RESEARCH
The Dans Lab is mainly focused on the study of the structure and dynamics of Nucleic Acids and their interactions with proteins, small ligands and the solvent atmosphere, from a molecular point of view. We use and develop all-atom force fields, and coarse-grained models for atomistic, nanoscopic and mesoscopic simulations. We also use and develop bioinformatic tools for the data mining of specialized databases containing structural information. All our projects are tackled from a multiscale perspective trying to connect the quantum world with the macroscopic level, from electrons and up to chromosomes.
CURRENT RESEARCH LINES
Interdisciplinary center (EI). 5-year project. Co-coordinator. Uruguay.
Centros Interdisciplinario (UdelaR): Centro de Estudios Interdisciplinarios de Biodiversidad Orientado a aplicaciones en Salud (CEIBOS). 2021-2025. Responsables: Dr Sonia Rodríguez Giordano, DEPBIO, Facultad de Química, UdelaR (Coordinator), Dr Pablo Dans, CENUR Litoral Norte (Salto), UdelaR, Dr. Carlos Testuri, INCO, Facultad de Ingeniería, UdelaR.
https://ceibos.ei.udelar.edu.uy/CSIC I+D project. 3 years. Member of the research team. Uruguay.
ProAgricultura: estudio de los beneficios de la acumulación de prolina en plantas mediante una aproximación multidiciplinaria. 2022-2024. Responsable Dr Santiago Signorelli, Facultad de Agronomía, UdelaR.EULAC-ANII project. 3-year project. Co-coordinator. Uruguay & Europeen Union.
ABSarbo. Aptamer-based strategies to create novel biotechnological tools against Arboviruses. Responsable Dr Calzada, Facultad de Ciencias. 2023-2025. The project involves 6 countries: Uruguay (headquarters), Peru, Mexico, Spain, Austria and Germany.
https://www.rediba.org/about-4CSIC I+D project. 2 years. Main responsable. Uruguay & EEUU.
Método de predicción estructural y dinámica de motivos inusuales de ADN: Estudio del espacio conformacional de aptámeros”, 2023-2025. CENUR Litoral Norte (Salto), Facultad de Ciencias, Institut Pasteur de Montevideo, Facultad de Medicina, U of Florida.Ascona B-DNA Consortium. Member of the consortium. Switzerland, Lithuania, Poland, Spain, Germany, EEUU, UK, Uruguay & France.
HexABC. The latest effort, 2021-2026, of the Ascona B-DNA (ABC) consortium. The study is focused on the systematic characterization of the physical properties of all 2080 unique hexanucleotides, from a collection of 950, 10μs-long MD simulations.
https://mmb.irbbarcelona.org/webdev/slim/ABC/public/FCE project. 2 years. Member of the research group. Uruguay.
Do AI dream of fluorinases? Artificial intelligence as a source of new enzymes for the biocatalytic synthesis of fluorinated compounds. 2024-2026. Responsible: Dr Paola Panizza, Facultad de Química, UdelaR.PhD project of MSc Gabriela da Rosa. Faculty of Chemistry. Co-director. Uruguay.
A new coarse-grained model of DNA for molecular dynamics simulations of chromatin. Facultad de Química (Dr Gianna Cecchetto, co-director), CENUR Litoral Norte, Comisión Académica de Posgrados (UdelaR).Master in Biotechnology project of Lic Gonzalo Lopez. Faculty of Science. Co-director. Uruguay.
Ingeniería in silico y experimental de aminasas reductivas: aplicación a la obtención de radiotrazadores para el diagnóstico PET de enfermedades neurodegenerativas. 2020-2023. Facultad de Química (Dr Paola Panizza and Dr Sonia Rodriguez, co-directors), CENUR Litoral Norte. Agencia Nacional de Investigación e Innovación.CENUR-UBA ATPase project. 1 year. Member of the research group. Argentina and Uruguay.
Unravelling the effect of Peroxynitrite on ATPase activity and structure. 2023-2024. University of Buenos Aires (UBA) and CENUR Litoral Norte (Prof Daniel Peluffo coordinator).FCE project. 2 years. Member of the research group. Uruguay.
Organización tridimensional y dinámica del genoma de Trypanosoma cruzi. 2023-2024. Institut Pasteur de Montevideo (Dr Florencia Viraqué main responsable), CENUR Litoral Norte.Crick Institute project. 2 years. Member of the research group. UK and Uruguay.
The role of T cell receptors (TCR) in driving cells into association with their target tissues. 2023-2025. Crick Institute (Dr Leticia Monin main responsable), CENUR Litoral Norte.MODxNA project. 2 years. Member of the research group. EEUU and Uruguay.
MODxNA database of thousands of DNA/RNA modified bases parameters for AMBER force field. 2023-2024. University of Utah, University of Maryland, IONIS Pharmaceuticals and CENUR Litoral Norte.Aptamers against T cruzi. 1 year. Member of the research group. Peru and Uruguay.
Development of aptamers against T cruzi. 2023-2024. Collaboration with the Centro de Investigación en Ciencias de la Salud, Facultad de Ciencias de la Salud, Universidad Peruana de Ciencias Aplicadas (Dr Polh Milón main responsable) and CENUR Litoral Norte. Member of REDIBA (https://www.rediba.org).Aptamers against Her2. 3-year project. Member of the research group. Uruguay.
Development of aptamers against Her2 receptor in breast cancer. 2022-2024. Collaboration with the group of Dr Calzada (head, co-funded by l'Oreal Uruguay) from Facultad de Ciencias, Universidad de la República and CENUR Litoral Norte. Member of REDIBA (https://www.rediba.org).Music from MD simulations of DNA duplexes. 5-year project. Coordinator. Uruguay.
Music from the molecule of life. 2022-2026. Collaboration with Nicolás Molla (music producer and composer) and CENUR Litoral Norte.tRNA and plastic art. 3-year project. Coordinator. Uruguay.
Creation of a travelling plastic-art-exhibition on the structure of transfer RNA molecules (tRNAs) released into the inter-cellular space. 2022-2024. Collaboration with Mariana Barraco (painter, art teacher and creator) and CENUR Litoral Norte.
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