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

 

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.


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)

 

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:

  • Selection of the leading strand during the formation of RISC complex (RNA - induced silencing complex) in mammalian cell lines. Ministry of Science and Higher Education research grant, 2016-2017, Principal investigator: Jolanta Lisowiec Wąchnicka
  • Thermodynamic insights into design of functionally optimized modified siRNAs and their experimental verification, NSC research grant: 2013/10/E/NZ1/00741, 2014-2018, Principal investigator: Anna Pasternak
  • Anticoagulant and antiproliferative properties of novel thrombin binding aptamer analogues, NSC research grant: 2015/19/N/NZ5/02246, 2016-2018, Principal investigator: Weronika Kotkowiak
  • 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
  • Synthesis of novel porphyrin derivatives with application potential for photodynamic therapy (PDT), NSC research grant Miniatura, 2017-2018, Principal investigator: Zofia Jahnz-Wechmann

 

Selected publications:

 

Bartyś N., Kierzek R., Lisowiec-Wąchnicka J. (2019) The regulation properties of RNA secondary structure in alternative splicing, BBA-Gene Regul. Mech. DOI: 10.1016/j.bbagrm.2019.07.002

 

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 Scientific Rep. 9(1), 2477

 

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. Nucleic Acids 2;10:304-316.

Gladysz M., Nowak A., Pasternak A., Milecki J. (2017) Synthesis and hybridization properties of oligonucleotide analogues with novel acyclic triazole internucleotide linkages. Bioorg Chem. 72,161-167.

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 ?-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.

Langkj?r 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.

Gurda D., Handschuh L., Kotkowiak W., Jakubowski H. (2015) Homocysteine and Its Metabolites Induce Pro-atherogenic Changes in Gene Expression in Human Vascular Endothelial Cells. Amino Acids, 47(7), 1319-39.

Magner D., Biala E., Lisowiec-Wachnicka J., Kierzek E., Kierzek R (2015) A tandem oligonucleotide approach for SNP selective RNA degradation using modified antisense oligonucleotides. PLoS ONE, 10(11), e0142139.

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

Kierzek E., Malgowska M., Lisowiec J., Turner D.H., Gdaniec Z., Kierzek R. (2014) The contribution of pseudouridine to stabilities and structure of RNAs. Nucleic Acids Res., 42(5), 3492-3501.

Jensen T. B.,  Henriksen J. R.,  RasmussenB. E., RasmussenL. M., AndresenT. L., Wengel J., Pasternak A. (2011) Thermodynamic  and  biological  evaluation  of  a  thrombin  binding  aptamer  modified  with  several  unlocked  nucleic  acid  (UNA)  monomers  and  a  2'-C-piperazino-UNA  monomer. Bioorg. Med. Chem., 19(16), 4739-4745.

Pasternak A., Wengel J. (2011) Unlocked nucleic acid – a simple modification with broad potential. Org. Biomol. Chem., 9, 3591-3597. (selected as an OBC HOT article)  

Pasternak A., Wengel J.(2011) Modulation of i-motif thermodynamic stability by the introduction of UNA (unlocked nucleic acid) monomers. Bioorg. Med. Chem. Lett., 21(2), 752-755.

Pasternak A., Hernandez F.J., Rasmussen L.M., Vester B., Wengel J. (2011) Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer. Nucleic Acids Res., 39 (3), 1155-1164.

Pasternak A., Wengel J. (2010) Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides. Nucleic Acids Res., 38(19),6697-6706. (placed on F1000 biology list)

Langkjær N., Pasternak A., Wengel J. (2009) UNA (unlocked nucleic acid): A flexible RNA mimic that allows engineering of nucleic acid duplex stability. Bioorg. Med. Chem., 17, 5420–5425. (placed on F1000 biology list)