A5069555359- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- RNA Interference and Gene Delivery
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Bacteriophages and microbial interactions
- Metal complexes synthesis and properties
- Biopolymer Synthesis and Applications
- Enzyme Structure and Function
- Chromosomal and Genetic Variations
- Molecular Junctions and Nanostructures
- Epigenetics and DNA Methylation
- Crystallography and molecular interactions
- MicroRNA in disease regulation
- RNA Research and Splicing
- Plant Virus Research Studies
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- RNA modifications and cancer
- Genetic Neurodegenerative Diseases
- Genetics and Neurodevelopmental Disorders
- CRISPR and Genetic Engineering
- Free Radicals and Antioxidants
- Conducting polymers and applications
Czech Academy of Sciences
2010-2024
Czech Academy of Sciences, Institute of Biophysics
2015-2024
Central European Institute of Technology
2012-2015
Central European Institute of Technology – Masaryk University
2012-2015
Masaryk University
1997-2015
Charles University
2012
Czech Academy of Sciences, Institute of Molecular Genetics
1992
The arrangement of the human telomeric quadruplex in physiologically relevant conditions has not yet been unambiguously determined. Our spectroscopic results suggest that core sequence G 3 (TTAG ) forms an antiparallel same basket type solution containing either K + or Na ions. Analogous sequences extended by flanking nucleotides form a mixture and hybrid (3 1) quadruplexes -containing solutions. We, however, show long DNA behaves way as basic motif. Both are also able to adopt structure:...
Secondary structures of the G-rich strand human telomere DNA fragments G 3 (TTAG ) n , = 1–16, have been studied by means circular dichroism spectroscopy and PAGE, in solutions physiological potassium cation concentrations. It has found that folding these into tetraplexes as well tetraplex thermostabilities enthalpy values depend on number TTAG repeats. The suggested topologies include, e.g. antiparallel parallel bimolecular tetraplexes, an intramolecular tetraplex, a consisting three chains...
DNA concentration has been recently suggested to be the reason why different arrangements are revealed for K+-stabilized human telomere quadruplexes by experimental methods requiring concentrations differing orders of magnitude. As Raman spectroscopy can applied samples ranging from those accessible absorption and CD spectroscopies up extremely concentrated solutions, gels even crystals; it used here clarify polymorphism a core telomeric sequence G3(TTAG3)3 in presence K+ Na+ ions throughout...
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich sequences, is reflected by typical changes CD and UV absorption spectra. By means spectroscopic methods, electrophoresis, chemical modifications other procedures, we characterized iM stability sequences with different cytosine block lengths interrupted various numbers types nucleotides. Particular attention was paid to the iMs at pH conditions close neutral. We...
Abstract We demonstrate that the characteristic circular dichroism (CD) features of parallel‐stranded DNA tetraplex d(G 4 ), especially strong band at 260 nm, are for B and A forms antiparallel duplex d(C G ). Hence, this evidently originates from intrastrand guanine–guanine stacking, which is therefore very similar in DNA. In addition, same type CD spectrum provided by ordered single strand d(GA) 10 . This observation suggests stabilized a core guanines stacked like parallel tetraplex. view...
Journal Article A Z-like form of poly(dA-dC).poly(dC-bT) in sotation? Get access Michaela Vorlíčková, Vorlíčková Search for other works by this author on: Oxford Academic PubMed Google Scholar Jaroslav Kypr, Kypr Štěpáanka Štokrová, Štokrová 1Institute Macromolecular Chemistry, Czechoslovak Academy Sciences162 06 Prague, Czechoslovakia Šponar 2Institute Organic Chemistry and Biochemistry, Sciences166 10 Nucleic Acids Research, Volume 10, Issue 3, 11 February 1982, Pages 1071–1080,...
8‐Oxoguanine is a ubiquitous oxidative base lesion. We report here on the effect of this lesion structure and stability quadruplexes formed by human telomeric DNA sequence 5′‐dG 3 (TTAG ) in NaCl KCl. CD, PAGE absorption‐based thermodynamic data showed that replacement any tetrad‐forming guanines 8‐oxoguanine did not hinder formation monomolecular, antiparallel NaCl. The modified were, however, destabilized both salts, extent depending position These results previous studies...
5-Hydroxymethylcytosine (5-hmC) was recently identified as a relatively frequent base in eukaryotic genomes. Its physiological function is still unclear, but it supposed to serve an intermediate DNA de novo demethylation. Using X-ray diffraction, we solved five structures of four variants the d(CGCGAATTCGCG) dodecamer, containing either 5-hmC or 5-methylcytosine (5-mC) at position 3 9. The observed resolutions were between 1.42 and 1.99 Å. Cytosine modification all cases influences neither...
Abstract Cytosine-rich DNA regions can form four-stranded structures based on hemi-protonated C.C+ pairs, called i-motifs (iMs). Using CD, UV absorption, NMR spectroscopy, and DSC calorimetry, we show that model (CnT3)3Cn (Cn) sequences adopt iM under neutral or slightly alkaline conditions for n > 3. However, the iMs are formed with long-lasting kinetics these melt significant hysteresis. Sequences 6 in two more separate steps, indicating presence of different species, proportion...
Abstract G-quadruplexes (G4s) formed within RNA are emerging as promising targets for therapeutic intervention in cancer, neurodegenerative disorders and infectious diseases. Sequences containing a succession of short GG blocks, or uneven G-tract lengths unable to form three-tetrad G4s (GG motifs), overwhelmingly more frequent than canonical motifs involving multiple GGG blocks. We recently showed that DNA is not able stable two-tetrad intramolecular parallel G4s. Whether can under...
Journal Article Conformational transitions of poly(dA-dT).poly(dA-dT) in ethanolic solutions Get access Michaela Vorlíčková, Vorlíčková 1Institute Biophysics, Czechoslovak Academy Sciences612 65 Brno Search for other works by this author on: Oxford Academic PubMed Google Scholar Pavel Sedláček, Sedláček 2Institute Organic Chemistry and Biochemistry, Sciences166 10 Prague, Czechoslovakia Jaroslav Kypr, Kypr Ŝponar Nucleic Acids Research, Volume 10, Issue 21, 11 November 1982, Pages 6969–6979,...
Conformational changes of poly(dA-dT) . induced by increasing ionic strength were studied using CD spectroscopy. It was found that a pronounced noncooperative inversion the long-wavelength part spectrum occurred at high concentrations CsF in solution. suggested great difference between geometries purine and pyrimidine residues helix characteristic structure concentrated solutions.
Transposable elements form a significant proportion of eukaryotic genomes. Recently, Lexa et al. (Nucleic Acids Res 42:968-978, 2014) reported that plant long terminal repeat (LTR) retrotransposons often contain potential quadruplex sequences (PQSs) in their LTRs and experimentally confirmed ability to adopt four-stranded DNA conformations. Here, we searched for PQSs human found are specifically localized the 3'-UTR LINE-1 elements, HERV strongly accumulated specific regions SVA elements....
G-quadruplexes are four-stranded nucleic acid structures that implicated in the regulation of transcription, translation and replication. Genome regions enriched putative G-quadruplex motifs include telomeres gene promoters. Tumour suppressor p53 plays a critical role regulatory pathways leading to cell cycle arrest, DNA repair apoptosis. In addition transcriptional mediated via sequence-specific binding, can selectively bind various non-B structures. present study, wild-type (wtp53) binding...
We have identified seven putative guanine quadruplexes (G4) in the RNA genome of tick-borne encephalitis virus (TBEV), a flavivirus causing thousands human infections and numerous deaths every year. The formation G4s was confirmed by biophysical methods on synthetic oligonucleotides derived from predicted TBEV sequences. TBEV-5, located at NS4b/NS5 boundary conserved among all known flaviviruses, tested along with its mutated variants for interactions panel G4 ligands, ability to affect...