Department of Structural Chemistry and Biology of Nucleic Acids

Prof. Ryszard Kierzek

Head of Department
rkierzek@ibch.poznan.pl
ext. 1143, 1113

Rafał Nowak MSc

PhD student

Dagny Lorent MSc

PhD student

PhD students

MSc Maria Tomaszewska
PhD student

Martina Prochota
PhD student

Grażyna Dominiak MSc, BEng

starszy specjalista chemik

Dr. Tomasz Czapik

chemist

Technical Staff:

Dr. Marta Szabat
asystent

Dr. Marta Soszyńska-Jóźwiak
asystent

Dr. Agnieszka Ruszkowska
adiunkt

Dr. Paweł Zmora
adiunkt

Researchers:

  • J. Piasecka, E. Lenartowicz, M. Soszynska-Jozwiak, B. Szutkowska, R. Kierzek E. Kierzek. RNA Secondary structure motifs of the influenza A virus as targets for siRNA-mediated RNA interference. Molecular Therapy-Nucleic Acids, 19, 627-642 (2020)

  • Ł. Pielok, M. Karczewski, W. Cierach, P. Zmora, E. Lenartowicz, J. Stefaniak. Portal hypertension as a result of the incomplete surgically treated advanced alveolar echinococcosis: a case description. BMC Gastroenterology, 20, 176 (2020)

  • W. Andralojc, M. Malgowska, J. Sarzynska, K. Pasternak, K. Szpotkowski, R. Kierzek, Z. Gdaniec. Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus. RNA, 25, 121-134 (2019)

  • P. Michalak, M. Soszyńska-Jozwiak, E. Biała, W.N. Moss, J. Kęsy, B. Szutkowska, E. Lenartowicz, R. Kierzek, E. Kierzek. Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides. Scientific Reports, 9, 3801 (2019)

  • M. Gładysz, W. Andralojc, T. Czapik, Z. Gdaniec, R. Kierzek. Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA. Scientific Reports, 9, 4385 (2019)

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

  • 172/ N. Bartyś, R. Kierzek, J. Lisowiec-Wachnicka, The regulation properties of RNA secondary structure in alternative splicing. Biochimica et biophysica acta. Gene regulatory mechanisms, 1862, 194401 (2019)

  • Ł. Pielok, S. Nowak, M. Kłudkowska, K. Frąckowiak, Ł. Kuszel, P. Zmora, J. Stefaniak. Massive Cryptosporidium infections and chronic diarrhoea in HIV-negative patients. Parasitology Research, 118, 1937-1942 (2019)

  • S.P. Nowak, P. Zmora, L. Pielok, L. Kuszel, R. Kierzek, J. Stefaniak, M. Paul. Case of plasmodium knowlesi malaria in Poland linked to travel in Southeast Asia. Emerging Infectious Diseases, 25, 1772-1773 (2019)

  • R. Rudiger, S.Y. Kupke, T. Laske, P. Zmora, U. Reichl. Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions. Plos Computational Biology, 15, e1006819 (2019)

  • A.A.L. Ong, J. Tan, M. Bhadra, C. Dezanet, K. Patil, M.S. Chong, R. Kierzek, J.L. Decout, X. Roca, G. Chen. RNA Secondary structure-based design of antisense peptide nucleic acids for modulating disease-associated aberrant Tau pre-mRNA alternative splicing. Molecules, 24, 3020 (2019)

  • K.J. Messina, R. Kierzek, M.A. Tracey, P.C. Bevilacqua. Small molecule rescue and glycosidic conformational analysis of the twister ribozyme. Biochemistry, 58, 4857-4868 (2019)

  • I. Deb, L. Popenda, J. Sarzynska, M. Małgowska, A. Lahiri, Z. Gdaniec, R. Kierzek. Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair. Scientific Reports, 9, 16278 (2019)

  • A. Spasic, S.D. Kennedy, L. Needham, M. Manoharan, R. Kierzek, D.H. Turner, D. Mathews. Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation. RNA, 24, 656-672 (2018)

  • W. Kotkowiak, J. Lisowiec-Wachnicka, J. Grynda, R. Kierzek, J. Wengel, A. Pasternak. Thermodynamic, anticoagulant, and antiproliferative properties of thrombin binding aptamer containing novel UNA derivative. Molecular Therapy-Nucleic Acids, 10, 304-316 (2018)

  • M. Szabat, E. Kierzek, R. Kierzek. Modified RNA triplexes: Thermodynamics, structure and biological potential. Scientific Reports, 8, 13023 (2018)

  • M. Szabat, R. Kierzek. Parallel-stranded DNA and RNA duplexes – structural features and potential applications. The FEBS Journal, 284, 3986-3999 (2017)

  • D. Magner, E. Biała, J. Lisowiec-Wąchnicka, R. Kierzek. Influence of mismatched and bulged nucleotides on SNP preferential RNase H cleavage of RNA-antisense gapmer heteroduplex. Scientific Reports, 7, 12532 (2017)

  • M. Soszynska-Jozwiak, P. Michalak, W.N. Moss, R. Kierzek, J. Kęsy, E. Kierzek. Influenza virus segment 5 (+) RNA – secondary structure and new targets for antiviral strategies. Scientific Reports, 7, 15041 (2017)

  • A. Kiliszek, L. Błaszczyk, R. Kierzek, W. Rypniewski. Stabilization of RNA hairpins using non-nucleotide linkers and circularization. Nucleic Acid Research, 45, e92 (2017)

  • A. Ruszkowska, E. Lenartowicz, W.N. Moss, R. Kierzek, E. Kierzek. Secondary structure model of the naked segment 7 influenza A virus genomic RNA. Biochemical Journal, 473, 4327-4348 (2016)

  • E. Lenartowicz, A. Nogales, E. Kierzek, R. Kierzek, L. Martinez-Sobrido, D.H. Turner. Antisense oligonucleotides targeting influenza A segment 8 genomic RNA inhibit viral replication. Nucleic Acids Therapeutics, 26, 277-285 (2016)

  • D. Gudanis, L. Popenda, K. Szpotkowski, R. Kierzek, Z. Gdaniec. Structural characterization of a dimer of RNA duplexes composed of 8-bromoguanosine modified CGG trinucleotide repeats: a novel architecture of RNA quadruplexes. Nucleic Acids Research, 44, 2409-2416 (2016)

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

  • W. Kotkowiak, A. Pasternak, R. Kierzek. Studies on transcriptional incorporation of 5′-N-Triphosphates of 5′-amino-5′-deoxyribonucleosides. PloS One, 11, e0148282 (2016)

  • E. Lenartowicz, J. Kęsy, A. Ruszkowska, M. Soszyńska-Jóźwiak, P. Michalak, W.N. Moss, D.H. Turner, R. Kierzek, E. Kierzek. Self-folding of naked segment 8 genomic RNA of influenza A virus. PloS One, 11, e0148281 (2016)

  • M. Szabat; T. Pędziński, T. Czapik, E. Kierzek, R. Kierzek, Structural aspects of the antiparallel and parallel duplexes formed by DNA, 2′-O-Methyl RNA and RNA Oligonucleotides. PloS One, 10, e0143354 (2015)

  • D. Magner, E. Biala, J. Lisowiec-Wąchnicka, E. Kierzek, R. Kierzek. A Tandem oligonucleotide approach for SNP-selective RNA degradation using modified antisense oligonucleotides. PloS One, 10, e0142139 (2015)

  • M. Soszyńska-Jóźwiak, P. Michalak, W.N. Moss, R. Kierzek, E. Kierzek. A conserved secondary structural element in the coding region of the influenza A virus nucleoprotein (NP) mRNA is important for the regulation of viral proliferation. PloS One, 10, e0141132 (2015)

  • J. Lisowiec, D. Magner, E. Kierzek, E. Lenartowicz, R. Kierzek. Structural determinants for alternative splicing regulation of the MAPT pre-mRNA. RNA Biology, 12, 330-342 (2015)

  • R. Kierzek, D.H. Turner, E. Kierzek. Microarrays for identifying binding sites and probing structure of RNAs. Nucleic Acids Research, 43, 1-12 (2015)

Selected publications

  • Cotranscriptional folding of influenza virus RNA in MDCK cells in presence of antisense oligonucleotides. A new method for next-generation sequencing based chemical mapping of RNA structure. NSC – OPUS 13 (PI: Professor Ryszard Kierzek) 

  • Thermodynamic parameters and rules towards the determination of RNA folding in in vivo-like conditions. RNA folding predictions for a better understanding of structure/function in mammalian cells. NSC – OPUS 17 (PI: Professor Ryszard Kierzek)

  • Molecular basics of type II transmembrane serine proteases (TTSPs)-mediated activation of influenza viruses. NSC – Beethoven Life 1 (PI: Doctor Pawel Zmora)

  • TMPRSS2 – a potential new drug target and a determinant of COVID19 outcome. NSC – Fast Track To Fund Research On SARS-CoV-2 (PI: Doctor Pawel Zmora)

  • The G-rich sequences in the influenza A virus genome – structural features and potential biological function in viral replication cycle. NCN – SONATA 15(PI: Doctor Marta Szabat)

Research activity

  • structure, dynamic and function of nucleic acids,
  • modified oligonucleotides,
  • thermodynamics of nucleic acids,
  • posttranscriptional RNA folding,
  • antisense oligonucleotides,
  • alternative splicing,
  • oligonucleotide microarrays,
  • microarray mapping,
  • conformational fixed nucleic acids,
  • retroviral RNA,
  • retrotransposons,
  • RNA therapeutics,
  • chemistry and molecular biology of RNA,
  • structural bioinformatics,
  • nucleic acids structure calculation,
  • trinucleotide repeats,
  • RNA bulged duplexes,
  • restricted conformation of modified purine nucleosides
  • RNA quadruplexes
  • type II transmembrane serine proteases (TTSPs)
  • virus entry
  • allele-specific degradation of pathogenic RNA with antisense oligonucleotides forming non-helical motifs with target RNA,

  • allele-specific degradation of pathogenic RNA with tandem antisense oligonucleotides,

  • modulation of RNA alternative splicing,

  • structure and thermodynamics of RNA multinucleotide repeats,

  • structure and functions of RNAs with conformational fixed nucleic acids, 

  • structure of RNA fragments composed of CGG, AGG and UGG trinucleotide repeats,

  • conformation of bulged RNA duplexes,

  • structural characterization of LNA-2'-O-MeRNA/RNA and 2'-O-MeRNA/RNA duplexes,

  • posttranscriptional RNA folding.

  • virus-host interactions

  • inhibitors of viral replication cycle

  • structure and potential function of G-rich RNA from the influenza virus genome

Research area

Keywords

Research Projects

Media Społecznościowe

Strona zrobiona w kreatorze stron internetowych WebWave

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