LABORATORY OF RNA CHEMISTRY

Head:Ryszard Kierzek

Research Staff:
Ewa Bia³a, El¿ieta Kierzek

Graduate Students:
Anna Pasternak, Karol Pasternak, Agata Fr±tczak

Keywords: oligonucleotides synthesis, modified nucleotides, locked nucleic acids and modified locked nucleic acids, thermodynamics of RNA, thermodynamics of modified oligonucleotides, thermodynamics of CNG RNA trinucleotides repeats, RNA self-cleavage, RNA microarrays, RNA structure analysis


The research in the group has recently focused on many problems of the chemical synthesis, thermodynamic properties, as well as on the structure and function of oligoribonucleotides and RNA. Recently, we have developed a new method of synthesizing of oligoribonucleotides containing N6-alkylated adenosines and 2-thiomethyl-N6-alkylpurine riboside nucleotides. The precursor type oligoribonucleotides were synthesized by phosphoramidite method on polymer support and a modification was introduced via post-synthetic procedure.
We have been involved in the studies of thermodynamic properties of oligoribonucleotides since 1984. At the moment, the group is focused on the influence of adenosine modifications on thermodynamic stability of oligoribonucleotides. The modifications include several natural nucleotides such as N6?isopentenyl-adenosine, N6-methyladenosine, 2-thiomethyl-N6-isopentenyladenosine, as well as artificial modifications of adenosine containing various N6-alkylated adenosines and 2-thiomethyl-N6-alkylated purine ribosides.
Our recent studies have focused on the influence of isocytidine, isoguanosine, 2?thiouridine, 4-thiouridine, all propynylated 2'-deoxynucleotides and LNA (Locked Nucleic Acid) nucleotides on thermal stability of RNA/RNA and RNA/DNA duplexes.



Current research activities:
  • chemical synthesis of nucleosides, nucleotides and oligoribonucleotides;
  • chemical synthesis of nucleosides, nucleotides and oligoribonucleotides containing modified nucleotides such as N6-alkylated adenosines and 2-thiomethyl-N6-alkylpurine ribosides, propynylated 2'-deoxynucleotides and LNA nucleotides;
  • thermodynamic stability of RNA/RNA and RNA/DNA duplexes;
  • thermodynamic stability of RNA/RNA and RNA/DNA duplexes containing modified nucleotides such as N6-alkylated adenosines and 2-thiomethyl-N6-alkylpurine riboside nucleotides, propynylated 2'-deoxynucleotides and LNA nucleotides;
  • determination of thermodynamic stability and secondary structure of RNA duplexes formed by trinucleotide repeats, such as CUG, CAG, CCG and CGG;
  • photocrosslinking RNA containing 2-azidoadenosine, 2-azidoguanosine, 4-thiouridine;
  • chemical stability of the 3'-5' and 2'-5' phosphordiester bonds placed in single stranded and double stranded RNA;
  • nonenzymatic cleavage of single stranded and double stranded RNA;
  • antisens oligonucleotides.


    SELECTED PUBLICATIONS

    E. Kierzek, R. Kierzek, D. H. Turner and I. E. Catrina
    Facilitating RNA Structure Prediction with Microarrays.
    Biochemistry, 45(2), 581-593 (2006)

    H. Ma, D.J. Proctor, E. Kierzek, R. Kierzek, P.C. Bevilacqua and M. Gruebele
    Exploring the Energy landscape of a small RNA hairpin.
    J. Am. Chem. Soc., 128, 1523-1530 (2006)

    E. Kierzek, D.H. Mathews, A. Ciesielska, D.H. Turner and R. Kierzek
    Nearest neighbor parameters for Watson-Crick complementary heteroduplex formed between 2’-O-methyl RNA and RNA oligonucleotides.
    Nucleic Acids Research, 34 (13), 3609-3614 (2006)

    R. Yajima, D.J. Proctor, R. Kierzek, E. Kierzek, P. C. Bevilacqua
    A conformationally restricted guanosine analogue reveals the catalytic relevance of three structures of an RNA enzyme.
    Chemistry and Biology, 14, 23-30 (2007)

    A. Pasternak, E. Kierzek, K. Pasternak, D. H. Turner and R. Kierzek
    A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2’-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2’-O-methyl RNA/RNA heteroduplexes.
    Nucleic Acids Research, 35 (12), 4055-4063, 2007

    C. Gang, R. Kierzek, I. Yildirim, T. R. Krugh, D. H. Turner and S. D. Kennedy
    Stacking Effects on Local Structure in RNA: The Structure of Tandem GA Pairs Changes When Flanking GC Pairs are Replaced by isoG-isoC Pairs
    J. Phys. Chem. B, 111, 6718-6727 (2007)

    M. Lewdorowicz, J. Jemielity, R. Kierzek, M. Shapira, J. Stepinski, R. Stolarski, and E. Darzynkiewicz
    Solid-supported synthesis of 5’ mRNA CAP-4 from Trypanosomatides.
    Nucleosides, Nucleotides and Nucleic Acids, in press

    M. Lewdorowicz, J. Stepinski, J. Jemielity, J. Zuberek, R. Kierzek, M. Shapira, J. Stepinski and E. Darzynkiewicz
    Syntheisis of 5’-mRNA CAP analogues (CAP-2 and CAP3) from Leishmana.
    Nucleosides, Nucleotides and Nucleic Acids, in press

    E. Kierzek, A. Fr±tczak, A. Pasternak, D. H. Turner and R. Kierzek
    Isoenergetic RNA microarrays, a new method to study the structure and interactions of RNA.
    International Proceedings Division, in press

    A. Pasternak, E. Kierzek, K. Pasternak, A. Fratczak, D. H. Turner and R. Kierzek
    The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure.
    Biochemistry, in press

    E. Kierzek, R. Kierzek, W. Moss, S. Christensen, T. Eickbush; D.T. Turner
    Isoenergetic Penta- and Hexanucleotide Microarray Probing and Chemical Mapping Provide a Secondary Structure Model for an RNA Element Orchestrating R2 Retrotransposon Protein Function.
    Nucleic Acids Research, in press