-1149-964X)
- Miłosz Wieczór (ORCID: https://orcid.org/0000-0003-4990-8629)
- Federica Battistini (ORCID: https://orcid.org/0000-0002-7544-0938)
- Gia Linh Hoang (ORCID: https://orcid.org/0000-0001-5922-2685)
- Michał Jurkowski
- Romain Poupon
- Agustín García-Doñate (ORCID: https://orcid.org/0009-0002-2159-965X)
- Rahul Sharma
- Subhamoy Deb
- Elliot W. Chan
- Gabriela da Rosa
- Ran Sun
- Thomas E. Cheatham
Institutions
- Centre National de la Recherche Scientifique (FR)
- University of Leeds (GB)
- University of Nottingham (GB)
- Gdańsk University of Technology (PL)
- Forschungszentrum Jülich (DE)
- Kaunas University of Technology (LT)
- Universidad de la República de Uruguay (UY)
- University of Utah (US)
- University of Cambridge (GB)
- Université Paris-Saclay (FR)
- Ionis Pharmaceuticals (United States) (US)
- University of Florida (US)
- Institute for Research in Biomedicine (ES)
- Sunny BioDiscovery (United States) (US)
- Institut Pasteur de Montevideo (UY)
- École Polytechnique Fédérale de Lausanne (CH)
- University of York (GB)
- Universitat de Barcelona (ES)
- University of Sheffield (GB)
- Louisiana Tech University (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-06-24
- DOI
- https://doi.org/10.1038/s41467-026-74390-5
- Primary Topic
- DNA and Nucleic Acid Chemistry
- Type
- article
- Field-Weighted Citation Impact
- 0.00