Structure and Dynamics of Nucleic Acids - Jiří Šponer
Structure and Dynamics of Nucleic Acids - Jiří Šponer


Judit Šponerová Judit Šponerová
Senior Researcher

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.

Content of research

  • Computational studies, combining a full range of leading computational methods (explicit solvent molecular dynamics simulations, quantum-chemical calculations, hybrid quantum-classical calculations and bioinformatics), will be used to unravel the key features of the RNA structure and the role of RNA in protein biosynthesis. The work will be initially devoted to ribosome and ribozymes where atomic resolution information is available. The research will be gradually extended to other RNA systems where enough experimental structural data is available.
  • Modern computational techniques can fill several major gaps in the present knowledge of the RNA function. We will classify RNA building blocks and their molecular interactions, to unravel the link between their physical-chemical properties and evolutionary patterns. We will analyse chemical reactions at the atomistic level of electronic structure description to capture catalytic strategies of ribozymes and to model prebiotic chemical reactions.
  • Extended studies will be carried out on selected DNA systems, mainly to understand the role of sequence-dependency of B-DNA structure and the principles of folding of quadruplex DNA.
  • Prebiotic chemical reactions will be studied using advanced electronic structure computations.
  • Free energy calculations, or molecular dynamics simulations, often critically depend on the adequacy of the molecular mechanical force fields and other methods describing the relationships between molecular structures and energies. Therefore, much effort will be devoted to the development and verification of these methods. This will mainly be done in the field of nucleic acids, where the main focus will be put on noncanonical architectures such as hairpin loops, which are notoriously difficult to describe by the force fields.