Biophysics of Nucleic Acids

Running projects

Role of guanine quadruplexes in chromatin architecture mediated by CTCF protein

Project ID code: 22-29738S
Provider: GAČR
Years: 2022 - 2024
Solver: Mgr. Daniel Renčiuk Ph.D.
Regulation of gene expression in Eukaryotes, mediated by promoter-enhancer interactions, is partially realized by organization of these regulatory elements into so called topologicallyassociating domains (TAD). The probability of the interaction and, subsequently, the employment of the enhancer regulatory machinery, is significantly higher within one TAD than within different ones. Key component of the boundaries between individual TADs is the CTCF protein bound to cohesin complex. Recently it was observed using bioinformatics tools that the TAD boundaries well correlate with the position of potential quadruplex-forming sites (G4). G4 are secondary structures of nucleic acids, based on pairing of four guanine residues through Hoogsteen hydrogen bonds. G4 existence in vivo was recently confirmed. In the project, we will study the interaction of different G4 types with CTCF protein and its variants by following direct interaction of purified molecules, using molecular biology and biophysics methods, and by using reporter systems in cell-based models.

Finished projects

The role of guanine quadruplexes in the RNA genome of tick-borne encephalitis virus, causal agent of severe neuroinfections

Project ID code: 20-20229S
Provider: GAČR
Years: 2020 - 2022
Solver: Mgr. Daniel Renčiuk Ph.D.
Abstract: Guanine quadruplexes (G4) represent structurally diverse group of unusual conformations of nucleic acids. Recently, their occurrence in vivo and some of their cellular roles was reported. RNA quadruplexes are very stable, even in comparison to DNA, which supports their formation in vivo and their involvement in cellular processes. They were reported in some RNA viruses, for example retroviruses or flaviviruses. The Flaviviridae family comprises viruses with singlestranded RNA genome, which are usually responsible for severe neural infections, like tickborne encephalitis virus (TBEV). In the project, we will identify and, using biophysical techniques, characterize quadruplexes in the TBEV genome. Subsequently, by studying the influence of G4-specific mutants and small-molecule ligands, as well as by direct quadruplex visualisation in the TBEV genome, we will assist in clarifying the role of quadruplexes in the TBEV replication cycle. The data obtained in this project will expand the knowledge of TBEV pathogenesis and might suggest future directions of therapy of TBEV infections. The goal: Prediction, identification and biophysical characterization of guanine quadruplexes (G4) in the RNA genome of the tick-borne encephalitis virus and clarifying the G4 role in viral replication cycle by studies of G4-specific viral mutants and by a visualization of the G4 in infected cell cultures.

Tetrastranded arrangements of DNA and their interactions

Project ID code: 19-17063S
Provider: GA ČR
Years: 2019 - 2021
Solver: prof. RNDr. Michaela Vorlíčková, DrSc.
Tetra-stranded structures of nucleic acids, namely guanine quadruplexes and cytosine i-motifs, are, due to their numerous regulatory functions in vivo, in the spotlight of the current molecular biology. Our observations indicate, in accordance with literature, that the conformational portfolio of such structures is much broader than expected based on standard search algorithms. These “less apparent” tetra-stranded structures may exist due to various base or sequence substitution effects along the strands and, as such, they may represent a fine-tuned regulation of cellular processes. In the project, we will characterize, using biophysical and molecular biological techniques, these less apparent tetra-stranded conformations, their interactions and some of their functional manifestations. In view of regulatory role of these structures, the identification of small variations in primary sequence that dramatically modulate secondary structure, either positively or negatively, has substantial importance in the context of recently emerging field of genome manipulations.

Polymorphic G-quadruplexes in gene promoters

Project ID code: 17-12075S
Provider: GA ČR
Years: 2017 - 2019

Identification and biophysical characterization of regulatory DNA elements of the gene for main pluripotency factor POU5F1

Project ID code: 17-19170Y
Provider: GA ČR
Years: 2017 - 2019

Nucleic acid regulatory sequences - polymorphism, dynamics, and interactions

Project ID code: 15-06785S
Provider: GA ČR
Years: 2015 - 2017

Regulation of the embryonic stem cell pluripotency factor Oct4 via guanine quadruplex in its promoter

Project ID code: 14-33947P
Provider: GA ČR
Years: 2014 - 2016

Evolutionary conserved structural features of centromeric and telomeric DNA

Project ID code: 13-28310S
Provider: GA ČR
Years: 2013 - 2016

DNA quadruplexes in the human genome associated with diseases and aging

Project ID code: P205-12-0466
Provider: GA ČR
Years: 2012 - 2016

Biophysics and bioinformatics of genomic DNA fragments very rich in guanine and adenine

Project ID code: IAA500040903
Provider: GA AV
Years: 2009 - 2013

Formation and dynamics of nucleic acid motifs involved in regulation of gene expression

Project ID code: GA202/09/0193
Provider: GA ČR
Years: 2009 - 2013

Biophysical properties of biologically and medically important regions of human DNA

Project ID code: IAA100040701
Provider: GA AV
Years: 2007 - 2011

Biophysics and bioinformatics of human genome regions with an extreme nucleotide distribution

Project ID code: GA202/07/0094
Provider: GA ČR
Years: 2007 - 2009

Tetraplexes in the human genome

Project ID code: GA204/07/0057
Provider: GA ČR
Years: 2007 - 2009

Pathological microsatelite expansion in the human genome

Project ID code: NR9147
Provider: MZ
Years: 2007 - 2009

Biophysical properties of (guanine+cytosine) and (adenine+thymine) regions in the DNA molecules of human chromosomes

Project ID code: IAA1004201
Provider: GA AV
Years: 2002 - 2006

Tetraplexes of DNA and their occurrence in the human genome

Project ID code: IAA4004201
Provider: GA AV
Years: 2002 - 2006

Conformational transitions in plasmid DNA.

Project ID code: IAA1004301
Provider: GA AV
Years: 2003 - 2005

Development of a method for prediction of the pathological trinucleotide repeat expansion in the human genome

Project ID code: NM7634
Provider: MZ
Years: 2003 - 2005

Conformational polymorphism of DNA molecules containing trinucleotide repeats associated with genetic diseases

Project ID code: 204/01/0561
Provider: GA ČR
Years: 2001 - 2003