Department of Structure and Dynamics of Nucleic Acids

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.

Classical explicit solvent molecular dynamics (MD) simulations characterize structural dynamics of nucleic acids with size of up to 100 or more nucleotides. The currently available simulations can be extended to multiple microsecond time scale. With this technique, nucleic acids are modeled at the atomistic level of descriptions using classical potential functions known also as empirical force fields. Approximations inherent to the force fields represent the main limitation of this approach.

Ab initio quantum chemical (QM) technique is state of the art physical-chemistry methodology that provides accurate and physically complete description of small model systems. The technique reveals direct structure – energy relations that cannot be obtained by any other technique. Such calculations have indispensable role in reference evaluation of nature and magnitude of all kinds of molecular energy contributions that shape up nucleic acids, such as base stacking, base pairing, backbone conformational preferences, etc. QM calculations allow to study chemical reactions at a level of electronic structure changes.

Structural bioinformatics aims, among other things, to provide classification of molecular interactions in nucleic acids based on structural and sequence data. 

In summary: our scientific goal is understanding of the most basic principles of structural dynamics, function and evolution of DNA and RNA.

Our methods are:

Classical Molecular Dynamics (MD) simulations.
Quantum-chemical (QM) methods.
Hybrid quantum-classical (QM/MM) methods, quantum molecular dynamics
Structural bioinformatics

Modern computations are extensively combined with many experimental techniques (NMR, X-Ray, high-energy lasers, biochemical techniques) mostly via numerous collaborations.

We collaborate with ~30 foreign and Czech laboratories. We publish about 20 papers annually and belong to the most cited Czech research groups. See the full list of papers on this web page.

We have excellent in-house computer facilities, which are regularly upgraded.

We currently work in several mutually interrelated research areas

  1. RNA structural dynamics, folding and catalysis.
  2. Protein-RNA complexes.
  3. DNA, with focus on G-quadruplexes.
  4. Diverse types of quantum-chemical studies on nucleic acids systems.
  5. Origin of life (prebiotic chemistry), i.e., creation of the simplest chemical life on our planet (or anywhere else in the Universe), with a specific attention paid to the formamide pathway to template-free synthesis of the first RNA molecules. This specific project includes also in house experimental research.

Besides studies of specific systems, we are also involved extensively in method testing/development, mainly in the field of parametrization of molecular mechanical force fields for DNA and RNA.