Department of Biomolecular NMR


 

Head:

Zofia Gdaniec, Prof.

 


 

Staff:
Daniel Baranowski, PhD;

Dorota Gudanis, PhD;

Witold Andrałojć, PhD;


PhD Students:

Karolina Zielińska, MSc

 


 

 
   

 

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Laboratory affiliated to the Department:

Laboratory of NMR

 

Keywords:

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

 

Research area:

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.

 

Ongoing research projects:

1. RNA hybrid duplex-quadruplex structures with dual functionality as a new tool for silencing of gene expression.

NSC – OPUS 7

2. 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

3. Synthesis and spectral studies of trifunctional modified antisense oligonucleotides.

NSC – MINIATURA 1

4. Synthesis of new 3,6,9-trisubstituted dervatives of 9-H-carbazole as fluorescent probe for DNA and RNa-quadruplexes detection.

NSC – MINIATURA 1

 

Selected publications from the last three years:

1. 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 simulation
J. Inorg. Biochem., 181, 65-73, (2018)

2. 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)

3. 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)

4. Andrałojć W, Hiruma Y, Liu W-M, Ravera E, Nojiri M, Parigi G, Luchinat C, and Ubbink M
Identification of productive and futile encounters in an electron transfer protein complex.
Proc. Natl. Acad. Sci. U. S. A., 114, E1840−E1847 (2017)

5. Andrałojć W,  Ravera E,  Salmon L,  Parigi G,  Al-Hashimi H M and  Luchinat  C
Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.
Phys. Chem. Chem. Phys.,18, 5743-5752 (2016)

6. 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 tRNAs
Nucleic Acids Res., 45, 2137–2149 (2017)

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

8. 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)

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

10. 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 Analysis
Nucleos. Nucleot. Nucl., 35, 4:178-194 (2016)

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