Department of Nucleic Acids Bioengineering
Assoc. Prof. Anna Pasternak, PhD
Natalia Bartyś, MSc
Carolina Roxo, MSc
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
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:
Most important research achievements:
Actual research projects:
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.
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)