Department of Structural Chemistry and Biology of Nucleic Acids


 

Head:
Prof. Ryszard Kierzek

 

 


Staff:

Dr. Dorota Magner,

Dr. Marta Soszyńska-Jóźwiak,

Dr. Joanna Sarzyńska,

Grażyna Dominiak MSc


 

PhD Students:

Marta Szabat MSc,

Tomasz Czapik MSc

 


 
 

 
Fig. 1.

 

 
Fig. 2


Links: 

 

  

 Calculators of thermodynamic parameters.

 

 

Affiliated Laboratory

Biomolecular NMR

 

Key words:

structure, dynamic and function of nucleic acids, modified oligonucleotides, thermodynamics of nucleic acids, posttranscriptional RNA folding, antisense oligonucleotides, alternative splicing, oligonucleotide microarrays, microarray mapping, conformational fixed nucleic acids, retroviral RNA, retrotransposons, RNA therapeutics, chemistry and molecular biology of RNA, structural bioinformatics, nucleic acids structure calculation, trinucleotide repeats, RNA bulged duplexes, restricted conformation of modified purine nucleosides

 

Scientific profile:

The outlines of research group are best described by its name Department of Structural Chemistry and Biology of Nucleic Acids. We are interested in investigations of structural chemistry and biology of RNAs based on experiences in chemical synthesis of oligonucleotides, studies of structure and interactions of RNAs, as well as research of nucleic acids thermodynamics. Compilation of those approaches is applied to influence the structure and functional activities of RNAs, including pathogenic RNAs related with human diseases. In the performed studies, RNA is a tool as well as target of therapeutic treatment. The chemical syntheses of oligonucleotides mostly concern incorporation into oligomer structurally and functionally defined nucleotides residues. The best example of that modified oligonucleotides are oligomers with syn or C3'-endo fixed nucleotide residues.

RNA structure related studies focus on two issues. First, it is determination of the secondary structure and interactions of RNA. A new method for determination of RNA secondary structure based on isoenergetic microarrays was developed. Microarrays mapping was successfully used to solve secondary structures of many RNAs as well as RNA/protein and RNA1/protein/RNA2 complexes. The second category of investigations is based on application of modified oligonucleotides with conformationally restricted (syn and C3'-endo) nucleotide residues to study hydrogen bonding, stacking and electrostatic interactions within RNA. The thermodynamic studies were mostly focused on developing thermodynamic rules of binding the modified oligonucleotides probes of isoenergetic microarrays to target RNAs.

In particular, the research focused on the influence of locked nucleic acids (LNA) on thermodynamic stabilities of RNA/LNA-2'-O-methyl-RNA duplexes. It was important to evaluate the influence of LNA residues on thermodynamic stability of complementary and mismatched LNA-2'-O-methyl-RNA/RNA duplexes with LNA residues placed at various positions within the duplex. Based on thermodynamic data, the nearest neighbor thermodynamic parameters of 2'-O-methylRNA/RNA and LNA-2'-O-methylRNA/RNA duplexes formations were determined and applied to prepare the calculators available on this website.

Recently, we are also very much involve on developing a new methods of the allele-selective degradation of pathogenic RNA. Both methods are based on different thermodynamic hybridization of antisense oligonucleotides with mutated and wild type forms of target RNA. First of the new methods is based on simultaneous application of two antisense oligonucleotides. One on them binds to mutated form of RNA and induce it degradation whereas second oligonucleotide preferentially bind to wild type RNA and inhibit it degradation. Second method is based on ability of RNase H cleavage of RNA caring different structural motifs within antisense oligonucleotide/target RNA duplex. Structural motifs form by the same antisense oligonucleotide with mutated RNA result in cleavage whereas structural motif created due to interaction with wild type RNA diminish or inhibit of RNA degradation.

 

Current research activity

  • Based on in vitro and cell lines approaches, the studies of allele-specific degradation of pathogenic RNA with antisense oligonucleotides forming non-helical motifs with target RNA,
  • Based on in vitro and cell lines approaches, the studies of allele-specific degradation of pathogenic RNA with tandem antisense oligonucleotides,
  • Based on in vitro and cell lines approaches, the studies modulation of RNA alternative splicing,
  • Studies of structure and thermodynamics of RNA multinucleotide repeats,
  • Studies of structure and functions of RNAs with conformational fixed nucleic acids,
  • Development of new methods to obtain through-space distances within RNAs
  • Structure of RNA fragments composed of CGG, AGG and UGG trinucleotide repeats,
  • Conformational studies of bulged RNA duplexes,
  • Structural characterization of LNA-2'-O-MeRNA/RNA and 2'-O-MeRNA/RNA duplexes,
  • Posttranscriptional RNA folding.

 

Most important research achievements:

  • Determination of the nearest neighbor thermodynamic parameters of RNA/RNA duplex. It was a result of the collaboration with Douglas Tuner (Department of Chemistry, University of Rochester, USA) started in 1985. All computer programs for the prediction of RNAs folding are based on those thermodynamic parameters,
  • Determination of the influence of various structural motifs of RNA such as: internal and bulge loops, hairpins, various single and multiple mismatches, terminal dangling ends on the thermodynamic stabilities of RNA double stranded regions,
  • Determination of the contribution of hydrogen bonding, stacking and electrostatic interactions on RNA/RNA, 2'-O-methyl-RNA/RNA and chimeric LNA-2'-O-methyl-RNA/RNA duplexes formation and stabilities,
  • Determination of the nearest neighbor thermodynamic parameters of 2'-O-methylRNA/RNA and chimerc LNA-2'-O-methyl-RNA/RNA duplexes formations,
  • Developing a new method for determination of RNAs secondary structure using microarrays. This method, called microarrays mapping, is based on application of isoenergetic microarrays. The thermodynamic foundations of isoenergetic microarrays were developed in our group based on broad studies of the thermodynamic stability of 2'-O-methyl-RNA/RNA and chimeric LNA-2'-O-methyl-RNA/RNA duplexes,
  • Determination of the secondary structure of several 5' regions of R2 retrotransposon RNAs (ca. 330 nucleotides long each) and small non-coding RNAs (DsrA RNA and OxyS RNA) and their complexes with Hfq protein using the developed microarrays mapping method,
  • Discovery of nonenzymatic self-cleavage of oligoribonucleotides, determination of structural elements affecting self-cleavage of some single stranded RNA,
  • Studies of the influence of various modified nucleotides on thermodynamic stability, the structure and interactions of several RNA structural motifs,
  • Application of oligonucleotides containing conformationally restricted nucleotides on the structure, interactions and biological activities of RNAs,
  • Developing of the new protective groups in oligoribonucleotide synthesis, first total synthesis of tRNA anticodon loop and arm heptanucleotide containing hypermodified nucleoside t6A,
  • First solid-phase synthesis of RNA fragments containing modified nucleoside,
  • Determining solution and crystal structures of non-canonical RNAs,

 

Current research projects:

Conformationally restricted oligonucleotides. Studies of the structure and structural determinants interactions of RNAs. UMO-2013/08/A/ST5/00295, 28 August 2013 -27 August 2018 r, NCN Maestro project.

 

Selected publications:

1/ I. Yildirim, S.D. Kennedy, H.A. Stern, J.M. Hart, R. Kierzek and D.H. Turner
Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.
Journal of Chemical Theory and Computation, 8, 172-181 (2012)

2/ A. Kiliszek, R. Kierzek, W.J. Krzyzosiak, W. Rypniewski
Crystallographic characterization of CCG repeats.
Nucleic Acids Research, 40, 8155-8162, (2012)

3/ W.N. Moss, L.I. Dela-Moss, E. Kierzek, R. Kierzek, S.F. Priore, D.H. Turner
The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin.
Plos One, 7, e38323, (2012)

4/ S.D. Kennedy, R. Kierzek, D.H. Turner
Novel Conformation o fan RNA structural switch.
Biochemistry, 51, 9257-9259 (2012)

5/ Y. Zhou, E. Kierzek, Z.P. Loo, M. Antonio, Y.H. Yau, Y.W. Chuah, S. Geifman-Shochat, R. Kierzek and G. Chen
Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides
Nucleic Acids Research, 41, 6664-6673 (2013)

6/ S.F. Priore, E. Kierzek, R.Kierzek, J.R. Baman; W.N. Moss; L.I. Dela-Moss, D.H. Turner
Secondary Structure of a Conserved Domain in the Intron of Influenza A NS1 mRNA
PloS One, 8, e70615 (2013)

7/ E. Kierzek, M. Malgowska, J. Lisowiec, D.H. Turner, Z. Gdaniec and R. Kierzek
The contribution of pseudouridine to stabilities and structure of RNAs.
Nucleic Acids Research, 42, 3492-3501 (2014)

8/ D.E. Condon, I. Yildirim, S.D. Kennedy, B.C. Mort, R. Kierzek and D. H. Turner
Optimization of an AMBER Force Field for the Artificial Nucleic Acid, LNA, and Benchmarking with NMR of L(CAAU).
J. Physical Chemistry B, 118, 1216-1228 (2014)

9/P. Sripakdeevong, M. Cevec, A.T. Chang, M.C. Erat, M. Ziegeler, Q. Zhao, G.E Fox, X. Gao, S.D. Kennedy, R. Kierzek, E.P. Nikonowicz, H. Schwalbe, R.K. O’Sigel, D.H. Turner and R. Das
Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts.
Nature Methods, 11, 413-416 (2014)

10/ M. Malgowska, D. Gudanis, R. Kierzek, E. Wyszko, V. Gabelica, Z. Gdaniec
Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats.
Nucleic Acids Research, 42, 10196-10207 (2014)

11/ I. Yildirim, E. Kierzek, R. Kierzek, G. Schatz
Interplay of LNA and 2ʹ-O-Methyl RNA in the Structure and Thermodynamics of RNA Hybrid Systems: A Molecular Dynamics Study using the Revised AMBER Force Field and Comparison with Experimental Results.
J. Physical Chemistry B, 118, 14177-14187 (2014)

12/ R. Kierzek, D.H. Turner, E. Kierzek
Microarrays for identifying binding sites and probing structure of RNAs.
Nucleic Acids Research, 43, 1-12 (2015)

13/ J. Lisowiec, D. Magner, E. Kierzek, E. Lenatrowicz, R. Kierzek
Structural determinants for alternative splicing regulation of the MAPT pre-mRNA.
RNA Biology, 12, 330-342 (2015)

14/ D. Condon, S. Kennedy, B. Mort, R. Kierzek, I. Yildirim, D.H. Turner
Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.
Journal of Chemical Theory and Computation, 11, 2729-27-42 (2015)

15/ D. Magner, E. Biala, J. Lisowiec-Wachnicka, E. Kierzek, R. Kierzek,
A Tandem Oligonucleotide Approach for SNP-Selective RNA Degradation Using Modified Antisense Oligonucleotides
PloS One, 10, e0142139 (2015)

16/ M. Szabat; T. Pedzinski, T. Czapik, E. Kierzek, R. Kierzek,
Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2'-O-Methyl RNA and RNA Oligonucleotides
PloS One, 10, e0143354 (2015)

17/ E. Lenartowicz, J. Kesy, A. Ruszkowska, M. Soszynska-Jozwiak, P. Michalak, W.N. Moss, D.H. Turner, R. Kierzek, E. Kierzek,
Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus
PloS One, 11, e0148281 (2016)

18/ W. Kotkowiak, A. Pasternak, R. Kierzek,
Studies on Transcriptional Incorporation of 5'-N-Triphosphates of 5'-Amino-5'-Deoxyribonucleosides
PloS One, 11, e0148282 (2016)

19/ M. Szabat, D. Gudanis, W. Kotkowiak, Z. Gdaniec, R. Kierzek, A. Pasternak,
Thermodynamic Features of Structural Motifs Formed by beta-L-RNA
PloS One, 11, e0149478 (2016)

20/ D. Gudanis, L. Popenda, K. Szpotkowski, R. Kierzek, Z. Gdaniec,
Structural characterization of a dimer of RNA duplexes composed of 8-bromoguanosine modified CGG trinucleotide repeats: a novel architecture of RNA quadruplexes.
Nucleic Acids Research, 44, 2409-2416 (2016)

21/ E. Lenartowicz, A. Nogales, E. Kierzek, R. Kierzek, L. Martinez-Sobrido, D.H. Turner,
Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication
Nucleic Acids Therapeutics, 26, 277-285 (2016)

22/ A. Ruszkowska, E. Lenartowicz, W.N. Moss, R. Kierzek, E. Kierzek,
Secondary structure model of the naked segment 7 influenza A virus genomic RNA.
Biochemical Journal, 473, 4327-4348 (2016)