Department of Biomolecular NMR

Prof. Zofia Gdaniec

Head of Department
zofia.gdaniec@ibch.poznan.pl
ext. 1151, 1156

Dr. Daniel Baranowski

adiunkt

Dr. Witold Andrałojć

adiunkt

Dr. Dorota Gudanis

adiunkt

Researchers:

Karolina Zielińska MSc

PhD student

PhD Students:

  • Andrałojć, W, Małgowska, M, Sarzyńska, J, Pasternak, K, Szpotkowski, K, Kierzek, R, Gdaniec, ZUnraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3′ terminus.RNA, 25, 121-134 (2019)

  • Gładysz, M, Andrałojć, W, Czapik, T, Gdaniec, Z, Kierzek,RThermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNASci. Rep. , 9, art 4385 (2019)

  • Czyrko, J, Śliwiak, J, Imiołczyk, B, Gdaniec, Z, Jaskolski, M, Brzezinski, MMetal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosaSci. Rep. , 8, art 11334 (2018)

  • Zhao, J, Xue, M, Gudanis, D, Gracz, H, Findenegg, G.H, Gdaniec, Z. Franzen, S,Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulationJ. Inorg. Biochem., 181, 65-73, (2018)

  • Lyons, S.M, Gudanis, D, Coyne, S.M, Gdaniec, Z, Ivanov, P,Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs.Nat. Commun., 8, 1127. (2017)

  • Jackowiak, P, Hojka-Osinska, A, Gasiorek, K, Stelmaszczuk, M, Gudanis, D, Gdaniec, Z, Figlerowicz, M,Effects of G-quadruplex topology on translational inhibition by tRNA fragments in mammalian and plant systems in vitro.Int. J. Biochem. Cell Biol., 92, 148–154 (2017)

  • Matuszewski, M, Wojciechowski, J, Miyauchi, K, Gdaniec, Z, Wolf, W. M, Suzuki, T, Sochacka, E,A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAsNucleic Acids Res., 45, 2137–2149 (2017)

  • Małgowska, M, Czajczyńska, K, Gudanis, D, Tworak, A, Gdaniec, Z,Overview of the RNA G-quadruplex structuresActa Biochim. Pol., 63, 609–621 (2016)

  • Gudanis, D, Popenda, Ł, Szpotkowski, K, Kierzek, R, Gdaniec, Z,Structural characterization of a dimer of RNA duplexes composed of 8-bromoguanosine modified CGG trinucleotide repeats: a novel architecture of RNA quadruplexes.Nucleic Acids Res., 44, 2409-2416 (2016)

  • Szabat, M, Gudanis, D, Kotkowiak, W, Gdaniec, Z, Kierzek, R, Pasternak, A,Thermodynamic Features of Structural Motifs Formed by beta-L-RNAPloS One, 11, e0149478 (2016)

  • Baraniak, D, Baranowski, D, Ruszkowski, P, Boryski, J,3′-O- and 5′-O-Propargyl Derivatives of 5-Fluoro-2′-Deoxyuridine: Synthesis, Cytotoxic Evaluation and Conformational AnalysisNucleos. Nucleot. Nucl., 35, 4:178-194 (2016)

  • Baranowski, D.S, Kotkowiak, W, Kierzek, R, Pasternak, A,Hybridization properties of RNA containing 8-methoxyguanosine and 8-benzyloxyguanosine.PLoS ONE, 10, e0137674 (2015)

  • Małgowska, M, Gudanis, D, Kierzek, R, Wyszko, E, Gabelica, V, Gdaniec, Z,Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeatsNucleic Acids Res., 42, 10196-10207 (2014)

  • Belter, A, Gudanis, D, Rolle, K, Piwecka, M, Gdaniec, Z, Naskręt-Barciszewska, M. Z, Barciszewski, J,Mature miRNAs form secondary structure, which suggests their function beyond RISCPLoS ONE, 9, e113848 (2014)

  • Kierzek, E, Małgowska, M, Lisowiec, J, Turner, D.H, Gdaniec, Z, Kierzek, R,The contribution of pseudouridine to stabilities and structure of RNAs.Nucleic Acids Res., 42, 3492-3501 (2014)

  • Brzezińska, J, Gdaniec, Z, Popenda, Ł, Markiewicz, W.T,Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue, N-[4,9,13-triazatridecan-1-yl]-2′-deoxycytidine.Biochem. Biophys. Acta General Subjects, 1840, 1163-1170 (2014)

Selected publications

  • RNA hybrid duplex-quadruplex structures with dual functionality as a new tool for silencing of gene expression. NSC – OPUS 7

  • Synthesis and structural studies of oligonucleotides with tRNA anticodon stem-loop sequences containing newly discovered modified nucleosides: ct6A, ms2ct6A, ges2U. Consortium with the Faculty of Chemistry, the Technical University of Lodz (leader). NSC – OPUS 13

  • Synthesis and spectral studies of trifunctional modified antisense oligonucleotides. NSC – MINIATURA 1

  • Synthesis of new 3,6,9-trisubstituted dervatives of 9-H-carbazole as fluorescent probe for DNA and RNa-quadruplexes detection. NSC – MINIATURA 1
     

Research activity

  • NMR spectroscopy,
  • structure and dynamics of nucleic acids,
  • quadruplexes,
  • duplex-quadruplex structural hybrids,
  • CGG, AGG and UGG trinucleotide repeats,
  • ligands,
  • conformation of modified nucleosides.

The primary focus of this group is on understanding the structure, function and dynamics of nucleic acids, particularly RNA. We apply both biophysical and biochemical techniques, with a strong emphasis on nuclear magnetic resonance spectroscopy (NMR). One of the major areas of our research involves structural studies of RNA quadruplexes, including their modes of interaction with various ligands. Our interests also focus on duplex-quadruplex structural hybrids, as promising tools for silencing gene expression.

  • Structural and functional studies of RNA duplex-quadruplex hybrids,
  •  Silencing of gene expression using small RNAs with dual functionality,
  •  Design and synthesis of G-quadruplex selective ligands,
  •  G-quadruplex interactions with ligands,
  • Structure of RNA fragments composed of CGG, AGG and UGG trinucleotide repeats,
  • Conformational analysis of 2’-OMe RNA duplexes,
  •  Structure elucidation of modified nucleosides with restricted conformation by means of homo- and heteronuclear NMR spectroscopy,
  •  Elucidating protein dynamics through nuclear relaxation studies.

 

Research area

Keywords

Research Projects

Media Społecznościowe

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Cooperation

Institute of Bioorganic Chemistry,
Polish Academy of Sciences
Z. Noskowskiego 12/14
61-704 Poznań
tel centrala: (+48) 61 852 85 03
fax: (+48) 61 852 05 32
e-mail: ibch@ibch.poznan.pl

Sekretariat Dyrektora, tel: 61 852 89 19

Adress