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New simplified DNA model for advanced computational simulations




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  • IRB Barcelona researchers develop a computational model that allows rapid and precise simulations of chromatin and facilitates detailed observation of structural modifications of the genome.
  • The work has been published in the journal Nucleic Acids Research.

DNA holds all the genetic information necessary for the development and functioning of living organisms. This molecule is organised in a structure called chromatin, within the cell nucleus. Given that the shape adopted by chromatin directly affects gene activity, a detailed study of the DNA structure is crucial to facilitate the prediction of its variations.

Scientists led by Dr. Modesto Orozco at IRB Barcelona have developed a simplified model of DNA called CGeNArate that allows rapid and precise computational simulations. This model uses a coarse-graining approach that consists of simplifying a complex system by reducing the number of degrees of freedom, thus grouping atoms into larger units called "grains."

In addition, it employs machine learning algorithms to reconstruct the atomic resolution of the simulated trajectories. This allows the structure and behaviour of DNA to be studied without the need to use complex and slow models, thus facilitating faster and more accessible research.

“This new model can be very useful for projects that call for detailed and rapid study of the DNA structure. Although the model is already functional, we are working to improve it and apply it to other components of the cell nucleus, which could open up new opportunities in biomedical research,” explains Dr. Orozco, head of the Molecular Modelling and Bioinformatics laboratory at IRB Barcelona and professor at the University of Barcelona.

Detailed genomic information

The researchers put the new tool to the test, validating its potential to obtain high-speed chromatin simulations. “The model allowed observation of the behaviour of a specific section of DNA in a yeast gene, the modelling of the DNA structure in mitochondria, the reproduction of the flexibility of different DNA structures in various contexts, and also the simulation of the formation of small circular DNA structures known as "minicircles," says David Farré-Gil, first author of the study and doctoral student in the same laboratory. These results demonstrate the effectiveness of the model for studying DNA and chromatin in detail.

This project has been financed by the Ministry of Science, Innovation and Universities, AGAUR, the Government of Catalonia and the Research and Innovation Programme of the European Union. The work has been carried out in collaboration with the University of Nottingham, thereby strengthening ties between European research institutions.


Related article:
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes
David Farré-Gil, Juan Pablo Arcon, Charles A. Laughton and Modesto Orozco
Nucleic Acids Research (2024) DOI: 10.1093/nar/gkae444

About IRB Barcelona

The Institute for Research in Biomedicine (IRB Barcelona) pursues a society free of disease. To this end, it conducts multidisciplinary research of excellence to cure cancer and other diseases linked to ageing. It establishes technology transfer agreements with the pharmaceutical industry and major hospitals to bring research results closer to society, and organises a range of science outreach activities to engage the public in an open dialogue. IRB Barcelona is an international centre that hosts 400 researchers and more than 30 nationalities. Recognised as a Severo Ochoa Centre of Excellence since 2011, IRB Barcelona is a CERCA centre and member of the Barcelona Institute of Science and Technology (BIST).