Structure and Dynamics of Nucleic Acids
Head: prof. RNDr. Jiří Šponer, DrSc.
About Us
Our main scientific goal is the basic understanding of the structural dynamics, function and evolution of nucleic acids. To achieve this goal, we use a portfolio of modern computational methods applied to a wide range of nucleic acids and protein systems. Our research is currently focused on explicit solvent atomistic molecular dynamics simulations, including state-of-the-art enhanced sampling methods.
The DSDNA research group is physically located at the Institute of Biophysics of the Czech Academy of Sciences (Královopolská 135, Brno).
Research Topics
The recently studied systems and scientific problems include ground-breaking simulations of the full binding processes of protein-RNA complexes (HuR RRM3 and SRSF1 RRM2), studies of folding pathways of DNA guanine quadruplexes, studies of DNA Holliday junction, folding simulations of small RNA motifs, and structural dynamics of recurrent RNA motifs (e.g. duplexes, kink-turns, U-turns, tetraloops, base pair mismatches). Besides applying computational methods to diverse biomolecular systems, we also significantly contribute to method development, mainly toward the improvement of nucleic acids simulation force fields.
Our research group has a set of powerful in-house computer clusters for state-of-the-art theoretical research and we have a wide range of established collaborations with foreign experimental laboratories in many of our research topics. For the topic of origin of life, where we try to understand the creation of the first RNA molecules on the early Earth, we also have an in-house experimental laboratory.
Main Objectives
- Studies of diverse RNA and protein-RNA systems
- Development of improved force fields for simulations of nucleic acids
- Template-free synthesis of first RNA molecules from monomers on early Earth
- Studies of basic principles of folding of guanine quadruplexes
- Studies of non-canonical DNA motifs (Holliday junction)
We carry out experimental studies of possible synthesis of first RNA molecules under prebiotically relevant conditions.
Our research into protein-RNA complexes recently led to the first visualisation of a complete binding process of HuR RRM3 complex. Sometimes assumed to be a simple on-off process, our study demonstrated the immense structural complexity involved in protein-RNA association.
Method development and improvement of the nucleic acid force fields remains our top priority. We recently identified and corrected a serious issue associated with the 0BPh interaction which is commonly found in A-RNA duplexes.
Team Members
- Sub-group leaders: RNDr. Miroslav Krepl, PhD; Vojtěch Mlýnský, PhD; Petr Stadlbauer, PhD; Judit E. Šponer, PhD
- PhD Students: Remi Coulon, Zhengyue Zhang, Toon Lemmens
- Bc/MSc Students: Barbora Knappeová
