Department of Structure and Dynamics of Nucleic Acids (DSDNA)


Prof. RNDr. Ji poner, DrSc.


We use a wide spectrum of state-of-the-art computational techniques, including explicit solvent molecular dynamics simulations, advanced ab initio quantum-chemical calculations and modern bioinformatics.
The main research aim is to provide unique insights into the role of molecular interactions in structure, dynamics, function and evolution of nucleic acids. In that sense, advanced computations can substantially complement experimental techniques. Our research is highly interdisciplinary and we wish to bring modern physical-chemistry insights into structural and molecular biology, biochemistry and bioinformatics. Our research has impact also in some other areas of chemistry, such as physical, supramolecular and bioinorganic chemistry.

Laboratory web:

Research areas:

  • Studies of structure, dynamics and molecular interactions of nucleic acids and their complexes with proteins using explicit solvent molecular dynamics simulations; main attention is paid to functional RNAs, such as ribosomal RNAs and catalytic RNAs
  • Studies of canonical and noncanonical DNA molecules
  • Quantum chemical modelling of processes relevant to the prebiotic synthesis of nucleic acid components
  • Structural bioinformatics of RNA (classification of molecular interactions in nucleic acids based on structural and sequence data)
  • Testing and refinement of force fields for atomistic simulations of nucleic acids
  • Reference quantum-chemical calculations of molecular interactions and conformational substates in nucleic acids

Main Objectives:

  • Investigation of the role of RNA and DNA in development and human diseases
  • Development of new methodologies for investigating the structure, interactions, and dynamics of biomolecules

Members of the laboratory also participate in research group Structure and Dynamics of Nucleic Acids in CEITEC.


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