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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Structure defined oligonucleotides for revealing fundamental insights into structure and function of RNAs

2013/08/A/ST5/00295

Keywords:

modified oligonucleotides RNA structure and function NMR ribozymes RNA thermodynamics RNA repeats RNA mapping

Descriptors:

  • ST5_16:
  • ST5_11: Smart materials – self assembled materials, external stimuli-responsive materials
  • 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 Bioorganicznej PAN

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: 14

Call: MAESTRO 4 - announced on 2012-12-15

Amount awarded: 2 997 800 PLN

Project start date (Y-m-d): 2013-08-28

Project end date (Y-m-d): 2019-08-27

Project duration:: 72 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. pakiet oprogramowania do przewidywania widm NMR (C/H/N/P/F - 1D i H/C/N - 2D) (60 000 PLN)
  2. spektrofotometr typu nanodrop (70 000 PLN)
  3. wirówka z chłodzeniem i rotorami (35 000 PLN)
  4. wyparka rotacyjna (typu speed-vac), z rotorami, wymrażalnikiem i pompą olejową (80 000 PLN)
  5. zestaw komputerowy (komputer, monitor, drukarka). (2 szt.) (14 000 PLN)
  6. Ph-metr z elektoodą.
  7. aparat do pomiaru suchości rozpszczalników organicznych (kulometr) (55 000 PLN)
  8. laboratoryjna waga analityczna (7 000 PLN)
  9. termomikser z blokiem wymiennym (2 szt.) (30 000 PLN)
  10. kaseta z ekranem do fosforimigera firmy Fuji (2 szt.) (30 000 PLN)
  11. pompa olejowa wysokiej próżni (10 000 PLN)
  12. Termomikser.
  13. Zasilacz do elektroforezy niskonapięciowe (9 000 PLN)
  14. aparat sekwencyjny do elektoforezy z zasilaczem (25 000 PLN)
  15. gradientowy aparat typu PCR (60 000 PLN)
  16. komora inkubacyjna.
  17. naczynie do przechowywania ciekłego azotu typu dewar (8 000 PLN)
  18. sterownik do syntetyzera RNA/DNA (20 000 PLN)
  19. zasilacz do elektroforezy wysokonapięciowej (9 000 PLN)
  20. Spektrofotometr Nanodrop One.
  21. system próżniowy z pompą membranową (2 szt.) (50 000 PLN)

Information in the final report

  • Publication in academic press/journals (27)
  1. Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair
    Authors:
    I. Deb, L. Popenda, J. Sarzynska, M. Małgowska, A. Lahiri, Z. Gdaniec, R. Kierzek
    Academic press:
    Scientific Reports (rok: 2019, tom: 9, strony: 16278), Wydawca: ATURE PUBLISHING GROUP, MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
    Status:
    Published
    DOI:
    10.1038/s41598-019-52637-0 - link to the publication
  2. Influenza virus segment 5 (+) RNA - secondary structure and new targets for antiviral strategies.
    Authors:
    M. Soszynska-Jozwiak, P. Michalak, W.N. Moss, R. Kierzek, J. Kesy, E. Kierzek
    Academic press:
    Scientific Reports (rok: 2017, tom: 7, strony: 15041), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s44598-017-15317-5 - link to the publication
  3. Stabilization of RNA hairpins using non-nucleotide linkers and circularization.
    Authors:
    A. Kiliszek, L. Blaszczyk, R. Kierzek, W. Rypniewski
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 45, strony: e92), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkx122 - link to the publication
  4. The contribution of pseudouridine to stabilities and structure of RNAs.
    Authors:
    E. Kierzek, M.Malgowska, J. Lisowiec, D.H. Turner, Z. Gdaniec and R. Kierzek
    Academic press:
    Nucleic Acids Research (rok: 2014, tom: 42, strony: 3492-3501), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkt1330 - link to the publication
  5. Structural determinants for alternative splicing regulation of the MAPT pre-mRNA. RNA Biology, 12, 330-342 (2015)
    Authors:
    J. Lisowiec, D. Magner, E. Kierzek, E. Lenatrowicz, R. Kierzek RNA. RNA Biology, 12, 330-342 (2015)
    Academic press:
    RNA Biology, 12, 330-342 (2015) (rok: 2015, tom: 12, strony: 330-342), Wydawca: TAYLOR & FRANCIS INC
    Status:
    Published
    DOI:
    10.1080/15476286.2015.1017214 - link to the publication
  6. 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
    Authors:
    M. Soszynska-Jozwiak, P. Michalak, W.N. Moss, R. Kierzek, E. Kierzek,
    Academic press:
    PloS One, 10, e0141132 (2015) (rok: 2015, tom: 10, strony: e0141132), Wydawca: PUBLIC LIBRARY SCIENCE
    Status:
    Published
    DOI:
    10.1371/journal.pone.0141132 - link to the publication
  7. A Tandem Oligonucleotide Approach for SNP-Selective RNA Degradation Using Modified Antisense Oligonucleotides
    Authors:
    D. Magner, E. Biala, J. Lisowiec-Wachnicka, E. Kierzek, R. Kierzek,
    Academic press:
    PloS One, 10, e0142139 (2015) (rok: 2015, tom: 10, strony: e0142139), Wydawca: PUBLIC LIBRARY SCIENCE
    Status:
    Published
    DOI:
    10.1371/journal.pone.0142139 - link to the publication
  8. Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats.
    Authors:
    M. Malgowska, D. Gudanis, R. Kierzek, E. Wyszko, V. Gabelica, Z. Gdaniec
    Academic press:
    Nucleic Acids Research (rok: 2014, tom: 42, strony: 10196-10207), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gku710 - link to the publication
  9. Modified RNA triplexes: Thermodynamics, structure and biological potential
    Authors:
    Szabat, M; Kierzek, E; Kierzek, R
    Academic press:
    Scientific Reports (rok: 2018, tom: 8, strony: 13023), Wydawca: NATURE PUBLISHING GROUP
    Status:
    Published
    DOI:
    10.1038/s41598-018-31387-5 - link to the publication
  10. RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference.
    Authors:
    J. Piasecka, E. Lenartowicz, M. Soszynska-Jozwiak, B. Szutkowska, R. Kierzek, E. Kierzek
    Academic press:
    Molecular Therapy-Nucleic Acids (rok: 2020, tom: 19, strony: 627-642), Wydawca: CELL PRESS, 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA
    Status:
    Published
    DOI:
    10.1016/j.omtn.2019.12.018 - link to the publication
  11. Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides.
    Authors:
    P. Michalak, M. Soszyńska-Jozwiak, E. Biała, W.N. Moss, J. Kęsy, B. Szutkowska, E. Lenartowicz, R. Kierzek, E. Kierzek
    Academic press:
    Scientific Reports (rok: 2019, tom: 9, strony: 3801), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-019-40443-7 - link to the publication
  12. Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus
    Authors:
    Lenartowicz E, Kesy J, Ruszkowska A, Soszynska-Jozwiak M, Michalak P, Moss WN, Turner DH, Kierzek R, Kierzek E
    Academic press:
    Plos One (rok: 2016, tom: 11, strony: e0148281), Wydawca: PUBLIC LIBRARY SCIENCE
    Status:
    Published
    DOI:
    10.1371/journal.pone.0148281 - link to the publication
  13. Small Molecule Rescue and Glycosidic Conformational Analysis of the Twister Ribozyme
    Authors:
    K.J. Messina, R. Kierzek, M.A. Tracey, P.C. Bevilacqua
    Academic press:
    Biochemistry (rok: 2019, tom: 58, strony: 4857-4868), Wydawca: AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
    Status:
    Published
    DOI:
    10.1021/acs.biochem.9b00742 - link to the publication
  14. Microarrays for identifying binding sites and probing structure of RNAs.
    Authors:
    R. Kierzek, D.H. Turner, E. Kierzek
    Academic press:
    Nucleic Acids Research (rok: 2015, tom: 43, strony: 45303), Wydawca: Oxford Press
    Status:
    Published
    DOI:
    10.1093/nar/gku1303 - link to the publication
  15. A Disease-Causing Intronic Point Mutation C19G Alters Tau Exon 10 Splicing via RNA Secondary Structure Rearrangement.
    Authors:
    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,
    Academic press:
    Biochemistry (rok: 2019, tom: 58, strony: 1565-1578), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.biochem.9b00001 - link to the publication
  16. High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations.
    Authors:
    P. Drożdżal, M. Gilski, R. Kierzek, L. Łomozik M. Jaskólski
    Academic press:
    J. Biol. Inorgan. Chem. (rok: 2015, tom: 20, strony: 595-602), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00775-015-1247-5 - link to the publication
  17. Secondary structure model of the naked segment 7 influenza A virus genomic RNA
    Authors:
    Ruszkowska A, Lenartowicz E, Moss WN, Kierzek R, Kierzek E
    Academic press:
    Biochemical Journal (rok: 2016, tom: 473, strony: 4327-4348), Wydawca: PORTLAND PRESS LTD
    Status:
    Published
    DOI:
    10.1042/BCJ20160651 - link to the publication
  18. Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2'-O-Methyl RNA and RNA Oligonucleotides
    Authors:
    M. Szabat; T. Pedzinski, T. Czapik, E. Kierzek, R. Kierzek
    Academic press:
    PloS One, 10, e0143354 (2015) (rok: 2015, tom: 10, strony: e0143354), Wydawca: PUBLIC LIBRARY SCIENCE
    Status:
    Published
    DOI:
    10.1371/journal.pone.0143354 - link to the publication
  19. Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication
    Authors:
    Lenartowicz E, Nogales A, Kierzek E, Kierzek R, Martinez-Sobrido L, Turner DH,
    Academic press:
    Nucleic Acids Therapeutics (rok: 2016, tom: 26, strony: 277-285), Wydawca: MARY ANN LIEBERT, INC
    Status:
    Published
    DOI:
    10.1089/nat.2016.0619 - link to the publication
  20. Thermodynamic Features of Structural Motifs Formed by beta-L-RNA
    Authors:
    Szabat M, Gudanis D, Kotkowiak W, Gdaniec Z, Kierzek R, Pasternak A
    Academic press:
    Plos One (rok: 2016, tom: 11, strony: e0149478), Wydawca: PUBLIC LIBRARY SCIENCE
    Status:
    Published
    DOI:
    10.1371/journal.pone.0149478 - link to the publication
  21. Influence of mismatched and bulged nucleotides on SNP preferential RNase H cleavage of RNA-antisense gapmer heteroduplexes.
    Authors:
    D. Magner, E. Biala, J. Lisowiec-Wachnicka, R. Kierzek
    Academic press:
    Scientific Reports (rok: 2017, tom: 7, strony: 12532), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-017-15317-5 - link to the publication
  22. Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation
    Authors:
    Spasic, A; Kennedy, SD; Needham, L; Manoharan, M; Kierzek, R; Turner, DH ; Mathews, DH
    Academic press:
    RNA (rok: 2018, tom: 24, strony: 656-672), Wydawca: COLD SPRING HARBOR LAB PRESS
    Status:
    Published
    DOI:
    10.1261/rna.064527.117 - link to the publication
  23. Parallel-stranded DNA and RNA duplexes - structural features and potential applications.
    Authors:
    M. Szabat, R. Kierzek
    Academic press:
    FEBS Journal (rok: 2017, tom: 284, strony: 3986-3998), Wydawca: Wiley (FEBS Press)
    Status:
    Published
    DOI:
    10.1111/febs.14187 - link to the publication
  24. Structural characterization of a dimer of RNA duplexes composed of 8-bromoguanosine modified CGG trinucleotide repeats: a novel architecture of RNA quadruplexes
    Authors:
    Gudanis D, Popenda L, Szpotkowski K, Kierzek R, Gdaniec Z
    Academic press:
    Nucleic Acids Research (rok: 2016, tom: 44, strony: 2409-2416), Wydawca: OXFORD UNIV PRESS
    Status:
    Published
    DOI:
    10.1093/nar/gkv1534 - link to the publication
  25. The regulation properties of RNA secondary structure in alternative splicing
    Authors:
    N. Bartys, R. Kierzek, J. Lisowiec-Wachnicka
    Academic press:
    Biochimica Biophysica Acta (rok: 2019, tom: 1862, strony: 194401), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bbagrm.2019.07.002 - link to the publication
  26. Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA.
    Authors:
    M. Gładysz, W. Andralojc, T. Czapik, Z. Gdaniec, R. Kierzek
    Academic press:
    Scientific Reports (rok: 2019, tom: 9, strony: 4385), Wydawca: Nature Publishing group
    Status:
    Published
    DOI:
    10.1038/s41598-019-40715-2 - link to the publication
  27. Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus.
    Authors:
    W. Andralojc, M. Malgowska, J. Sarzynska, K. Pasternak, K. Szpotkowski, R. Kierzek, Z. Gdaniec
    Academic press:
    RNA (rok: 2019, tom: 25, strony: 121-134), Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Published
    DOI:
    10.1261/rna.068163.118 - link to the publication

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