Department of Nucleic Acids Bioengineering

Dr. habil. Anna Pasternak

Head of Department
apa@ibch.poznan.pl
ext.1279

Researchers:

Dr. Jolanta Lisowiec-Wąchnicka BEng.

adiunkt

Dr. Weronika Kotkowiak

asystent

Technical Staff:

Dr. Zofia Jahnz-Wechmann

starszy specjalista chemik

Natalia Bartyś MSc

PhD student/biologist

PhD students:

Carolina Roxo MSc

PhD student

Research Projects

  • modified nucleosides,
  • modified oligonucleotides,
  • G-quadruplexes,
  • triplexes,
  • i-motif,
  • alternative splicing regulation,
  • RNA,
  • DNA
  • aptamers,
  • therapeutic oligonucleotides,
  • diagnostics,
  • theranostics,
  • cancer treatment,
  • siRNAs,
  • nucleic acids thermodynamics,

Research area

Keywords

  • development of novel molecular tools and devices based on nucleic acids and their analogues,

  • chemical synthesis of modified nucleosides and oligonucleotides,

  • thermodynamic and structural (CD, TDS) analysis of various nucleic acids motifs (e.g. G-quadruplexes, triplexes, i-motif),

  • thermodynamics of siRNAs,

  • regulation of siRNA strand selection by RISC complex using modified nucleotides,

  • allele-selective degradation of mRNA via chemically modified siRNAs,

  • alternative splicing regulation in cancer cell lines,

  • development of potent anticoagulants based on modified oligonucleotides,

  • in vitro studies of chemically modified G-quadruplexes and their antiproliferative properties,

  • chemical synthesis of novel dyes with potential photodynamic activity.

As co-investigators:

  • in vitro studies of dye-oligonucleotide conjugates as useful tools for photodynamic therapy (Principal investigator: Michał Kotkowiak, PhD, Faculty of Technical Physics, Institute of Physics, Poznan University of Technology, Poznań, Poland),

  • studies on therapeutic potential of antisense oligonucleotides in gene silencing process (Prof. Jesper Wengel, University of Southern Denmark, Odense)

 

Research activity

  • Novel bispecific G-quadruplex conjugates as potential anticancer agents, NSC PRELUDIUM 18 research grant: 2019/35/N/NZ7/02777, Principal Investigator: Carolina Roxo

  • Bifunctional antisense oligonucleotides - optimization of alternative splicing regulation in cancer cell lines, NSC research grant: UMO-2016/21/D/NZ5/01906, 2017-2020, Principal investigator: Jolanta Lisowiec-Wąchnicka

  • Structural determinants of anticancer properties of G-rich oligonucleotides, grant NCN: UMO-2017/25/B/NZ7/00127, 2018-2021, Principal Investigator: Anna Pasternak

Selected publications

  • Bartyś N., Kierzek R., Lisowiec-Wąchnicka J. (2019) The regulation properties of RNA secondary structure in alternative splicing. Biochim Biophys Acta Gene Regul Mech. 1862(11-12), 194401.

  • Roxo C., Kotkowiak W., Pasternak A. (2019) G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives Molecules 24(20): 3781.

  • Kotkowiak W., Wengel J., Scotton C., Pasternak A. (2019) Improved RE31 analogues containing modified nucleic acid monomers: thermodynamic, structural and biological effects. J. Med. Chem. 62(5), 2499-2507.

  • Lisowiec-Wąchnicka J., Bartyś N., Pasternak A. (2019) A systematic study on the influence of thermodynamic asymmetry of 5′-ends of siRNA duplexes in relation to their silencing potency Sci. Rep. 9:2477, 1-12.

  • Lisowiec-Wąchnicka J., Znosko B., Pasternak A. (2019) Contribution of 3′T and 3′TT overhangs to the thermodynamic stability of model siRNA duplexes. Biophys. Chem. 246, 35–39.

  • Kotkowiak W., Czapik T., Pasternak A. (2018) Novel isoguanine derivative of unlocked nucleic acid – investigations of thermodynamics and biological potential of modified thrombin binding aptamer. PLoS ONE 13(5):e0197835.

  • Kotkowiak W., Lisowiec-Wachnicka J., Grynda J., Kierzek R., Wengel J., Pasternak A. (2018) Thermodynamic, anticoagulant and antiproliferative properties of thrombin binding aptamer containing novel UNA derivative. Mol. Ther. Nucl. Acids, 2;10:304-316.

  • Jahnz-Wechmann Z., Lisowiec-Wachnicka J., Framski G., Kosman J., Boryski J., Pasternak A. (2017) Thermodynamic, structural and fluorescent characteristics of DNA hairpins containing functionalized pyrrolo-2′-deoxycytidines. Bioorg. Chem, 71, 294-298.

  • Szabat M., Gudanis D., Kotkowiak W., Gdaniec Z., Kierzek R., Pasternak A. (2016) Thermodynamic features of structural motifs formed by β-L-RNA. PLoS ONE, 11(2), e0149478.

  • Kotkowiak W., Pasternak A., Kierzek R. (2016) Inhibition of transcription with 5’-N-triphosphates of 5’-amino-5’-deoxyribonucleosides. PLoS ONE, 11(2), e0148282.

  • Langkjær N, Wengel J, Pasternak A. (2015) Watson-Crick hydrogen bonding of unlocked nucleic acids. Bioorg. Med. Chem. Lett., 25(22), 5064-6.

  • Lisowiec J., Magner D., Kierzek E., Lenartowicz E., Kierzek R. (2015) Structural determinants for alternative splicing regulation of the MAPT pre-mRNA. RNA Biol., 12(3), 330-42.

  • Baranowski D., Kotkowiak W., Kierzek R., Pasternak A. (2015) Hybridization properties of RNA containing 8-methoxyguanosine and 8-benzyloxyguanosine. PLoS ONE, 10(9), e0137674.

  • Kotkowiak W., Kotkowiak M., Kierzek R., Pasternak A. (2014) Unlocked nucleic acids – the implications of increased conformational flexibility for RNA/DNA triplex formation. Biochem. J., 464 (2), 203-211

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