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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Vitamin B12 as a delivery vehicle for antibacterial oligonucleotide analogues

2014/12/W/ST5/00589

Keywords:

vitamin B12 bacterial cells translation antibiotics modified oligonucleotides

Descriptors:

  • ST5_23:

Panel:

ST5 - Materials: materials synthesis, structure-properties relations, advanced and functional materials with designed properties, (macro)molecular architecture, material engineering

Host institution :

Instytut Chemii Organicznej PAN

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Dorota Gryko 

Number of co-investigators in the project: 10

Call: SYMFONIA 2 - announced on 2013-12-16

Amount awarded: 3 116 800 PLN

Project start date (Y-m-d): 2014-12-11

Project end date (Y-m-d): 2019-12-10

Project duration:: 60 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. komputer.
  2. komputery z oprogramowaniem i drukarką (2 szt.) (10 000 PLN)
  3. miniwirówka.
  4. wirówka laboratoryjna.
  5. Wysokosprawny chromatograf cieczowy (250 000 PLN)
  6. mała wytrząsarka.
  7. prosty spektrofotometr.
  8. termocykler do przygotowywania rekacji PCR w czasie rzeczywistym (52 000 PLN)
  9. wyparka próżniowa.
  10. pompa próżniowa.
  11. spektrofotometr (44 000 PLN)
  12. aparat do pionowej elektroforezy białek i moduł do transferu (8 800 PLN)
  13. monitor.
  14. stacja robocza do symulacji i wizualizacji (10 000 PLN)

Information in the final report

  • Publication in academic press/journals (32)
  1. Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides.
    Authors:
    Sapna G. Thoduka, Paul A. Zaleski, Zofia Dąbrowska, Marcin Równicki, Joanna Stróżecka, Anna Górska, Mikołaj Olejniczak, Joanna Trylska
    Academic press:
    Biopolymers (rok: 2017, tom: 107, strony: 23004), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/bip.23004 - link to the publication
  2. Antimicrobial synergy between mRNA targeted peptide nucleic acid and antibiotics in E. coli
    Authors:
    Jaime Ivan Castillo, Marcin Równicki, Monika Wojciechowska, Joanna Trylska,
    Academic press:
    Bioorg. & Med. Chem. Lett. (rok: 2018, tom: 28, strony: 3094–3098), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bmcl.2018.07.037 - link to the publication
  3. Synthetic Approaches toward Vitamin B12 Conjugates
    Authors:
    Aleksandra J. Wierzba, Sidra Hassan, Dorota Gryko
    Academic press:
    Asian Journal of Organic Chemistry (rok: 2019, tom: 8, strony: 45467), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/ajoc.201800579 - link to the publication
  4. The Tetraarylpyrrolo[3,2‑b]pyrrolesFrom Serendipitous Discovery to Promising Heterocyclic Optoelectronic Materials
    Authors:
    Maciej Krzeszewski, Dorota Gryko, and Daniel T. Gryko
    Academic press:
    Accounts of Chemical Research (rok: 2017, tom: 50, strony: 2334-2345), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.accounts.7b00275 - link to the publication
  5. Interactions of 2'-O-methyl Oligoribonucleotides with the RNA Models of the 30S Subunit A-site
    Authors:
    Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski, Joanna Trylska
    Academic press:
    PLoS ONE (rok: 2018, tom: 13, strony: 13(1):e0191138), Wydawca: Scijournal.org
    Status:
    Published
    DOI:
    10.1371/journal.pone.0191138 - link to the publication
  6. Computational methods used to explore transport events in biological systems
    Authors:
    T. Pieńko, J. Trylska
    Academic press:
    Journal of Chemical Information and Modeling., 59(5):1772-1781, 2019 (rok: 2019, tom: 59, strony: 1772-17781), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jcim.8b00974 - link to the publication
  7. Improved force fields for peptide nucleic acids with optimized backbone torsion parameters
    Authors:
    Maciej Jasiński, Michel Feig, Joanna Trylska
    Academic press:
    J. Chem. Theory Comput. (rok: 2018, tom: 14, strony: 3603–3620), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jctc.8b00291 - link to the publication
  8. Inhibition of Escherichia coli growth by vitamin B12-peptide nucleic acid conjugates
    Authors:
    M. Równicki, Z. Dąbrowska, M. Wojciechowska, A. J. Wierzba, K. Maximova, D. Gryko, J. Trylska
    Academic press:
    ACS Omega (rok: 2019, tom: 4, strony: 819-824), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acsomega.8b03139 - link to the publication
  9. Molecular dynamics simulations of L-RNA involving homo- and heterochiral complexes
    Authors:
    Marta Dudek, Joanna Trylska
    Academic press:
    J. Chem. Theory Comput. (rok: 2017, tom: 13, strony: 1244-1253, 2017), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jctc.6b01075 - link to the publication
  10. Photoinduced Vitamin B12-Catalysis for Deprotection of (Allyloxy)arenes
    Authors:
    Maciej Giedyk, Joanna Turkowska, Sandra Lepak, Marcin Marculewicz, Keith ó Proinsias, Dorota Gryko
    Academic press:
    Organic Letters (rok: 2017, tom: 19, strony: 2670-2673), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.orglett.7b01012 - link to the publication
  11. Synthesis of Corroles and Their Heteroanalogs
    Authors:
    Rafał Orłowski, Dorota Gryko,Daniel T. Gryko
    Academic press:
    Chemical Reviews (rok: 2017, tom: 117, strony: 3102-3137), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.chemrev.6b00434 - link to the publication
  12. Thermal stability of peptide nucleic acid complexes
    Authors:
    M. Jasiński, J. Miszkiewicz, M. Feig, J. Trylska
    Academic press:
    Journal of Physical Chemistry B (rok: 2019, tom: 123, strony: 8168-8177), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.9b05168 - link to the publication
  13. Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells
    Authors:
    Marcin Równicki, Monika Wojciechowska, Aleksandra J. Wierzba, Jakub Czarnecki, Dariusz Bartosik, Dorota Gryko, Joanna Trylska
    Academic press:
    Scientific Reports (rok: 2017, tom: 7, strony: 7644-), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-017-08032-8 - link to the publication
  14. meso-Modified cobalamins – synthesis, structure, and properties
    Authors:
    Aleksandra J. Wierzba, Aleksandra Wincenciuk, Maksymilian Karczewski, Valentine I. Vullev, Dorota Gryko
    Academic press:
    Chemistry A European Journal (rok: 2018, tom: 24, strony: 10344-10356), Wydawca: Wiley-VCH
    Status:
    Published
    DOI:
    10.1002/chem.201801807 - link to the publication
  15. 5'-Vitamin B12 derivatives suitable for bioconjugation via the amide bond
    Authors:
    A. Jackowska, M. Chromiński, M. Giedyk, D. Gryko
    Academic press:
    Organic & Biomolecular Chemistry (rok: 2018, tom: 16, strony: 936-943), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c7ob02898a - link to the publication
  16. Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target
    Authors:
    Marta Kulik a, b, 1, 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
  17. Interactions of 2'-O-methyl Oligoribonucleotides with the RNA Models of the 30S Subunit A-site
    Authors:
    Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski, Joanna Trylska,
    Academic press:
    PLoS ONE (rok: 2018, tom: 13, strony: e0191138), Wydawca: PLOS
    Status:
    Published
    DOI:
    Interactions - link to the publication
  18. Modeling nucleic acids at the residue-level resolution, in: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes - from bioinformatics to molecular quantum mechanics
    Authors:
    F. Leonarski, J. Trylska
    Academic press:
    Springer series on Bio- and Neurosystems (rok: 2019, tom: 8, strony: 117-161), Wydawca: Springer
    Status:
    Published
    DOI:
    doi - link to the publication
  19. 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: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.6b02081 - link to the publication
  20. Vitamin B12 transports modified RNA into E. coli and S. Typhimurium cells
    Authors:
    M. Giedyk, A. Jackowska, M. Równicki, M. Kolanowska, J. Trylska, D. Gryko
    Academic press:
    Chemical. Communications (rok: 2019, tom: 55, strony: 763-766), Wydawca: RSC
    Status:
    Published
    DOI:
    10.1039/C8CC05064C - link to the publication
  21. Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin
    Authors:
    Katarzyna Kulczycka-Mierzejewska, Joanna Sadlej, Joanna Trylska,
    Academic press:
    J. Mol. Model (rok: 2018, tom: 24, strony: 191), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00894-018-3689-5 - link to the publication
  22. Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides
    Authors:
    Sapna G. Thoduka, Paul A. Zaleski, Zofia Dąbrowska, Marcin R!ownicki, Joanna Stróżecka , Anna Górska, Mikołaj Olejniczak, Joanna Trylska
    Academic press:
    Biopolymers (rok: 2017, tom: 107, strony: 23004-23023), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/bip.23004 - link to the publication
  23. Vitamin B12 Deficiency Induces Imbalance in Melanocytes Homeostasis—A Cellular Basis of Hypocobalaminemia Pigmentary Manifestations
    Authors:
    Zuzanna Rzepka, Michalina Respondek, Jakub Rok, Artur Beberok , Keith ó Proinsias, Dorota Gryko, Dorota Wrześniok
    Academic press:
    International Journal of Molecular Sciences (rok: 2018, tom: 19, strony: 2845-2858), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms19092845 - link to the publication
  24. Vitamin B12-peptide nucleic acids use the BtuBreceptor to pass through theEscherichia colioutermembrane
    Authors:
    Tomasz Pieńko, Jakub Czarnecki, Marcin Równicki, Monika Wojciechowska, Aleksandra J.Wierzba, Dorota Gryko, Dariusz Bartosik, Joanna Trylska
    Academic press:
    Biophysical Journal (rok: 2021, tom: 120, strony: 725–737), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bpj.2021.01.004 - link to the publication
  25. Artificial activation of Escherichia coli mazEF and hipBA toxin–antitoxin systems by antisense peptide nucleic acids as an antibacterial strategy,
    Authors:
    Marcin Równicki, Tomasz Pieńko, Jakub Czarnecki, Monika Kolanowska, Dariusz Bartosik, Joanna Trylska
    Academic press:
    Frontiers in Microbiology (rok: 2018, tom: 9, strony: 2870), Wydawca: JCR, Clarivate Analytics
    Status:
    Published
    DOI:
    10.3389/fmicb.2018.02870 - link to the publication
  26. Conformational Dynamics of Cyanocobalamin and Its Conjugates with Peptide Nucleic Acids
    Authors:
    Tomasz Pieńko, Aleksandra J. Wierzba, Monika Wojciechowska, Dorota Gryko, Joanna Trylska
    Academic press:
    The Journal of Physical Chemistry B (rok: 2017, tom: 121, strony: 2968-2979), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.7b00649 - link to the publication
  27. Interactions of aminoglycoside antibiotics with rRNA
    Authors:
    Joanna Trylska, Marta Kulik
    Academic press:
    Biochem. Soc. Trans. (rok: 2016, tom: 44, strony: 987-993), Wydawca: Portland Press
    Status:
    Published
    DOI:
    10.1042/BST20160087 - link to the publication
  28. Molecular Dynamics Simulations of L‑RNA Involving Homo- and Heterochiral Complexes
    Authors:
    Marta Dudek, Joanna Trylska
    Academic press:
    J. Chem. Theory Comput. (rok: 2017, tom: 13, strony: 1244-1253), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jctc.6b01075 - link to the publication
  29. Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA
    Authors:
    Monika Wojciechowska, Marta Dudek, Joanna Trylska
    Academic press:
    Biopolymers (rok: 2018, tom: 109, strony: e23116), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/bip.23116 - link to the publication
  30. Truncated vitamin B12 derivative with the phosphate group retained
    Authors:
    Sidra Hassan, Agnieszka Jackowska, Dorota Gryko
    Academic press:
    Journal of Porphyrins and Phtalocyanines (rok: 2019, tom: 23, strony: 554–560), Wydawca: World Scientific
    Status:
    Published
    DOI:
    10.1142/S1088424619500421 - link to the publication
  31. Vitamin B12 Suitably Tailoed for Disulfide-Based Conjugation
    Authors:
    Aleksandra Wierzba,† Monika Wojciechowska, Joanna Trylska, Dorota Gryko
    Academic press:
    Bioconjugate Chemistry (rok: 2016, tom: 27, strony: 189-197), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.bioconjchem.5b00599 - link to the publication
  32. Vitamin B12 transports modified RNA into E. coli and S. Typhimurium cells
    Authors:
    Maciej Giedyk, Agnieszka Jackowska,Marcin Równicki, Monika Kolanowska, Joanna Trylska, Dorota Gryko
    Academic press:
    Chemical Communications (rok: 2019, tom: 55, strony: 763-766), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c8cc05064c - link to the publication

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