A5107092937- Origins and Evolution of Life
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Astro and Planetary Science
- Photoreceptor and optogenetics research
- Advanced Chemical Physics Studies
- RNA modifications and cancer
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- Metal complexes synthesis and properties
- Bacterial Genetics and Biotechnology
- Crystallography and molecular interactions
- Photosynthetic Processes and Mechanisms
- Astrophysics and Star Formation Studies
- Mass Spectrometry Techniques and Applications
- Molecular Spectroscopy and Structure
- Spectroscopy and Quantum Chemical Studies
- Chemical Reaction Mechanisms
- Advanced biosensing and bioanalysis techniques
- Isotope Analysis in Ecology
- Chemical Analysis and Environmental Impact
- Organometallic Complex Synthesis and Catalysis
- Astronomy and Astrophysical Research
Czech Academy of Sciences, Institute of Biophysics
2015-2024
Institut für Urheber- und Medienrecht
2024
University College London
2024
Palacký University Olomouc
2009-2023
Regional Centre of Advanced Technologies and Materials
2018-2023
Charles University
2022
Czech Academy of Sciences
2009-2019
Central European Institute of Technology
2011-2019
Central European Institute of Technology – Masaryk University
2011-2019
Sapienza University of Rome
2015
Significance This paper addresses one of the central problems origin life research, i.e., scenario suggesting extraterrestrial impact as source biogenic molecules. Likewise, results might be relevant in search molecules universe. The work is therefore highly actual and interdisciplinary. It could interesting for a very broad readership, from physical organic chemists to synthetic biologists specialists astrobiology.
Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of bases in structured Protein Data Bank (PDB) hydrogen-bond with phosphates other nucleotides. By extracting superimposing base-phosphate (BPh) from a reduced-redundancy subset structures PDB, we identified recurrent phosphate-binding sites on bases. Quantum chemical calculations were carried out model systems...
Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base has been extensively studied by experimental theoretical methods. Advanced quantum-chemical calculations clarified that common interaction, which in first approximation can be described as combination of three most basic contributions to molecular interactions, namely, electrostatic London dispersion attraction short-range repulsion. There not any specific π-π energy term associated...
The formation of nucleobases from formamide during a high-energy density event, i.e., the impact an extraterrestrial body into planetary atmosphere, was studied by irradiation ice and liquid samples with high-power laser in presence potential catalysts. FTIR spectroscopy, time-resolved emission GC-MS were subsequently used to monitor dissociation this molecule stable molecular fragments (HCN, H2O, HNCO, H2, CO, NH3) unstable species (HNC, •CN, •NH). kinetic thermodynamic models event...
Abstract For the emergence of life, abiotic synthesis RNA from its monomers is a central step. We found that in alkaline, drying conditions bulk and at heated air‐water interfaces, 2′,3′‐cyclic nucleotides oligomerised without additional catalyst, forming up to 10‐mers within day. The oligomerisation proceeded pH range 7–12, temperatures between 40–80 °C was marginally enhanced by K + ions. Among canonical ribonucleotides, cGMP most efficiently. Quantification performed using HPLC coupled...
The formamide-based synthesis of nucleic acids is considered as a nonaqueous scenario for the emergence biomolecules from inorganic matter. In current study, we scrutinized chemical composition formamide ices mixed with an FeNi meteorite material treated laser-induced dielectric breakdown plasma created in nitrogen buffer gas. These experiments aimed to capture first steps those transformations that may lead formation nucleobases during impact extraterrestrial icy body containing on early...
The formation of the first C-C bonds from formaldehyde represents rate-limiting step formose reaction. However, free-energy surface associated with such a process has never been determined in condensed phase. By means ab initio molecular dynamics and metadynamics techniques here we report on landscape underlying synthesis glycolaldehyde aqueous solution. Moreover, numerical samples (both neat water solution) have exposed to intense electric fields. application electrostatic gradients...
The origin of life on Earth is one the most fascinating questions contemporary science. Extensive research in past decades furnished diverse experimental proposals for emergence first informational polymers that could form basis early terrestrial life. Side by side with experiments, fast development modern computational chemistry methods during last 20 years facilitated use silico modelling tools to complement experiments. Modern computations can provide unique atomic-level insights into...
SIBFA polarizable molecular mechanics (PMM) and quantum-chemical (ab initio Hartree−Fock DFT) computations are performed on the binding of hydrated Zn(II) Mg(II) cations to 5'-guanosine monophosphate, a basic building block nucleic acids, probing both C2' endo C3' conformations. The interaction energies hydrates, ΔEint, compared in three distinct arrangements: (A) simultaneous dication O1 N7, (B) direct through-water conversely, (C) N7. With sugar, bidentate complex A has marginally more...
Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many the families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization all 13 crystallographically detected members this family provided means B3LYP/6-31G RIMP2/aug-cc-pVDZ Further, a prediction made for remaining 3 WC/SE pairs which are yet to be seen...
Due to the presence of 2'-OH hydroxyl group ribose, RNA molecules utilize an astonishing variability base pairing patterns build up their structures and perform biological functions. Many key families have no counterparts in DNA. In this study, trans Watson−Crick/sugar edge (trans WC/SE) pair family has been characterized using quantum chemical molecular mechanics calculations. Gas-phase optimized geometries from density functional theory (DFT) calculations RIMP2 interaction energies are...
Trans Hoogsteen/sugar edge (H/SE) RNA base pairs form one of the six families that utilize 2′-hydroxyl group ribose for pairing and play key roles in stabilizing folded molecules. Here, we provide a detailed quantum chemical characterization intrinsic structures interaction energies this pair family, along with evaluation solvent screening effects by continuum approach. We report DFT-optimized geometries MP2 all 10 crystallographically identified members representative set them, using...
In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these areas, while largely separated contemporary literature, have substantial potential complement each other could significantly contribute our understanding the exciting world acids. We identify questions amenable combined application modern ab initio methods...
Abstract NMR chemical shifts are highly sensitive probes of local molecular conformation and environment form an important source structural information. In this study, the relationship between nucleic acids glycosidic torsion angle, χ , has been investigated for two commonly occurring sugar conformations. We have calculated by means DFT all atoms in eight DNA RNA mono‐nucleosides as a function these variables. From calculations, structures potential energy surfaces were determined using...
Abstract The formation of nucleosides in abiotic conditions is a major hurdle origin-of-life studies. We have determined the pathway general reaction leading to one-pot synthesis ribo- and 2′-deoxy-ribonucleosides from sugars purine nucleobases under proton irradiation presence chondrite meteorite. These simulate presumptive space or on an early Earth fluxed by slow protons solar wind, potentially mimicking plausible prebiotic scenario. (i) requires neither pre-activated precursors nor...
Abstract Recent synthetic efforts aimed at reconstructing the beginning of life on our planet point plausibility scenarios fueled by extraterrestrial energy sources. In current work we show that beyond nucleobases sugar components first informational polymers can be synthesized in this way. We demonstrate a laser-induced high-energy chemistry combined with TiO 2 catalysis readily produces mixture pentoses, among them ribose, arabinose and xylose. This might highly relevant to Late Heavy...
Chemical environments of young planets are assumed to be significantly influenced by impacts bodies lingering after the dissolution protoplanetary disk. We explore chemical consequences these under reducing planetary atmospheres dominated carbon monoxide, methane, and molecular nitrogen. Impacts were simulated using a terawatt high-power laser system. Our experimental results show that one-pot impact-plasma-initiated synthesis all RNA canonical nucleobases simplest amino acid glycine is...
Synthesis of nucleobases in nonaqueous environments is an alternative way for the emergence terrestrial life, which could solve fundamental problem connected to hydrolytic instability nucleic acid components aqueous environment. In this contribution, we present a plausible reaction route prebiotic synthesis formamide, does not require participation formamide trimer and aminoimidazole-carbonitrile intermediates. The computed activation energy proposed pathway noticeably higher than that...
Cis and trans sugar edge/sugar edge (SE/SE) binding patterns are essential building units of RNAs. For example, SE/SE interactions form the A-minor motifs, most important tertiary interaction type in functional This study provides an in-depth structure stability analysis for these two base pair families. Gas-phase-optimized geometries reported 12 cis 7 pairs contrasted to their X-ray counterparts. Interaction energies computed at RIMP2 level theory using density-functional-theory-optimized...
M-DNA is a type of metalated DNA that forms at high pH and in the presence Zn, Ni, Co, with metals placed between each base pair, as G−Zn−C. Experiments have found could be promising candidate for variety nanotechnological applications, it speculated metal d-states enhance conductivity, but controversy still clouds these findings. In this paper, we carry out comprehensive ab initio study eight G−Zn−C models gas phase to help discern structure electronic properties Zn-DNA. Specifically,...