LABORATORY OF RNA BIOCHEMISTRY

Head: Jerzy Ciesiołka

Research Staff:
Mariola Dutkiewicz, Jan Wrzesiński

Research Support:
Barbara Smólska

Ph.D. Students:
Leszek Błaszczyk, Agata Świątkowska, Agnieszka Wichłacz

Undergraduate Students:
Monika Matelska, Jacek Pieczyński



Keywords:
ribozymes, RNA structure, RNA-metal ion interactions, combinatorial oligonucleotide libraries, in vitro selection method, nucleic acids-based technologies, non-coding RNA regions, RNA viruses

Our research is directed toward understanding the role of specific interactions of RNA with metal ions in ribozymes as well as searching for other RNA molecules in which metal ions play an important structural or regulatory role. We are also interested in studying the principles of the formation of folded, biologically active RNA structures. For the past four years the major efforts of our team have focused on the structure and function of ri-bozymes derived from hepatitis delta virus.
RNA structure and RNA-metal ion interactions are studied using a variety of chemical and enzymatic probes with special emphasis on limited, metal ion-induced RNA cleavages. A powerful technique, selection-amplification, is used to select for catalytically active vari-ants of delta ribozymes and to search for novel RNA motifs capable of binding selected divalent metal ions.
Recently, we have also commenced the studies aimed at the application of ribozymes and antisense oligonucleotides for site-specific degradation of positive strand RNA viruses. The goal of ongoing studies is to establish the rules which could facilitate designing antisense oligonucleotides, robizymes and small interfering RNAs to target highly structured, non-coding regions of hepatitis C viral RNA.

Current research activities:

application of in vitro selection method to search for catalitically active variants of delta ribozymes ;

determination of the factors that limit the effectiveness of delta ribozyme technology;

search for RNA molecules that specifically bind selected divalent metal ions using the affinity selection-amplification methodology;

elucidation of the role of specific interactions of RNA with divalent metal ions in the delta ribozymes and metal ion-binding aptamers by the bucleotide analog interference mapping (NAIM) approach);

structural characterization of the conserved, untranslated regions of selected, positive strand RNA viruses;

application of the nucleic acids-based strategies for site-specific degradation of viral RNAs.



SELECTED PUBLICATIONS

J. Wrzesiński, M. Łęgiewicz, J. Ciesiołka
Mapping of accessible sites for oligonucleotide hybridization on hepatitis delta virus ribozymes.
Nucleic Acids Res. 28, 1785-1793 (2000).

J. Ciesiołka, J. Wrzesiński, M. Łęgiewicz, B. Smólska, M. Dutkiewicz
Ribozymes of the hepatitis delta virus: Recent findings on their structure, mechanism of catalysis and possible applications.
Acta Biochim. Pol. 48, 409-418 (2001).

J. Wrzesiński, M. Łęgiewicz, B. Smólska, J. Ciesiołka
Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions.
Nucleic Acids Res. 29, 4482-4492 (2001).

M. Jeżowska-Bojczuk, W. Szczepanik, W. Leśniak, J. Ciesiołka, J. Wrzesiński, W. Bal
DNA and RNA damage by Cu(II)-amikacin complex.
Eur. J. Biochem. 269, 5547-5556 (2002).

M. Dutkiewicz, J. Ciesiołka
Strategy of directed RNA degradation and selected examples of its use in antiviral therapy.
Biotechnologia 1(56), 57-70 (2002).

W. Szczepanik, E. Dworniczek, J. Ciesiołka, J. Wrzesiński, J. Skała, M. Jeżowska-Bojczuk
In vitro oxidative activity of cupric complexes of kanamycin A in comparision to in vivo bactericidal efficacy.
Journal of Inorganic Biochem. 94, 355-364 (2003).

W. Szczepanik, J. Ciesiołka, J. Wrzesiński, J. Skała, M. Jeżowska-Bojczuk
Interaction of aminoglycosides and their copper (II) complexes with nucleic acids-implication to the toxicity of these drugs.
Dalton Trans. 8, 1488-1494 (2003).

M. Łęgiewicz, J. Ciesiołka
Hepatitis delta virus (HDV) ribozymes.
Postępy Biochem. 50, 19-31 (2004).

A. Wichłacz, M. Łęgiewicz, J. Ciesiołka
Generating in vitro transcripts with homogenous 3' ends using trans-acting antigenomic delta ribozyme.
Nucleic Acids Res. 32, e39 (2004).

M. Dutkiewicz, J. Ciesiołka
Structural characterization of the highly conserved 98-base sequence at the 3' end of HCV RNA genome and the complementary sequence located at the 5’ end of the replicative viral strand.
Nucleic Acids Res. 33, 693-703 (2005).

L. A. Kirsebom, J. Ciesiołka
Lead (II) – induced cleavage of RNA. In: R. K. Hartmann, A. Bindereif, A. Schön, E. Westhof (eds.).
Handbook of RNA Biochemistry. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, 214-228 (2005).

J. Wrzesiński, J. Ciesiołka
Characterization of structure and metal ions specificity of Co2+-binding RNA aptamers.
Biochemistry, 44, 6257-6268 (2005).

J. Wrzesiński, W. Szczepanik, J. Ciesiołka, M. Jeżowska-Bojczuk
tRNAPhe cleavage by aminoglycosides is triggered off by formation of an abasic site.
Biochem. Biophy. Res. Commun. 331, 267-271 (2005).

M. Łęgiewicz, A.Wichłacz, B. Brzezicha, J. Ciesiołka
Antigenomic delta ribozyme variants with mutations in the catalytic core obtained by the in vitro selection method.
Nucleic Acids Res. 34, 1270-1280 (2006).

J. Wrzesiński, M. Brzezowska, W. Szczepanik, M. Jeżowska-Bojczuk, J. Ciesiołka
Inhibition of the catalytic activity of trans-acting antigenomic d ribozyme by selected antibiotics and their Cu2+ complexes.
Biochem. Biophy. Res. Commun. 349, 1394-1400 (2006).

M. Dutkiewicz, A. Świątkowska, J. Ciesiołka
Structure and function of the non-coding regions of hepatitis C viral RNA.
Postępy Biochem. 52, 62-71 (2006).

A. Świątkowska, M. Dutkiewicz, J. Ciesiołka
Structural features of target RNA molecules greatly modulate the cleavage efficiency of trans-acting delta ribozymes.
Biochemistry, 46, 5523-5533 (2007).