Home
Current Research
Team
Ryszard Kierzek
Ewa Biala
Agata Fratczak
Michal Jenek
Anna Marciniak
Dorota Wojciechowska
Publications
Collaborations
Calculators
Prof. Ryszard Kierzek

rkierzek[at]ibch.poznan.pl

Scientific interest of Ryszard Kierzek

The most important of Ryszard Kierzek projects concerned: (a) chemical synthesis of nucleosides, nucleotides, plus natural and modified oligonucleotides; (b) researches into the thermodynamics of natural and modified RNAs; (c) investigations of nonenzymatic self-cleavage of oligoribonucleotides; (d) studies of various aspects of the structural biology and chemistry of RNA; (e) developing a new type of microarrays (isoenergetic microarrays) and their application to the study of the structure and interactions of RNA; (f) the application of short modified oligonucleotides to the selective cleavage of target pathogenic RNAs with the aim of inhibiting their biological activity.
Some of the most important scientific achievements are presented in details below.

Chemical synthesis of natural and modified oligonucleotides
Ryszard Kierzek has been working on the chemical synthesis of natural and modified nucleosides, nucleotides and oligonucleotides since 1973. The most significant achievements on this subjects are: developing methods for the selective deprotection of 2-cyanoethyl and 2,2,2-trichloroethyl phosphorous protecting groups; contribution to the first chemical synthesis of modified heptanucleotide corresponding to tRNAPhe anticodon loop; contribution in developing methods of the chemical synthesis of DNA oligonucleotides using the block triester approach on solid support (including chemical synthesis of large fragments of interferon and gonadotripin genes); developing methods for the chemical synthesis of oligoribonucleotides with 2'-O-tetrahydropyranyl protecting groups on solid support using the phosphoramidite approach; developing methods for the chemical synthesis of branched RNA and RNA containing additional 2'-O-phosphates; performing chemical synthesis of variously modified oligonucleotides (over 30 different modifications); chemical synthesis of oligonucleotides containing LNA-2,6-diaminopurine riboside and LNA-2-thiouridine.

Thermodynamics of natural and modified RNA
Towards a better understanding of the thermodynamic properties of RNA, Ryszard Kierzek main contributions have been: the determination of the thermodynamic parameters for RNA duplex formation; the determination of the influence of RNA structural motifs (e.g. bulges, internal loops, hairpins, 5'- and 3'-dangling ends, single mismatches, terminal mismatches, noncanonical base pairs (e.g. G-U, G-A)) on the thermodynamics of RNA molecules; evaluation of the influence of over 40 natural and artificially modified nucleotides on the thermodynamic stability of RNA duplexes; determination of the thermodynamic parameters of 2'-O-methylRNA/RNA and chimeric LNA-2'-O-methylRNA/RNA duplex formation.
The thermodynamics of RNA duplex stability and the structural motifs listed above have been parameterized and are almost universally used in the computational prediction of RNA secondary structure (e.g. by such programs as Mfold, RNAstructure, and the Vienna RNA package).

Isoenergetic microarrays, a new method to study the structure and interactions of RNA
The development and application of isoenergetic microarrays was initiated in the RNA Chemistry group around 2004. The motivation behind this project is to apply high throughput methods (microarrays) to the analysis of RNA structure via profiling the probe binding accessibility of a structured RNA. The novelty of this approach is two-fold: firstly, this is the first application of microarray technology to the study of the structure and interactions of RNA; secondly, this is the first use of socalled "isoenergetic" microarrays. The goal in developing isoenergetic microarrays is to make target binding independent of sequence, but highly selective to structure. This was accomplished by incorporating several base (diaminopurine riboside) and backbone (LNA, 2'-O-methyl) modifications into oligonucleotide probes, whose effects are such that the thermodynamic stability of duplex formation is enhanced and as uniform as possible across the probe library. The design of the modified microarray probes was preceded by extensive studies of the thermodynamic stability of 2'-O-methylRNA/RNA and chimeric LNA-2'-O-methylRNA/RNA duplexes. So far, this method of probing of RNA structure by microarray has been successfully applied towards elucidating the secondary structure of five retrotransposon RNAs (ca 330 nucleotides each). Recently, microarray mapping was successfully used to study RNA/protein interactions, to study RNA conformational dynamic and investigate the regulatory function of RNA.

Education
Professorship (2000) Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
Habilitation (1988) (Doctor of Sciences) habilitation thesis, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
Ph.D. degree (1978) Chemistry, A. Mickiewicz University, Department of Chemistry, Poznań, Poland
MS degree (1974) Chemistry, A. Mickiewicz University, Department of Chemistry, Poznań, Poland
Scientific Positions
2000 - present Professor, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, head of the Laboratory of RNA Chemistry
1988 - 2000 Associate Professor, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, head of the Laboratory of RNA Chemistry
1978 - 1988 Research Fellow, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
1974 - 1978 Graduate Student, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań and A. Mickiewicz University, Department of Chemistry, Poznań

International Training (total 98 months)

  • Visiting Professor, Department of Chemistry, University of Rochester, Dr. Douglas H. Turner, total 80 months
  • Research Fellow, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Dr. Marvin H. Caruthers, 6 months
  • Postdoctoral Fellow, Department of Molecular Genetics, Beckman Research Institute of the City of Hope, Duarte, Dr. Keichi Itakura, 12 months



    • Currently supervised scientific projects

  • RNA microarrays as new tools of structural and functional genomic to studies the structure and interactions of native RNA, 15.10.2005–14.10.2008. Supported by Ministry of Sciences and Higher Education.
  • Modified oligonucleotides as allele specific therapeutic and regulators of pathogenic human genes, 21.12.2007-18.12.2010. Supported by Ministry of Sciences and Higher Education.


    • Awards Related to the Scientific Activity

  • Elected as EU representative to the reviewers committee of the Human Frontier Science Program, 2004-2008
  • Fogatry International Research Collaboration Award (FIRCA), National Institutes of Health (NIH), USA, finical support for Polish-American scientific collaboration, 2002-2006
  • Fogatry International Research Collaboration Award (FIRCA), National Institutes of Health (NIH), USA, finical support for Polish-American scientific collaboration, 1998-2002
  • Group award from the president of Polish Academy of Sciences, 1987
  • Group award from the president of Polish Academy of Sciences, 1977


    • List of Supervised Graduate Students
    advisor of completed PhD theses:
    2008 Dr. Karol Pasternak
    2008 Dr. Anna Pasternak
    2005 Dr. Magdalena Broda
    2003 Dr. Elzbieta Kierzek
    1998 Dr. Arkadiusz Bibiłło
    1998 Dr. Krzysztof Ziomek
    Full list of publications, total citations: 4556, Hirsch index: 36
    1 W.Z. Antkowiak, E. Biala, P. Dembek, R. Kierzek, K. Grzeskowiak, A. Kraszewski, M. Wiewiórowski, Further studies on synthesis and properties of the protected triester nucleotides as a new key intermediate for the synthesis of oligoribonucleotides. Nucleic Acids Res., spec. publ. No 1, 133-136 (1975)
    2 R.W. Adamiak, M.Z. Barciszewska, E. Biala, K. Grzeskowiak, R. Kierzek, A. Kraszewski, W.T. Markiewicz, M. Wiewiórowski, Nucleoside 3'-phosphotriesters as key intermediates for the oligonucleotide synthesis. An improved preparation of nucleoside 3'-phosphotriesters, their 1H NMR characterization and new condition for removal of 2-cyanoethyl group. Nucleic Acids Res., 3, 3397-3408 (1976)
    3 R.W. Adamiak, E. Biala, K. Grzeskowiak, R. Kierzek, A. Kraszewski, W.T. Markiewicz, J. Stawinski, M. Wiewiórowski, Nucleoside 3'-phosphotriesters as key intermediates for the oligoribonucleotide synthesis. IV. New method for removal of 2,2,2-trichloroethyl group and 31P NMR as a new tool for analysis of deblocking of internucleotide phosphate protecting groups. Nucleic Acids Res., 4, 2321-2329 (1977)
    4 R.W. Adamiak, E.Biala, K. Grzeskowiak, R. Kierzek, A. Kraszewski, W.T. Markiewicz, J. Okupniak, J. Stawiñski, M. Wiewiórowski, The chemical synthesis of the anticodon loop of an eukaryotic initiator tRNA containing the hypermodified nucleoside N-(N-threonylcarbonyl)-adenosine. Nucleic Acids Res., 5, 1889-1905 (1978)
    5 R.W. Adamiak, E. Biala, K. Grzeskowiak, R. Kierzek, A. Kraszewski, W.T. Markiewicz, J. Stawiñski, M. Wiewiórowski, Studies on polynucleotide synthesis. in: Phosphorus Chemistry directed towards Biology, ed. W.J. Stec, Pergamon Press, Oxford New York, 9-12 (1980)
    6 W.T.Markiewicz, R.W.Adamiak, E.Biala, K.Grzeskowiak, R.Kierzek, A.Kraszewski, J.Stawiñski, M.Wiewiórowski, Further studies on oligoribonucleotide synthesis. Nucleic Acids Res., symp. ser., 7, 115-127 (1980)
    7 R. Kierzek, H. Ito, R. Bhatt, K. Itakura, Selective N-deacylation of N,O-protected nucleosides by zinc bromide. Tetrahedron Lett., 22, 3761-3764 (1981)
    8 J.J. Rossi, R. Kierzek, T. Huang, P.A. Valker, K. Itakura, An alternate method for synthesis of double stranded DNA segments. J. Biol. Chem., 257, 9226-9229 (1982)
    9 J.J. Rossi, R. Kierzek, T. Huang, P.A. Valker, K. Itakura, The role of synthesis of DNA in the preparation of structural genes coding for proteins. „From Gene to Protein: Translation into Biotechnology”, Academic Press Inc., p.213-219 (1982)
    10 A.B. Legocki, A. Konieczny, C. Madrzak, P. Strozycki, A. Wolanski, R. Kierzek Nodule specific induction of host genes in yellow lupin. Structure and function of plant genomes. O. Ciferii and L. Dure III Eds., Plenum Press, New York, London, p. 263-267 (1983)
    11 W.T. Markiewicz, E. Biala, R. Kierzek, Application of the tetraisopropyldisiloxane-1,3-diyl group in the chemical synthesis of oligoribonucleotides. Bull. Acad. Polon. Sci., ser. chim., 32, 433-451 (1984)
    12 R. Kierzek, The synthesis of 5'-O-dimethoxytrityl N-acyl 2'-deoxynucleosides. Improved transient protection approach. Nucleosides and Nucleotides, 5, 641-649 (1985)
    13 R. Kierzek, D.W. Kopp, M. Edmonds, M.H. Caruthers, Chemical synthesis of branched RNA. Nucleic Acids Res., 14, 4751-4764 (1986)
    14 S.M. Freier, R. Kierzek, M.H. Caruthers, T. Neilson, D.H. Turner, Free energy contributions of G:U and other terminal mismatches to helix stability. Biochemistry, 25, 3209-3213 (1986)
    15 S.M. Freier, R. Kierzek, J.A. Jaeger, N. Sugimoto, M.H. Caruthers, T. Neilson, D.H. Turner, Improved free energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA, 83, 9373-9377 (1986)
    16 D.H. Turner, S.M. Freier, N. Sugimoto, D.R. Hickey, J.A. Jaeger, A. Sinclair, D. Alkema, T. Neilson, M.H. Caruthers, R. Kierzek, Improved parameters for prediction of RNA secondary structure and insights into why RNA forms doubles helixes. 3D Structure and dynamics of RNA /P.H. van Knippenberg, C.W. Hilbers, Bosch Eds Plenum New York, p 1-13 (1986)
    17 N. Sugimoto, R. Kierzek, S.M. Freier, D.H. Turner, Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry, 25, 5755-5759 (1986)
    18 S.M. Freier, N. Sugimoto, A. Sinclair, D. Alkema, T. Neilson, R. Kierzek, M.H. Caruthers, D.H. Turner, Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: An empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry, 25, 3214-3219 (1986)
    19 R. Kierzek, M.H. Caruthers, C.E. Longfellow, D. Swinton, D.H. Turner, S.M. Freier, Polymer supported RNA synthesis and its application to test the nearest neighbor model for duplex stability. Biochemistry, 25, 7840-7846 (1986)
    20 M.H. Caruthers, D. Dellinger, K. Prosser, A.D. Barone, J.W. Dubendorff, R. Kierzek, M. Rosendahl, Nucleic acid synthesis and applications to molecular biology. Chemica Scripta, 26, 25-30 (1986)
    21 L.J. McBride, R. Kierzek, S.L. Beaucage, M.H. Caruthers, Amidine protecting groups for oligonucleotide synthesis. J. Am. Chem. Soc., 108, 2040-2048 (1986)
    22 R. Kierzek, M. Rozek, W.T. Markiewicz, Some steric aspects of synthesis of oligoribonucleotides by phosphoramidite approach on solid support. Nucleic Acids Res., symp. ser., 18, 201-205 (1987)
    23 W.T. Markiewicz, R. Kierzek, B. Hernes, A new method of synthesis of 4-N-alkyl substituted cytosine derivatives via 4-N-arylsulfonyl or alkylsulfonyl intermediates. Nucleosides and Nucleotides, 6, 269-273 (1987)
    24 R. Kierzek, W.T. Markiewicz, Synthesis of 5'-0-dimethoxytrityl 4-N-(6 trifluoro-acetamidohexyl)-2'-deoxycytidine and its application in the synthesis of biotin labelled oligonucleotides. Nucleosides and Nucleotides, 6, 463-466 (1987)
    25 R. Kierzek, W.T. Markiewicz, B. Imiolczyk, Synthesis of 2'-5-oligonucleotides on solid support by phosphoramidite method. "Biophosphates and their Analogues Synthesis, Structure, Metabolism and Activity", eds. K.S. Bruzik, W.J. Stec, Elsevier Sci. Publ., 179-184 (1987)
    26 D.H. Turner, N. Sugimoto, R. Kierzek, S.D. Dreiker, Free energy increments for hydrogen bonds in nucleic acid base pairs. J. Am. Chem. Soc., 109, 3783-3785 (1987)
    27 N. Sugimoto, R. Kierzek, D.H. Turner, Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry, 26, 4554-4559 (1987)
    28 N. Sugimoto, R. Kierzek, D.H. Turner, Sequence dependence for the energetics of terminal mismatches in ribooligonucleotides. Biochemistry, 26, 4559-4562 (1987)
    29 D.H. Turner, N. Sugimoto, J.A. Jaeger, C.E. Longfellow, S.M. Freier, R. Kierzek, Improved parameters for prediction of RNA structure. Cold Spring Harbor Symposia on Quantitative Biology, vol. LII, 123-133 (1987)
    30 M.H. Caruthers, R. Kierzek, J.Y. Tang, Synthesis of oligonucleotides using the phosphoramidite method. "Biophosphates and their Analogues Synthesis, Structure, Metabolism and Activity", eds. K.S. Bruzik, W.J. Stec, Elsevier Sci. Publ., 3-21 (1987)
    31 R. Kierzek, M. Rozek, W.T. Markiewicz, Some steric aspect of synthesis of oligoribonucleotides by phosphoramidite approach on a solid support. Bull. Pol. Ac.:Chem, 35, 508-517 (1987)
    32 D.H. Turner, N. Sugimoto, S.D. Dreiker, S.M. Freier, R. Kierzek, Hydrogen bonding and stacking contributions to nucleic acid stability. Proteins to Ribosomes, Adenine Press p. 249-259 (1988)
    33 N. Sugimoto, R. Kierzek, D.H. Turner, Kinetics for reaction of a circularized intervening sequence with CU, UCU, CUCU, and CUCUCU: mechanistic implications from the dependence on temperature, and on oligomer and Mg+2 concentrations. Biochemistry, 27, 6384-6392 (1988)
    34 N. Sugimoto, M. Tomka, R. Kierzek, P. Bevilacqua, D.H. Turner, Effects of substrate structure on the kinetics of circle opening reactions of the self splicing intervening sequence from Tetrahymena thermophila: evidence for substrate and Mg+2 binding interactions. Nucleic Acids Res., 17, 355-371 (1989)
    35 A.P. Williams, C.E. Longfellow, S.M. Freier, R. Kierzek, D.H. Turner, Laser temperature jump, spectroscopic and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry, 28, 4283-4291 (1989)
    36 N. Sugimoto, N. Sasaki, R. Kierzek , D.H. Turner, Binding of a fluorescent oligonucleotide to a circularized intervening sequence from Tetrahymena thermophila. Chem. Lett., 2223-2226 (1989)
    37 M. Welnicki, J. Skrzeczkowski, A. Soltynska, P. Jonczyk, W.T. Markiewicz, R. Kierzek, B. Imiolczyk, W. Zagórski, Characterization of synthetic DNA probe detecting potato spindle tuber virioid. J. Virological Methods, 24, 141-152 (1989)
    38 R .Kierzek, W.T. Markiewicz, A general method of synthesis of 5'-O-dimethoxytrityl-3'-O-tetrahydropyranyl-N-acylribonucleosides. Bull. Pol. Ac.:Chem., 38, 33-40 (1990)
    39 C.E. Longfellow, R. Kierzek , D.H. Turner, Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry, 29, 278-285 (1990)
    40 J. SantaLucia Jr., R. Kierzek, D.H. Turner, Effects of G A mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry, 29, 8813-8819 (1990)
    41 J.D. Reilly, S.K. Freeman, R.F. Melhan, R. Kierzek, M.H. Caruthers, M. Edmonds T.W. Munns, Antibodies specific for branched oligoribonucleotides. Anal. Biochem., 185, 125-130 (1990)
    42 N. Sugimoto, M. Sasaki, R. Kierzek , D.H. Turner, Inhibition of deoxyribo-oligonucleotides on the circle opening of the intervening sequence from Tetrahymena thermophila. Chem. Lett., 747-748 (1990)
    43 J. SantaLucia Jr., R. Kierzek , D.H. Turner, Functional group substitutions as probes of hydrogen bonding between G A mismatches in RNA internal loops. J. Am. Chem. Soc., 113, 4313-4322 (1991)
    44 A. Peritz, R. Kierzek, N. Sugimoto, D.H. Turner, Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops. Biochemistry, 30, 6428-6436 (1991)
    45 J. SantaLucia Jr., R. Kierzek, D.H. Turner, Stabilities of consecutive A-C, C-C, G-G, U-C and UU mismatches in RNA internal loops: evidence for stable hydrogen bonded U-U and C-C+ pairs. Biochemistry, 30, 8242-8251 (1991)
    46 L. He, R. Kierzek, J. SantaLucia Jr., A.E. Walter, D.H. Turner, Nearest neighbor parameters for G U mismatches: 5'GU 3'/3'UG 5' is destabilizing in the contexts CGUG/GUGC, UGUA/AUGU and AGUU/UUGA but stabilizing in GGUC/CUGG. Biochemistry, 30, 11124-11132 (1991)
    47 R. Kierzek, W.T. Markiewicz, The synthesis of 5'-O-triphosphate-4-N-(omega- aminoalkyl)deoxycytidine, a useful precursor to the generation of different labeled triphosphates. Nucleosides and Nucleotides, 10, 1257-1275 (1991)
    48 J. SantaLucia Jr., R. Kierzek, D.H. Turner, Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science, 256, 217-219 (1992)
    49 R. Kierzek, L. He, D.H. Turner, Association of 2'-5' oligoribonucleotides. Nucleic Acids Res., 20, 1685-1690 (1992)
    50 R. Kierzek, Nonenzymatic hydrolysis of oligoribonucleotides. Nucleic Acids Res., 20, 5079-5084 (1992)
    51 R. Kierzek, Hydrolysis of oligoribonucleotides: influence of sequence and length. Nucleic Acids Res., 20, 5073-5077 (1992)
    52 P.C. Bevilacqua, R. Kierzek, K.A. Johnson, D.H. Turner, Dynamics of ribozyme binding of substrate revealed by fluorescence detected stopped flow. Science, 258, 1355-1358 (1992)
    53 R. Kierzek, Y. Li, D.H. Turner, P.C. Bevilacqua, 5'-Amino pyrene provides a sensitive, non perturbing fluorescent probe of RNA secondary and tertiary structure formation. J. Am. Chem. Soc., 115, 4985-4992 (1993)
    54 S. Moran, R. Kierzek, D.H. Turner, Binding of guanosine and 3'-splice site analogues to a group I ribozyme: interactions with functional groups of guanosine and additional nucleotides. Biochemistry, 32, 5247-5257 (1993)
    55 M. Culver, S.M. McCraith, M. Zillmann, R. Kierzek, N. Michaud. R.D. LaReau. D.H. Turner , E.M. Phizicky, A novel NAD derivative produced during transfer RNA splicing: ADP-ribose 1''-2'' cyclic phosphate. Science, 261, 266-208 (1993)
    56 R. Kierzek, The stability of trisubstituted internucleotide bond in the presence of vicinal 2'-hydroxyl. Chemical synthesis of the uridyl-(2'-phosphate)-3'-5'-uridine. Nucleotides and Nucleosides, 13, 1757-1768 (1994)
    57 R. Kierzek, Wlasciwosci katalityczne kwasów rybonukleinowych (RNA) (The catalytic properties of ribonucleic acids) „Nowe tendencje w biologii molekularnej i inzynierii genetycznej” (The new trends, in molecular biology and genetic engineering), (J. Barciszewski, K. Lastowski, T. Twardowski, Editors), Sorus, Poznañ, p. 137-185 (1996)
    58 R. Kierzek, The effect of support and mobile phase on diastereoisomers separation of monophosphate of DNA and RNA oligomers by high performance liquid chromatography. Collect. Czech. Chem. Commun., 61, 161-163 (1996)
    59 R. Kierzek, Nonenzymatic hydrolysis of oligoribonucleotides III. Stereochemistry and influence of chimeric DNA/RNA on nonenzymatic hydrolysis of oligoribonucleotides. Collect. Czech. Chem. Commun., 61, 253-257 (1996)
    60 L. Profenno, R. Kierzek, S. Testa, D. Turner, Guanosine binds to the tetrahymena ribozyme in more than one step, and its 2’-OH and the nonbridging pro-Sp-phsphoryl oxygen at the cleavage site are required for productive docking. Biochemistry, 36, 12477-12485 (1997)
    61 T. Xia, J. SantaLucia, M.E. Burkard, R. Kierzek, S.J. Schroeder, C. Cox and D.H. Turner, Parameters for expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pair. Biochemistry, 37, 14719-14735 (1998)
    62 R. Kierzek, Właściwości termodynamiczne kwasów rybonukleinowych., „Na pograniczu chemii i biologii”, H. Koroniak, J. Barciszewski, W.T. Markiewicz, K. Ziemnicki (eds), Wydawnictwo Naukowe UAM, p. 369-416 (1998)
    63 S.L. Spinelli, R. Kierzek. D.H. Turner, E.M. Phizicky, Transient ADP-ribosylation of a 2’-phosphate implicated in its removal from ligated tRNA during splicing in yeast. J. Biol. Chem., 274, 2637-2644 (1999)
    64 A. Bibiłło, K. Ziomek, M. Figlerowicz, R. Kierzek, Nonenzymatic hydrolysis of oligoribonucleotides V. The elements affecting the process of self-hydrolysis. Acta Biochemica Polonica, 46, 145-153 (1999)
    65 A. Bibiłło, M. Figlerowicz, R. Kierzek, The nonenzymatic hydrolysis of oligoribonucleotides VI. The role of biogenic polyamines. Nucleic Acids Res., 27, 3931-3937 (1999)
    66 M.E. Burkard, R. Kierzek, D.H. Turner, Thermodynamics of unpaired terminal nucleotides on short RNA helixes corralates with stacking at helix termini in larger RNAs. J. Mol. Biol., 290, 967-982 (1999)
    67 R. Kierzek, M.E. Burkard, D.H. Turner, The thermodynamics of single mismatches in RNA duplxes. Biochemistry, 38, 14214-14223 (1999)
    68 S.M. Testa, M.D. Disney, D.H. Turner, R. Kierzek, Thermodynamics of RNA-RNA duplexes with 2- and 4-thiouridenes: implications for antisense design and targeting a group intron. Biochemistry, 38, 16655-16662 (1999)
    69 K. Ziomek, R. Kierzek, Przewidywanie struktur drugorzędowych kwasów rybonukleinowych (RNA) metodą termodynamiczną. Postępy Biochemii, 45, 74-80 (1999)
    70 K. Ziomek, R. Kierzek, Drugorzędowe motywy strukturalne RNA. Postępy Biochemii, 45, 80-87 (1999)
    71 R. Kierzek, M.A. Steiger, S.L. Spinelli, D.H. Turner, E.M. Phizicky, The chemical synthesis of oligoribonucleotides with selectively placed 2’-O-phosphates. Nucleosides, Nucleotides & Nucleic Acids, 19, 917-933 (2000)
    72 A. Bibiłło, M. Figlerowicz, K. Ziomek, R. Kierzek, The nonenzymatic hydrolysis of oligoribonucleotides VII. Structural elements affecting hydrolysis. Nucleosides, Nucleotides & Nucleic Acids, 19, 977-994 (2000)
    73 X. Chen, J. A. McDowell, R. Kierzek, T. R. Krugh, and D. H. Turner, Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G•U pairs: one hydrogen bond for each G•U pair in r(GGCGUGCC)2 and two for each G•U pair in r(GAGUGCUC)2. Biochemistry, 39, 8970-8982 (2000)
    74 X. Chen, R. Kierzek and D. H. Turner, Stability and Structure of RNA Duplexes containing isoguanosine and isocytidine. J. Am. Chem. Soc., 123, 1267-1274 (2001)
    75 E. Kierzek, R. Kierzek, Influence of N6-isopentenyladenosine (i6A) on thermal stability of RNA duplexes. Biophysical Chemistry, 91, 135-140 (2001)
    76 R. Kierzek, Nonenzymatic cleavage of oligoribonucleotides. Methods in Enzymology, vol. 341A, p. 657-675, Ed. A.W. Nicholson, Academic Press, San Diego, London, Boston, New York, Sydney, Tokyo, Toronto (2001)
    77 M. Alejska, A. Kurzyńska-Kokorniak, M. Broda, R. Kierzek and M. Figlarowicz, How RNA viruses exchange their genetic material. Acta Biochemica Polonica, 48, 391-407 (2001)
    78 E. Kierzek, E. Biała and R. Kierzek, Elements of thermodynamics in RNA evolution. Acta Biochemica Polonica, 48, 485-493 (2001)
    79 M. A. Steiger, R. Kierzek, D. H. Turner and E. M. Phizicky, Substrate Recognition by a Yeast 2'-Phosphotransferase Involved in tRNA Splicing and by Its Escherichia coli Homolog. Biochemistry, 40, 14098-14105 (2001)
    80 K. Ziomek, E. Kierzek, E. Biała and R. Kierzek, The thermal stability of RNA duplexes containing modified base pairs placed at internal and terminal positions of the oligoribonucleotides. Biophysical Chemistry, 97, 233-241 (2002)
    81 K. Ziomek, E. Kierzek, E. Biała and R. Kierzek, The influence of various modified nucleotides placed as 3’-dangling end on thermal stability of RNA duplexes. Biophysical Chemistry, 97, 243-249 (2002)
    82 D.E. Proctor, E. Kierzek, R. Kierzek and P.C. Bevilacqua, Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine. J. Am. Chem. Soc., 125, 2390-2391 (2003)
    83 E. Kierzek and R. Kierzek, The synthesis of oligoribonucleotides containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines via post-synthetic modifications of precursor oligomers. Nucleic Acids Research, 31, 4461-4471 (2003)
    84 E. Kierzek and R. Kierzek, The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines. Nucleic Acids Research, 31, 4472-4480 (2003)
    85 E. Kierzek, R. Kierzek, The synthesis of oligoribonucleotides containing N6 alkyladenosines and 2-methylthio-N6-alkyladenosines. Current Protocols in Nucleic Acids Chemistry, 4.23.1-4.23.21 John Wiley & Sons, Inc (2004)
    86 R.Kierzek, Structural considerations for the spontaneous cleavage of RNA. Procceding in Nucleic Acids and Molecular Biology, Vol. 13, p. 33-48, Artificial nucleases, M.A. Zenkova (Ed.), Springer-Verlag, Berlin Heidelberg (2004)
    87 D J. Proctor, H. Ma, E. Kierzek, R. Kierzek, M. Gruebele, and P. C. Bevilacqua, Folding Thermodynamics and Kinetics of YNMG RNA Hairpins: Specific Incorporation of 8-Bromoguanosine Leads to Stabilization by Enhancement of the Folding Rate. Biochemistry, 43, 14004-14014 (2004)
    88 M. Lewdorowicz, Y. Yoffe, J. Zuberek, J. Jemielity, J. Stepinski, R. Kierzek, R. Stolarski, M. Shapira and E. Darzynkiewicz. Chemical synthesis and binding activity of trypanosomatid cap-4 structure. RNA, 10, 1469-1478 (2004)
    89 M. Broda, R. Kierzek, Mutacje dynamiczne trójnukleotydowych powtórzeń DNA w genomie człowieka oraz ich związek z chorobami neurologicznymi. redaktorzy H. Koroniak i J. Barciszewski (eds), „Na pograniczu biologii i chemii”, Wydawnictwo Naukowe UAM, p 51-95 (2004)
    90 E. Kierzek, A. Ciesielska, K. Pasternak, D.H. Mathews, D.H. Turner and R. Kierzek, The influence of locked nucleic acid residues on thermodynamic properties of 2’-O-methyl RNA/RNA hetroduplexes. Nucleic Acids Research, 33, 5082-5093 (2005)
    91 M. Broda, E. Kierzek, Z. Gdaniec, T. Kulinski and R. Kierzek, Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure. Biochemistry, 44, 10873-10882 (2005)
    92 M. Lewdorowicz, J. Jemielity, R. Kierzek, M. Shapira, J. Stepinski, R. Stolarski, and E. Darzynkiewicz, Solid-support synthesis of 5’ mRNA CAP-4 from trypanosomatides. Collection symposium Series, 7, 433-435 (2005)
    93 E. Kierzek, R. Kierzek, D. H. Turner and I. E. Catrina, Facilitating RNA Structure Prediction with Microarrays. Biochemistry, 45, 581-593 (2006)
    94 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)
    95 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, 3609-3614 (2006)
    96 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)
    97 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 thethermodynamic properties of 2’-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Research, 35, 4055-4063, (2007)
    98 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)
    99 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, 26, 1329-133 (2007)
    100 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, 26, 1339-1348 (2007)
    101 E. Kierzek, A. Frątczak, A. Pasternak, D. H. Turner and R. Kierzek, Isoenergetic RNA microarrays, a new method to study the structure and interactions of RNA. 2nd European Conference on Chemistry for Life Sciences, Wroclaw, Medimond, International Proceedings Division, p. 25-30, Bologna, Italy (2007)
    102 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, 47,1249-1258 (2008)
    103 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, 36, 1770-1782 (2008)
    104 A. Pasternak, R. Kierzek, Modyfikowane nukleotydy jako narzędzia molekularne sluzace do kontrolowanej zmiany właściwości fizykochemicznych RNA. Na pograniczu chemii i biologii, tom XVII, p. 41-87, Wydawnictwo UAM (2008)
    105 K. Kubiak, J. Kazmierczak-Baranska, E. Sochacka, R. Kierzek, M. Janicka, K.Brzuska and B. Nawrot, Modulation of silencing activity of siRNAs by chemical modifications. Collection symposium series, 70, 264-267 (2008)
    106 A. Pasternak, R. Kierzek, Z. Gdaniec and M. Gdaniec, A locked derivative of 8-aza-7-deazaadenosine. Acta Crystalographica, C64, 467-470 (2008)