hexABC seeking the physical code of DNA
Year: 2026
Type: article
Abstract: 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.
Source: Nature Communications
Authors: Federica Battistini, Miłosz Wieczór, 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, 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
Institutions: Institute for Research in Biomedicine, Universitat de Barcelona, Centre National de la Recherche Scientifique, Université Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, University of York, University of Florida, Universidad de la República de Uruguay, University of Cambridge, Forschungszentrum Jülich, Gdańsk University of Technology, École Polytechnique Fédérale de Lausanne, Louisiana Tech University, University of Utah, Institut Pasteur de Montevideo, University of Leeds, University of Sheffield, University of Nottingham, Ionis Pharmaceuticals (United States), Kaunas University of Technology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Funders: Institute for Research in Biomedicine, European Commission, Institució Catalana de Recerca i Estudis Avançats, Ministerio de Ciencia e Innovación, Infrastruktura PL-Grid, Horizon 2020 Framework Programme, Agència de Gestió d'Ajuts Universitaris i de Recerca, Instituto de Salud Carlos III, European Regional Development Fund, Academic Computer Centre Cyfronet, AGH University of Science and Technology
OpenAlex ID: W7165778597