Department of Nucleic Acids Bioengineering

 

Head:

Assoc. Prof. Anna Pasternak, PhD
 

 



Staff:


Jolanta Lisowiec-Wąchnicka,PhD; Zofia Jahnz-Wechmann,PhD;
Weroniak Kotkowiak, PhD

 


PhD Students:

Natalia Bartyś, MSc

Carolina Roxo, MSc

 

 


 

 

 

 


 

 

 

 

 

Key words:

modified nucleosides, modified oligonucleotides, G-quadruplexes, triplexes, aptamers, nanoparticles, therapeutic oligonucleotides, diagnostics, theranostics, cancer treatment, siRNAs, nucleic acids thermodynamics, thermodynamic stability of nucleic acids structural motifs

 

#Hashtag: #RNA, #DNA, #G-quadruplexes, #triplexes, #thermodynamics, #aptamers, #tumors, #cancer, #oligonucleotides, #splicing

 

Scientific profile:

Department of Nucleic Acids Bioengineering was established in June 2016. We are highly interested in the development of novel molecular tools and devices based on nucleic acids and their analogues. We believe that a variety of chemical modifications gives an opportunity to modulate physicochemical and biological properties of oligonucleotides in predictable and controllable manner. Oligonucleotides with improved properties can be applied as useful therapeutic or highly specific diagnostic tools. Our research team includes biologists and chemists, therefore we easily combine our knowledge to reach various interdisciplinary scientific goals. We are highly experienced in chemical synthesis of modified nucleosides and oligonucleotides, thermodynamic and structural (CD, TDS) analysis of various nucleic acids motifs (particularly in highly-ordered structures e.g. G-quadruplexes, triplexes, i-motif), in vitro experiments on cell lines (HeLa, HFL-1, HUVEC, Huh-7), RNA secondary structure determination, alternative splicing analysis, RT-PCR and qPCR experiments.

Scientific profile:

• 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. duplexes, G-quadruplexes, triplexes, i-motif)

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

• selective degradation of mRNA via chemically modified molecular tools

• regulation of alternative splicing in cancer cell lines using bifunctional antisense oligonucleotides (BASO)

• characterization of interactions between antisense oligonucleotides and splicing factors

• studies on the influence of chemical and structural modifications on interactions between regulatory oligonucleotides and splicing factors

• development of potent anticoagulants based on modified oligonucleotides• in vitro studies of chemically modified G-quadruplexes and their antiproliferative properties

Current research activity:

Own research projects:
  • studies on thermodynamics of natural siRNAs, determination of individual nearest-neighbor hydrogen bond model (INN-HB) parameters of 3’TT dangling ends within RNA duplexes
  • determination of the influence of various modified nucleosides on thermodynamic stability of siRNA duplexes
  • 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)
  • anticoagulant properties of Cu2O nanoparticles and their conjugates (Principal investigator: Marta Woźniak-Budych, PhD, NanoBioMedical Centre, A. Mickiewicz University, Poznan, Poland)

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

 

Most important research achievements:

  • implications of increased conformational flexibility induced by unlocked nucleic acids for RNA/DNA triplex formation
  • design, synthesis, physicochemical and biological characterization of chemically modified analogues of thrombin binding aptamer (TBA)
  • hybridization properties of various RNA and DNA structures containing unlocked nucleic acids (UNA); a result of the collaboration with Prof. Jesper Wengel (Nucleic Acid Center, University of Southern Denmark, Odense, Denmark)
  • structural determinants for alternative splicing regulation of the MAPT pre-mRNA
  • thermodynamic basis of construction of isoenergetic microarrays; a result of the collaboration with Prof. Ryszard Kierzek (IBCh PAS, Poznań)
  • thermodynamics of modified nucleosides (LNAs, 3’-terminal pyrene) for the design of isoenergetic 2’-O-methyl-LNA chimeric oligonucleotide probes of RNA structure; a result of the collaboration with Prof. Ryszard Kierzek (IBCh PAS, Poznań)

 

Actual research projects:

  • 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, NSC research grant: UMO-2017/25/B/NZ7/00127, 2018-2021, Principal Investigator: Anna Pasternak

  • Novel bispecific G-quadruplex conjugates as potential anticancer agents, NSC research grant: 2019/35/N/NZ7/02777, 2020-2023, Principal Investigator: Carolina Roxo

 

Selected publications: 

  • Danielsen M., Lou C., Lisowiec‐Wąchnicka J., Pasternak A., Jørgensen P., Wengel J. (2020) Gapmer Antisense Oligonucleotides Containing 2',3'-Dideoxy-2'-fluoro-3'-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing Chem. Eur. J. 26(6), 1368-1379.

  • 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.

  • Tan J., Yang L.,Lerk Ong A.A., Shi J., Zhong Z., Leng Lye M., Liu S., Lisowiec-Wachnicka J., Kierzek R., Roca X., Chen G. (2019) A disease-causing intronic point mutation C19G alters tau exon 10 splicing via RNA secondary structure rearrangement. Biochemistry 58 (12) 1565-1578.

  • 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.

  • Jahnz-Wechmann Z., Framski G. R., Januszczyk P.A., Boryski J. (2016) Base-Modified Nucleosides: Etheno Derivatives, Front. Chem., 4(19). 

  • 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

 

Achievements of our team members (since 2016)

Team work

  • 2020 Scientific Award of the Institute of Bioorganic Chemistry, Polish Academy of Sciences for the best scientific article made in the Institute in 2019 (Kotkowiak W., Wengel J., Scotton C.J., Pasternak A. Improved RE31 analogues containing modified nucleic acid monomers: thermodynamic, structural and biological effects. J Med Chem, 62(5), 2499-2507).

  • 2020 Scientific Award of the Institute of Bioorganic Chemistry, Polish Academy of Sciences for the best review article made in the Institute in 2019 (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).

  • 2019 Scientific Award of the Institute of Bioorganic Chemistry, Polish Academy of Sciences for the best scientific article made in the Institute in 2018 (Kotkowiak W., Lisowiec-Wachnicka J., Grynda J., Kierzek R., Wengel J. and Pasternak A. (2018) Thermodynamic, anticoagulant and antiproliferative properties of thrombin binding aptamer analogues containing novel UNA derivative. Mol.Ther. Nucleic Acids, 10:304–316).

Weronika Kotkowiak, PhD

  • 2016 Scholarship from the President of Polish Academy of Sciences for outstanding achievements, Warsaw, Poland

  • 2016 KNOW Scholarship (2 months) for a short-term training and research internship, Poznań, Poland

 

Natalia Bartyś, MSc

  • 2018/2019 Scholarship for the best PhD students