Research
Nucleic acids in their full dynamic context
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 Deep Learning approaches for 3D prediction and 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 up to chromosomes.
Bacterial genomics & antimicrobial resistance
A second main research line of DansLab tackles the genomics and molecular biology of antimicrobial resistance, with a particular focus on ESKAPE pathogens. We follow how clinical isolates evolve under last-resort antibiotics, characterising the genetic and metabolic determinants behind resistance, hetero-antagonism and the emergence of small-colony variants.
Combining whole-genome sequencing, comparative genomics, transcriptomics and structural modelling, we map the spread of carbapenemases (NDM, KPC, OXA-type) across hospital outbreaks in Latin America, dissect mechanisms of spontaneous resistance in vitro, and probe non-canonical drivers. The goal is to translate that mechanistic insight into actionable knowledge for clinical surveillance and into the design of next-generation therapies built on ASOs, siRNAs, aptamers and oligotherapeutics in general.
Current research lines & projects
16 ongoing or recently active projects, spanning consortia, PhD/MSc co-directions, and outreach.
CEIBOS — Centro de Estudios Interdisciplinarios de Biodiversidad Orientado a aplicaciones en Salud
2021–2025Interdisciplinary Center (EI)·Co-coordinator·Uruguay5-year UdelaR interdisciplinary center. Lead: Dr Sonia Rodríguez Giordano (DEPBIO, Facultad de Química, UdelaR, Coordinator). Co-coordinators: Dr Pablo Dans (CENUR Litoral Norte, Salto, UdelaR) and Dr Carlos Testuri (INCO, Facultad de Ingeniería, UdelaR).
ceibos.ei.udelar.edu.uy/ →HexABC — Ascona B-DNA Consortium
2021–2026International consortium·Member of the consortium·Switzerland · Lithuania · Poland · Spain · Germany · USA · UK · Uruguay · FranceLatest ABC effort: systematic characterization of the physical properties of all 2080 unique hexanucleotides from a collection of 950 10 μs all-atom MD simulations.
mmb.irbbarcelona.org/webdev/slim/ABC/public/ →ABSarbo — Aptamer-based strategies against arboviruses
2023–2025EULAC-ANII project·Co-coordinator·Uruguay (HQ) · Peru · Mexico · Spain · Austria · GermanyAptamer-based biotechnological tools against arboviruses. Lead: Dr Calzada (Facultad de Ciencias, UdelaR). 6-country consortium.
www.rediba.org/about-4 →Conformational space of DNA aptamers
2023–2025CSIC I+D project·Main responsible·Uruguay · USAStructural and dynamic prediction of unusual DNA motifs — conformational space of aptamers. Partners: CENUR Litoral Norte (Salto), Facultad de Ciencias, Institut Pasteur de Montevideo, Facultad de Medicina, University of Florida.
ProAgricultura — Proline accumulation in plants
2022–2024CSIC I+D project·Member of the research team·UruguayMultidisciplinary study of the benefits of proline accumulation in plants. Lead: Dr Santiago Signorelli, Facultad de Agronomía, UdelaR.
Do AI dream of fluorinases? — AI-designed enzymes
2024–2026FCE project·Member of the research group·UruguayArtificial intelligence as a source of new enzymes for the biocatalytic synthesis of fluorinated compounds. Lead: Dr Paola Panizza, Facultad de Química, UdelaR.
Coarse-grained DNA model for chromatin MD
ongoingPhD project (PEDECIBA Química / UdelaR)·Co-director·UruguayPhD project of MSc Gabriela da Rosa: A new coarse-grained model of DNA for molecular dynamics simulations of chromatin. Co-director: Dr Gianna Cecchetto (Facultad de Química). CAP fellowship.
In silico engineering of reductive aminases
2020–2023MSc project (UdelaR / ANII)·Co-director·UruguayMSc in Biotechnology project of Lic. Gonzalo Lopez. In silico and experimental engineering of reductive aminases applied to obtaining radiotracers for PET diagnostics of neurodegenerative diseases. Co-directors: Dr Paola Panizza, Dr Sonia Rodriguez (Facultad de Química).
ATPase × peroxynitrite
2023–2024CENUR–UBA project·Member of the research group·Argentina · UruguayEffect of peroxynitrite on ATPase activity and structure. Coordinator: Prof. Daniel Peluffo (UBA / CENUR Litoral Norte).
3D organization and dynamics of the Trypanosoma cruzi genome
2023–2024FCE project·Member of the research group·UruguayLead: Dr Florencia Viraqué (Institut Pasteur de Montevideo) with CENUR Litoral Norte.
T-cell receptors and tissue homing
2023–2025Crick Institute project·Member of the research group·United Kingdom · UruguayRole of T cell receptors (TCR) in driving cells into association with their target tissues. Lead: Dr Leticia Monin (Crick Institute) with CENUR Litoral Norte.
MODxNA — modified nucleic acid parameters for AMBER
2023–2024International collaboration·Member of the research group·USA · UruguayDatabase of thousands of DNA/RNA modified-base parameters for the AMBER force field. Partners: University of Utah, University of Maryland, IONIS Pharmaceuticals, CENUR Litoral Norte.
Aptamers against Trypanosoma cruzi
2023–2024REDIBA collaboration·Member of the research group·Peru · UruguayDevelopment of aptamers against T. cruzi. Lead: Dr Pohl Milón (Universidad Peruana de Ciencias Aplicadas) with CENUR Litoral Norte. Member of REDIBA.
www.rediba.org →Aptamers against Her2 (breast cancer)
2022–2024REDIBA / l'Oréal Uruguay·Member of the research group·UruguayDevelopment of aptamers against the Her2 receptor in breast cancer. Co-funded by l'Oréal Uruguay. Lead: Dr Calzada (Facultad de Ciencias, UdelaR) with CENUR Litoral Norte. Member of REDIBA.
www.rediba.org →Music from the molecule of life
2022–2026Outreach project·Coordinator·Uruguay5-year project on music from MD simulations of DNA duplexes, in collaboration with Nicolás Molla (music producer and composer) and CENUR Litoral Norte.
tRNA and plastic art (ARN for Export)
2022–2024Outreach project·Coordinator·UruguayTravelling plastic-art exhibition on the structure of transfer RNA molecules (tRNAs) released into the inter-cellular space. Collaboration with Mariana Barraco (painter, art teacher and creator) and CENUR Litoral Norte.