Publications

 

2021
2020
2019
2018
- Press release from the University of Bern in English
2016
  • Gebetsberger,  J., Wyss, L., Mleczko,  A.M., Reuther,  J., and Polacek,  N. (2016). A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress. RNA Biol., doi.org/10.1080/15476286.2016.1257470
  • Luidalepp H., Berger S., Joss O., Tenson T. and Polacek N. (2016). Ribosome Shut-Down by 16S rRNA Fragmentation in Stationary-Phase Escherichia coli. J Mol Biol. 2016 Apr 8. pii: S0022-2836(16)30048-1.
2015
2014
2013
2012
  • Gebetsberger, J., Zywicki, M., Künzi, A. and Polacek N. (2012). tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA in Haloferax volcanii. Archea doi:10.1155/2012/260909
  • Erlacher, M. and Polacek, N. (2012). Probing functions of the ribosomal peptidyl transferase center by nucleotide analog interference. Methods Mol. Biol. 848:215-226
  • Graber, D., Trappl, K., Steger, J., Geiermann A.S., Rigger, L., Moroder H., Polacek, N. and Micura, R.(2012). Deoxyribozyme-based, semisynthetic access to stable peptidyl-tRNAs exemplified by tRNA(Val) carrying a macrolide antibiotic resistance peptide. Methods Mol. Biol. 848:201-213.
  • Zywicki, M., Bakowska-Zywicka, K. and  Polacek, N. (2012). Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res.: doi:10.1093/nar/gks020
2011
  • Geiermann, A.-S., Polacek, N. and Micura R. (2011). Native chemical ligation of hydrolysis-resistant 3’-peptidyl-tRNA mimics. J. Am. Chem. Soc. 133:19068-19071.
  • Erlacher, M., Chirkova, A., Voegele, P. and Polacek, N. (2011). Generation of chemically engineered ribosomes for atomic mutagenesis studies on protein biosynthesis. Nature Prot., 6:580-592.
  • Polacek, N. (2011). The ribosome meets synthetic biology. ChemBioChem 19: 2122-2124.
  • Trappl, K., and Polacek, N. (2011). The ribosome: A molecular machine powered by RNA. In: Metal Ions Life Sci. 9 (Structural and Catalytic Roles of Metal Ions in RNA):253-275.
2010
  • Graber, D., Moroder, H., Steger, J., Trappl, K., Polacek, N. and Micura, R. (2010). Reliable semi-synthesis of hydrolysis-resistant 3’-peptidyl-tRNA conjugates containing genuine tRNA modifications. Nucleic Acids Res., 38:6796-6802.
  • Clementi, N., Chirkova, A., Puffer, B., Micura, R. and Polacek, N. (2010). Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation. Nature Chem. Biol., 6:344-351.
  • Chirkova, A., Erlacher, M., Clementi, N., Zywicki, M., Aigner, M., and Polacek, N. (2010). The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center. Nucleic Acids Res., 38:4844-4855.
  • Clementi, N., and Polacek, N. (2010). Ribosome-associated GTPases: The role of RNA for GTPase activation. RNA Biol., 7:521-527.
  • Chirkova, A., Erlacher, M., Micura, R, and Polacek, N. (2010). Chemically engineered ribosomes: a new frontier in synthetic biology. Curr. Org. Chem., 14:148-161.
2009
  1. Hutzinger, R., Feederle, R., Mrazek, J., Schiefermeier, N., Balwierz, P.J., Zavolan, M., Polacek, N., Delecluse H.-J., and Hüttenhofer, A. (2009). Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathogens, 5:e1000547.
  2. Nandy, C., Mrazek, J., Stoiber, H., Grässer, F.A., Hüttenhofer, A., and Polacek, N. (2009). Epstein-Barr virus-induced expression of a novel human vault RNA. J. Mol. Biol., 388:776-784.
  3. Moroder, H., Steger, J., Graber, D., Fauster, K., Trappl, K., Marquez, V., Polacek, N., Wilson, D. W., and Micura, R. (2009). Non-hydrolyzable RNA-peptide conjugates: a powerful advance in the synthesis of mimics for 3'-peptidyl tRNA termini. Angew. Chem., 48:4056-4060.
  4. Rieder, U., Lang, K., Kreutz, C., Polacek, N., and Micura, R. (2009). Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers. ChemBioChem., 10:1141-1144.
  5. Erlacher, M. D., and Polacek, N. (2009). Role of RNA backbone groups for ribosomal catalysis. Biotechnologia, 1 (84):65-80.
2008
  • Lang, K., Erlacher, M. D., Wilson, D. N., Micura, R., and Polacek, N. (2008). The role of 23S ribosomal RNA residue A2451 in peptide bond formation revealed by atomic mutagenesis. Chem Biol, 15:485-492.
  • Erlacher, M. D., and Polacek, N. (2008). Ribosomal catalysis: The evolution of mechanistic concepts for peptide bond formation and peptidyl-tRNA hydrolysis. RNA Biol., 5:5-12.
  • Mankin, A.S., and Polacek, N. (2008). SPARK – A new peptidyl transferase activity assay. In: Champney S. eds. New Antibiotic Targets. Totowa, NJ: Humana Press Inc., Methods in Molecular Medicine 142:107-116.
2007
  • Amort, M., Wotzel, B., Bakowska-Zywicka, K., Erlacher, M. D., Micura, R., and Polacek, N. (2007). An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination. Nucleic Acids Res., 35:5130-5140.
  • Mrazek, J., Kreutmayer, S. B., Grässer, F. A., Polacek, N., and Hüttenhofer, A. (2007). Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV infected human B cells. Nucleic Acids Res., 35:e73.
    2006
  • Qin, Y., Polacek, N., Vesper, O., Staub, E., Einfeldt, E., Wilson, D., and Nierhaus, K.H. (2006). The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 127:721-733.
  • Erlacher, M.D., Lang, K., Wotzel, B., Rieder, R., Micura, R., and Polacek, N. (2006). Efficient ribosomal peptidyl transfer critically relies on the presence of the ribose 2'-OH at A2451 of 23S rRNA. J. Am. Chem. Soc. 128:4453-4459.
2005
  • Erlacher, M.D., Lang, K., Shankaran, N., Wotzel, B., Hüttenhofer, A., Micura, R., Mankin, AS. and Polacek, N. (2005). Chemical engineering of the peptidyl transferase center reveals an important role of the 2’-hydroxyl group of A2451. Nucleic Acids Res. 33:1618-1627.
  • Thang, TH., Polacek, N., Zywicki, M., Huber, H., Brügger, K., Garrett, R., Bachellerie, JP., and Hüttenhofer, A. (2005). Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol. Micro. 55:469-481.
  • Hüttenhofer, A., Schattner, P., and Polacek, N. (2005). Non-coding RNAs: hope or hype? Trends Genet. 21:289-297.
  • Polacek, N., and Mankin, A.S. (2005). The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition. Crit. Rev. Biochem. Mol. 40:285-311.
2003
  • Polacek, N., Gomez, MJ., Ito, K., Xiong, L., Nakamura, Y., and Mankin, AS. (2003). The critical role of the universally conserved A2602 of 23S ribosomal RNA in the release of the nascent peptide during translation termination. Mol. Cell 11:103-112.
2002
  • Polacek, N., Swaney, S., Shinarbarger, D., and Mankin, AS. (2002). SPARK-A novel method to monitor ribosomal peptidyl transferase activity. Biochem. 41:11602-11610.
  • Dorner, S., Polacek, N., Schulmeister, U., Panuschka, C., and Barta, A. (2002). Molecular aspects of ribosomal peptidyl transferase. Biochem. Soc. Trans. 30:1131-1137.
2001
  • Xiong, L., Polacek, N., Sander, P., Böttger, EC., and Mankin AS. (2001). pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive. RNA 7:1365-1369.
  • Polacek, N., Gaynor, M., Yassin, A. and Mankin, AS. (2001). Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature 441:498-501.
  • Barta, A., Dorner, S., Polacek, N. (2001). Mechanism of ribosomal peptide bond formation. Science 291:203a.
  • Polacek, N. (2001). Peptidyl transferase directed drugs: Inhibitors of an RNA-enzyme? In: Schroeder R., Wallis M.G., eds. RNA-binding Antibiotics. Georgetown, Texas: Landes Bioscience, 1-11.
2000
  • Polacek, N., Patzke, S., Nierhaus, K.H. and Barta, A. (2000). Periodic conformational changes in rRNA: Monitoring the dynamics of translating ribosomes. Mol. Cell 6:159-171.
1998
  • Polacek, N. and Barta, A. (1998). Metal ion probing of rRNAs: Evidence for evolutionarily conserved divalent cation binding pockets. RNA 4:1282-1294.
1997
  • Winter, D., Polacek, N., Halama, I., Streicher, B. and Barta, A. (1997). Lead-catalysed specific cleavage of ribosomal RNAs. Nucleic Acids Res. 25:1817-1824.
  • Oehler, R., Polacek, N., Steiner, G. and Barta, A. (1997). Interaction of tetracycline with RNA: photoincorporation into ribosomal RNA of Escherichia coli. Nucleic Acids Res. 25:1219-1224.