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Thermodynamic parameters and rules towards the determination of RNA folding in in vivo-like conditions. RNA folding predictions for a better understanding of their structure and function in mammalian cells.

2019/33/B/ST4/01422

Keywords:

RNA RNA thermodynamics native RNA structure folding RNA in the cells duplexes and structural motifs of RNA.

Descriptors:

  • ST4_001:
  • ST4_009:
  • ST4_003:

Panel:

ST4 - Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development

Host institution :

Instytut Chemii Bioorganicznej Polskiej Akademii Nauk

woj. wielkopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Ryszard Kierzek 

Number of co-investigators in the project: 4

Call: OPUS 17 - announced on 2019-03-15

Amount awarded: 1 812 200 PLN

Project start date (Y-m-d): 2020-02-25

Project end date (Y-m-d): 2025-02-24

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

Project status: Project completed

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (18)
  1. Secondary Structure of Subgenomic RNA M of SARS-CoV-2
    Authors:
    M. Soszynska-Jozwiak, A. Ruszkowska, R. Kierzek, C.A. O'Leary, W.N. Moss and E. Kierzek
    Academic press:
    VIRUSES-BASEL (rok: 2022, tom: 14, strony: 322), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/v14020322 - link to the publication
  2. Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs.
    Authors:
    T. Czapik, J. Piasecka, R. Kierzek, E. Kierzek
    Academic press:
    Molecular Therapy – Nucleic Acids (rok: 2022, tom: 29, strony: 64-74), Wydawca: CELL PRESS 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139
    Status:
    Published
    DOI:
    10.1016/j.omtn.2022.05.035 - link to the publication
  3. Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine.
    Authors:
    E. Kierzek, X. Zhang, R. Watson, S. Kennedy, M. Szabat, R. Kierzek, and D. Mathews
    Academic press:
    Nature Communications (rok: 2022, tom: 13, strony: 1271), Wydawca: NATURE PORTFOLIOHEIDELBERGER PLATZ 3, BERLIN 14197, GERMANY
    Status:
    Published
    DOI:
    10.1038/s41467-022-28817-4 - link to the publication
  4. RNA Secondary Structure as a First Step for Rational Design of the Oligonucleotides towards Inhibition of Influenza A Virus Replication
    Authors:
    M. Szabat, D. Lorent, T. Czapik, M. Tomaszewska, E. Kierzek, R. Kierzek
    Academic press:
    Pathohens (rok: 2020, tom: 9, strony: 925), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/pathogens9110925 - link to the publication
  5. Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in A Cellular Environment.
    Authors:
    B. Szutkowska, K. Wieczorek, R. Kierzek, P. Zmora, J.M. Peterson, W.N. Moss, D.H. Mathews and E. Kierzek
    Academic press:
    International Journal of Molecular Sciences (rok: 2022, tom: 23, strony: 2452), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms23052452 - link to the publication
  6. A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine.
    Authors:
    M. Szabat, M. Prochota, R. Kierzek, E. Kierzek, D. H. Mathews
    Academic press:
    Journal of Molecular Biology (rok: 2022, tom: 434, strony: 167632), Wydawca: CADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
    Status:
    Published
    DOI:
    10.1016/j.jmb.2022.167632 - link to the publication
  7. Secondary Structure of Subgenomic RNA M of SARS-CoV-2
    Authors:
    M. Soszynska-Jozwiak, A. Ruszkowska, R. Kierzek, C.A. O'Leary, W.N. Moss and E. Kierzek
    Academic press:
    Viruses-Basel (rok: 2022, tom: 14, strony: 322), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/v14020322 - link to the publication
  8. METTL16, Methyltransferase-like Protein 16: Current Insights into Structure and Function
    Authors:
    Ruszkowska A.
    Academic press:
    International Journal of Molecular Sciences (rok: 2021, tom: 22, strony: 2176), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22042176 - link to the publication
  9. Secondary Structure of Subgenomic RNA M of SARS-CoV-2
    Authors:
    M. Soszynska-Jozwiak, A. Ruszkowska, R. Kierzek, C.A. O'Leary, W.N. Moss and E. Kierzek
    Academic press:
    Viruses-Basel (rok: 2022, tom: 14, strony: 322), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/v14020322 - link to the publication
  10. Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus - application of 4-thiouridine photocrosslinking
    Authors:
    M. Soszynska-Jozwiak, M. Pszczola, J. Piasecka, J.M. Peterson, W.N. Moss, K. Taras-Goslinska, R. Kierzek, E. Kierzek
    Academic press:
    Journal of Biological Chemistry (rok: 2021, tom: 297, strony: 101245), Wydawca: ASBMB
    Status:
    Published
    DOI:
    10.1016/j.jbc.2021.101245 - link to the publication
  11. Structural variants and modifications of hammerhead ribozymes targeting influenza A virus conserved structural motifs.
    Authors:
    T. Czapik, J. Piasecka, R. Kierzek, E. Kierzek
    Academic press:
    Molecular Therapy – Nucleic Acids (rok: 2022, tom: 29, strony: 64-74), Wydawca: CELL PRESS 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139
    Status:
    Published
    DOI:
    10.1016/j.omtn.2022.05.035 - link to the publication
  12. A Structural Potential of Rare Trinucleotide Repeat Tracts in RNA
    Authors:
    D. Magner, R. Nowak, E. Lenartowicz Onyekaa, A. Pasternak, R. Kierzek
    Academic press:
    International Journal of Molecular Sciences (rok: 2022, tom: 23, strony: 5850), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms23105850 - link to the publication
  13. Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in A Cellular Environment
    Authors:
    B. Szutkowska, K. Wieczorek, R. Kierzek, P. Zmora, J.M. Peterson, W.N. Moss, D.H. Mathews and E. Kierzek
    Academic press:
    International Journal of Molecular Sciences (rok: 2022, tom: 23, strony: 2452), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms23052452 - link to the publication
  14. Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA
    Authors:
    P. Michalak, J. Piasecka, B. Szutkowska, R. Kierzek, E. Biala, W.N. Moss and E. Kierzek
    Academic press:
    VIRUSES-BASEL (rok: 2021, tom: 13, strony: 525), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/v13030525 - link to the publication
  15. Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine.
    Authors:
    E. Kierzek, X. Zhang, R. Watson, S. Kennedy, M. Szabat, R. Kierzek, and D. Mathews
    Academic press:
    Nature Communications (rok: 2022, tom: 13, strony: 1271), Wydawca: NATURE PORTFOLIOHEIDELBERGER PLATZ 3, BERLIN 14197, GERMANY
    Status:
    Published
    DOI:
    10.1038/s41467-022-28817-4 - link to the publication
  16. Secondary Structure of Subgenomic RNA M of SARS-CoV-2
    Authors:
    M. Soszynska-Jozwiak, A. Ruszkowska, R. Kierzek, C.A. O'Leary, W.N. Moss and E. Kierzek
    Academic press:
    VIRUSES-BASEL (rok: 2022, tom: 14, strony: 322), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/v14020322 - link to the publication
  17. Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in A Cellular Environment.
    Authors:
    B. Szutkowska, K. Wieczorek, R. Kierzek, P. Zmora, J.M. Peterson, W.N. Moss, D.H. Mathews and E. Kierzek
    Academic press:
    International Journal of Molecular Sciences (rok: 2022, tom: 23, strony: 2452), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms23052452 - link to the publication
  18. Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine
    Authors:
    E. Kierzek, X. Zhang, R. Watson, S. Kennedy, M. Szabat, R. Kierzek, and D. Mathews
    Status:
    Accepted for publication

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