Electrochemistry and structure of nucleic acids

(Miroslav Fojta)

We investigate the relationships between primary (sequence), secondary (global and local conformation), and tertiary (superhelicity and topology) DNA structure and its interactions with charged electrode surfaces. These interactions are manifested in the electrochemical (oxidation and reduction) and surface (adsorption and two-dimensional condensation) behavior of DNA and its components. Special attention is devoted to mechanism of reduction of guanine residues and roles of other components in this process.

Until recently, electrochemical reduction of nucleic acids was feasible primarily at mercury-based electrodes, whereas their oxidation was largely limited to carbon electrodes. Our recent findings have demonstrated that nucleic acid reduction can also be studied at pyrolytic graphite electrodes, enabling both reduction and oxidation measurements to be performed on the same electrode surface. In parallel, the availability of two distinct electrode materials for cathodic measurements—where DNA structural effects on electrochemical signals are particularly pronounced—broadens the range of experimental variables available for optimizing structure-sensitive DNA analyses.

As part of our research into the relationship between the structure and electrochemical properties of DNA, we focus extensively on the behavior of G-quadruplexes (G4) and sequences capable of forming these structures, as well as on the interactions between G4s and specific ligands—potential drugs designed to target G4 structures.

We also conduct detailed investigations into how the micro- and nanostructure, as well as the surface chemistry, of carbon electrodes influence the electrochemical responses of polymeric nucleic acids, their monomeric components, and related classes of compounds.

Electrochemistry of modified nucleic acids

(Luděk Havran)

The group focuses on the application of chemically labeled DNA molecules in the development of electrochemical biosensors. Labeled DNA is prepared either through the incorporation of chemically modified nucleobases by DNA polymerases or by direct chemical modification of synthetic oligonucleotides. The incorporated nucleobase analogues carry electrochemically active substituents or functional groups that enable subsequent modification reactions. In addition to conventional electroactive labels based on a variety of redox-active moieties, boron cluster compounds are also employed as unique electrochemical tags.

Our research further includes systematic studies of the effects of chemical modifications on DNA structure and on its electrochemical behavior at different types of working electrodes. The development of these approaches is aimed primarily at biochemical biosensors for monitoring a wide range of DNA-related processes and interactions, including DNA hybridization, DNA damage, and DNA–protein interactions.

Another type of modified DNA consists of molecules containing unnatural (synthetic) bases, which are introduced to expand the genetic alphabet in the field of synthetic biology. These often possess specific electrochemical properties that differ from those of natural nucleic acid components, enabling their electrochemical incorporation into "semisynthetic" organisms.

Biomolecules at charged surfaces

(Veronika Ostatná)

The Biomolecules on Charged Surfaces research group focuses on the study of biomolecules at electrically charged interfaces and the development of sensitive electrochemical methods for their analysis.

The group investigates how surface charge and interfacial properties influence the behavior of proteins, nucleic acids, glycans, and their complexes. A major part of the research is dedicated to the preparation and characterization of micro- and nanostructured surfaces, including metallic and carbon-based materials, designed for biomolecule detection.

For many years, the group has specialized in protein analysis using constant-current chronopotentiometry, a label-free technique capable of monitoring subtle structural changes and molecular interactions. This approach is applied to the study of protein denaturation, aggregation, oligomerization, and specific interactions with DNA, ligands, and other proteins.

Another important research direction is the electrochemical analysis of glycans, oligosaccharides, polysaccharides, and glycoproteins, including the differentiation of structures associated with tumor biomarkers. The group also develops strategies based on chemical labeling, such as the use of osmium complexes, to enhance the sensitivity and selectivity of carbohydrate structure detection.

Through these activities, the group aims to advance the understanding of processes occurring at biomolecule–surface and complex–surface interfaces, thereby contributing to the development of new biomedical and analytical applications.