Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Interactions of peptide nucleic acids with biologically relevant RNA motifs

2012/05/B/NZ1/00035

Keywords:

peptide nucleic acid (PNA) structure and function of RNA peptides molecular dynamics simulations spectroscopy isothermal titration calorimetry

Descriptors:

  • NZ1_3: Biophysics
  • ST4_13: Solid-state chemistry, surface physicochemistry
  • NZ2_7: Bioinformatics

Panel:

NZ1 - Molecular biology, structural biology, biotechnology: molecular biology, structural biology, biotechnology

Host institution :

Uniwersytet Warszawski, Centrum Nowych Technologii Uniwersytetu Warszawskiego

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Joanna Trylska 

Number of co-investigators in the project: 5

Call: OPUS 3 - announced on 2012-03-15

Amount awarded: 997 120 PLN

Project start date (Y-m-d): 2013-02-26

Project end date (Y-m-d): 2016-06-25

Project duration:: 40 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Wysokosprawny analityczno-preparatywny system chromatograficzny (HPLC) z wysokociśnieniowym dynamicznym mikserem gradientów, piecem do kolumn, pompą o niskiej pulsacji wraz z celami pomiarowymi (analityczną i preparatywną), kolektorem frakcji i kolumnami chromatograficznymi (analityczną i preparatywną). (232 000 PLN)
  2. Liofilizator z pompą próżniową odporną chemicznie. (60 000 PLN)

Information in the final report

  • Publication in academic press/journals (15)
  • Book publications / chapters in book publications (1)
  1. Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field
    Authors:
    Filip Leonarski , Fabio Trovato, Valentina Tozzini , Andrzej Leś, and Joanna Trylska
    Academic press:
    J. Chem. Theory Comput. (rok: 2013, tom: 9(11), strony: 4874–4889), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/ct4005036 - link to the publication
  2. RedMDStream: Parameterization and simulation toolbox for coarse-grained molecular dynamics models
    Authors:
    Filip Leonarski, Joanna Trylska
    Academic press:
    Biophysical Journal (rok: 2015, tom: 108(8), strony: 1843-1847), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.bpj.2015.03.023 - link to the publication
  3. Scanning of 16S ribosomal RNA for peptide nucleic acid targets
    Authors:
    Anna Górska, Agnieszka Markowska-Zagrajek, Marcin Równicki, Joanna Trylska
    Academic press:
    J. Phys. Chem. B (rok: 2016, tom: 120, strony: 8369-8378), Wydawca: American Chemical Society
    Status:
    Accepted for publication
    DOI:
    10.1021/acs.jpcb.6b02081 - link to the publication
  4. Electrostatic Interactions in Aminoglycoside-RNA Complexes
    Authors:
    Marta Kulik, Anna M. Goral, Maciej Jasiński, Paulina M. Dominiak, Joanna Trylska
    Academic press:
    Biophysical Journal (rok: 2015, tom: 108(3), strony: 655-665), Wydawca: Cell Press Journals
    Status:
    Published
    DOI:
    10.1016/j.bpj.2014.12.020 - link to the publication
  5. MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids
    Authors:
    Anna Górska, Maciej Jasiński, Joanna Trylska
    Academic press:
    Nucleic Acids Research (rok: 2015, tom: 43(17), strony: e114), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkv559 - link to the publication
  6. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics
    Authors:
    Katarzyna Kulczycka-Mierzejewska, Joanna Trylska, Joanna Sadlej
    Academic press:
    Journal of Molecular Modelling (rok: 2016, tom: 22(20), strony: 45302), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00894-015-2881-0 - link to the publication
  7. Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target
    Authors:
    Marta Kulik, Agnieszka Markowska-Zagrajek, Monika Wojciechowska, Renata Grzela, Tomasz Wituła, Joanna Trylska
    Academic press:
    Biochimie (rok: 2017, tom: 138, strony: 32-42), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.biochi.2017.04.001 - link to the publication
  8. Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study
    Authors:
    Joanna Panecka, Marek Havrila, Kamila Reblova, Jiri Sponer, Joanna Trylska
    Academic press:
    Journal of Physical Chemistry B (rok: 2014, tom: 118, strony: 6687−6701), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/jp5030685 - link to the publication
  9. Using Sequence-Specific Oligonucleotides To Inhibit Bacterial rRNA
    Authors:
    Joanna Trylska, Sapna G. Thoduka , Zofia Dąbrowska
    Academic press:
    ACS Chemical Biology (rok: 2013, tom: 8(6), strony: 1101–1109), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/cb400163t - link to the publication
  10. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site
    Authors:
    Joanna Panecka, Jiri Sponer, Joanna Trylska
    Academic press:
    Biochimie (rok: 2015, tom: 112, strony: 96-110), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.biochi.2015.02.021 - link to the publication
  11. Hamowanie wzrostu bakterii przez peptydowe kwasy nukleinowe i ich rola w biotechnologii
    Authors:
    Agnieszka Markowska-Zagrajek, Marcin Równicki, Joanna Trylska
    Academic press:
    Postępy Mikrobiologii (rok: 2014, tom: 53(3), strony: 255-263), Wydawca: Polskie Towarzystwo Mikrobiologów
    Status:
    Published
    DOI:
    brak - link to the publication
  12. Interactions of amikacin with the RNA model of the ribosomal A-site: Computational, spectroscopic and calorimetric studies
    Authors:
    Marta Dudek, Julia Romanowska, Tomasz Wituła, Joanna Trylska
    Academic press:
    Biochimie (rok: 2014, tom: 102, strony: 188-202), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.biochi.2014.03.009 - link to the publication
  13. Interplay of the Bacterial Ribosomal A-Site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study
    Authors:
    Joanna Panecka, Cameron Mura, Joanna Trylska
    Academic press:
    PLOS One (rok: 2014, tom: e111811, strony: 45308), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0111811 - link to the publication
  14. Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site
    Authors:
    Marta Kulik, Joanna Trylska
    Academic press:
    RAIRO Operations Research (rok: 2016, tom: 50, strony: 375-386), Wydawca: EDP Sciences
    Status:
    Published
    DOI:
    10.1051/ro/2015041 - link to the publication
  15. Interactions of aminoglycoside antibiotics with ribosomal RNA
    Authors:
    Joanna Trylska, Marta Kulik
    Academic press:
    Biochemical Society Transactions (rok: 2016, tom: 44, strony: 987-993), Wydawca: Portland Press
    Status:
    Accepted for publication
    DOI:
    10.1042/BST20160087 - link to the publication
  1. Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
    Authors:
    Filip Leonarski, Joanna Trylska
    Book:
    Modeling Nucleic Acids at the Residue-Level Resolution (rok: 2014, tom: 1, strony: 109-149), Wydawca: Springer-Verlag Berlin Heidelberg Springer Berlin Heidelberg
    Status:
    Published
    DOI:
    link to the publication

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