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 bioinformatical 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

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The Barcelona Institute of
Science and Technology
Ignite grant to M.V. Neguembor and P.D. Dans

From optical microscopy to near-atomic resolution of  Human genes and chromosomes

This joint IRB Barcelona - CRG - UdelaR - Institut Pasteur de Montevideo project aims to integrate high-resolution STORM microscopy, HiC and MNase-seq data to coarse-grained models of chromatin and chromosomes to reveal the organization of the 3D structure during reprogramming and differentiation of human cells.

GENSTORM team: Maria Victoria Neguembor [CRG], Diana Buitrago [IRB], Rafael Lema [IRB], Jürgen Walther [IRB], Juan Pablo Arcon [IRB], Ximena Garate [CRG], Laura Martin [CRG], Pablo Romero [IRB], Marta Gut [CNAG-CRG], Julie Blanc [CNAG-CRG], Jumana AlHaj Abed [HARVARD], Melike Lakadamyali [UPENN], Chao-ting Wu [HARVARD], Isabelle Brun Heath [IRB], Modesto Orozco [IRB],
Pablo D. Dans [
UDELAR-IPMONT-IRB], and Maria Pia Cosma [CRG].

Read the pre-print about the impact of methylation PDF

The impact of CpG methylation, UV radiation and oxidative stress on the 3D organization of Yeast nucleus

This joint IRB Barcelona - CNAG/CRG - UdelaR - Institut Pasteur de Montevideo project aims to integrate HiC data, MNase-seq data, and expression profiles to coarse-grained models of chromatin, chromosomes and whole haploid yeast nucleus.

Team: Diana Buitrago [IRB], Mireia Labrador [IRB], Juan Pablo Arcon [IRB], Rafael Lema [IRB] Oscar Flores [IRB] Anna Esteve-Codina [CNAG-CRG], Julie Blanc [CNAG-CRG], Nuria Villegas [IRB], David Bellido [UB], Marta Gut [CNAG-CRG], Pablo D. Dans [UDELAR-IPMONT-IRB], Simon C. Heath [CNAG-CRG], Ivo Gut [CNAG-CRG], Isabelle Brun Heath [IRB], and Modesto Orozco[IRB].

Read the 
pre-print  PDF

All-atom force field parameters for epigenetically modified nucleobases

This joint IRB Barcelona - CSIC Madrid - AstraZeneca - UdelaR - Institut Pasteur de Montevideo project aims to develop force field parameters for 5-hydroxymethyl-cytosine (5HC) and 6-methyl-adenine (6MA) in the context of DNA. QM calculations, MD simulations, NMR, DNA melting and nucleosome reconstitution experiments are integrated to produce high-quality and trustable parameters compatible with PARMBSC1.

TeamFederica Battistini [IRB], Pablo D. Dans [UDELAR-IPMONT-IRB], 

Montserrat Terrazas [IRB], Chiara L. Castellazzi [IRB], Guillem Portella [ASTRAZENECA], Mireia Labrador [IRB], Isabelle Brun-Heath [IRB], Irene Gómez-Pinto [CSIC], Carlos González [CSIC], and Modesto Orozco [IRB].

Development of a coarse-grained model of chromatin for Molecular Dynamics simulations

This UdelaR - Institut Pasteur de Montevideo - IRB project aims to develop a new coarse-grained model of DNA and chromatin. The model will include epigenetic modifications at the DNA and histone level, and the possibility to integrate micro-C data to run experimentally-biased molecular dynamics simulations. This research line is part of the PhD project of Gabriela da Rosa.

TeamGabriela da Rosa [UDELAR-IPMONT], Leandro Grille [UDELAR-PMONT], Rafael Lema [IRB], Isabelle Brun-Heath [IRB], Modesto Orozco [IRB], and Pablo D. Dans [UDELAR-IPMONT-IRB].

The conformational landscape of RNA molecules: From base pairing to tertiary motifs.

This UdelaR - Institut Pasteur de Montevideo - IRB project aims to develop tools and increase our knowledge on the conformational landscape of RNA molecules. In particular, we are using our R package (veriNa3D) to unravel the pseudo-torsional space of RNA by analyzing specialized databases containing non-redundant structural information. One of the final aims of this project is to develop a tool for the validation of RNA structures and provide a useful framework for the development of new coarse-grained models. This research line is part of the PhD project of Diego Gallego and the postdoc project of Leandro Grille.

TeamLeandro Grille [UDELAR-IPMONT], Diego Gallego [IRB], Eric Matamoros [IRB], Modesto Orozco [IRB], and Pablo D. Dans [UDELAR-IPMONT-IRB].

Structure, dynamics, and stability of tRNA-halves molecules

This UdelaR - Institut Pasteur de Montevideo project aims to analyze with the use of computational tools (all-atom and coarse-grained MD simulations) the stability and the possible formation of new tRNA-halves monomers, dimers and tetramers using all the available tRNA sequences found in the human genome. This project was written-by and granted (Fondo Clemente Estable - ANII) to Dr. Leonardo Darré, and then transferred to the Dans Lab. This research line is part of the postdoc project of Leandro Grille.

TeamLeandro Grille [UDELAR-IPMONT], Juan Pablo Tosar [UDELAR-IPMONT], Leonardo Darré [ex-IPMONT], Alfonso Cayota [UDELAR-IPMONT], Sergio Pantano [IPMONT], and Pablo D. Dans [UDELAR-IPMONT-IRB].

DNA-solvent interactions: cations, water, and small ligands

This UdelaR - Institut Pasteur de Montevideo - IRB - ABC project aims to study the interaction between DNA and the solvent atmosphere. In particular, we are working on DNA-cations, DNA hydration and the interaction of DNA with LYS/ARG residues by using atomistic all-atom simulations and validating our results through experiments. The hydration of all the possible tetranucleotides (136 unique combinations) is being analyzed in collaboration with the Ascona B-DNA Consortium (ABC).

Team: Federica Battistini [IRB], Benjamin Martin [UCSF], Milosz Wieczór [IRB], Nuria Villegas [IRB], Isabelle Brun-Heath [IRB], Montserrat Terrazas [IRB], Modesto Orozco [IRB], Pablo D. Dans [UDELAR-IPMONT-IRB], and the ABC members.

 

FUNDED RESEARCH COLLABORATIONS

A study on the genetics, the activity, and the structure of cannabinoid synthase from cannabis

FCE-ANII project granted to Prof. Astrid Agorio (IIBCE). Member of the research group.

In the framework of this project, Prof. Dans is co-directing with Prof. Agorio the Master degree in Biology of Lic. Leticia Chao (UdelaR, PEDECIBA Biología).

Determination, activity, and structure of antimicrobial peptides extracted from native plants

FCE-ANII project granted to Prof. Gianna Cecchetto (UdelaR) and Dr. Susana Rodriguez. Member of the research group. This is a long-term collaboration between the Dans Lab. and the Microbiology group of the Faculty of Chemistry (UdelaR). To date, two articles related to this research line were published in 2018 and 2019 (take a look to our publication list). Gabriela da Rosa is part of this joint project.
 

Interview in La Diaria (uruguayan newspaper) in July 2018 to Cecchetto and Rodriguez about our work. The interview was done by Leo Lagos (in spanish) PDF 

Elucidating the ligninolytic system: from transcriptome to enzymatic activity

CSIC I+D project granted to Prof. Gianna Cecchetto (UdelaR). Member of the research group.

This is a long-term collaboration between the Dans Lab. and the group of Prof. Cecchetto from the Faculty of Chemistry (UdelaR). Gabriela da Rosa is part of this joint project.

 
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