Table Of Content

RNA Biochemistry and Biotechnology NATO Science Series A Seri es presenting the results of activities sponsored by the NATO Science Committee. The Series is published by 10S Press and Kluwer Academic Publishers, in conjunction with the NATO Scientific Affairs Division. A. Life Sciences 10S Press B. Physics Kluwer Academic Publishers C. Mathematical and Physical Sciences Kluwer Academic Publishers D. Behavioural and Social Sciences Kluwer Academic Publishers E. Applied Sciences Kluwer Academic Publishers F. Computer and Systems Sciences 10S Press 1. Disarmament Technologies Kluwer Academic Publishers 2. Environmental Security Kluwer Academic Publishers 3. High Technology Kluwer Academic Publishers 4. Science and Technology Policy 10S Press 5. Computer Networking 10S Press NATO-PCO-DATA BASE The NATO Science Series continues the series of books published formerly in the NATO ASI Series. An electronic index to the NATO ASI Series provides full bibliographical references (with keywords and/or abstracts) to more than 50000 contributions from internatonal scientists published in aII sections of the NATO ASI Series. Access to the NATO-PCO-DATA BASE is possible via CD-ROM "NATO-PCO-DATA BASE" with user-friendly retrieval software in English, French and German (WTV GmbH and DATAWARE Technologies Inc. 1989). The CD-ROM of the NATO ASI Series can be ordered from: PCO, Overijse, Belgium Series 3. High Technology - VoI. 70 RNA Biochemistry and Biotechnology edited by Jan Barciszewski Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan, Poland and Brian F.C. Clark Institute of Molecular and Structural Biology, University of Aarhus, Denmark Springer-Science+Business Media, B.V. Proceedings of the NArO Advanced Research Workshop on RNA Biochemistry and Biotechnology Poznan, Poland October 10-17,1998 A C.I.P. Catalogue record for this book is available from the Library of Congress. ISBN 978-0-7923-5862-6 ISBN 978-94-011-4485-8 (eBook) DOI 10.1007/978-94-011-4485-8 Printed on acid-free paper AII Rights Reserved © 1999 Springer Science+Business Media Dordrecht Originally published by Kluwer Academic Publishers in 1999 Softcover reprint of the hardcover 1 st edition 1999 No part of the material protected by this copyright notice may be reproduced or utilized in any.form or by any means, electronic or mechanical,including photocopying, recording or by any information storage and retrieval system, without written permission from the copyright owner. TABLE OF CONTENTS PREFACE ix LIST OF CONTRIBUTORS xi 1) WbyRNA? J. Barciszewski and B.F. C. Clark 2) Algorithms and thermodynamics for RNA secondary 11 structure prediction: a practical guide M. Zuker, D.H. Mathews and D.H. Turner 3) Recurrent RNA motifs: Analysis at the basepair level 45 N.B. Leontis and E. Westhof 4) Towards the 3D structure of 5S rRNA 63 M. Perbandt, S. Lorenz, M. Vallazza, V.A. Erdmann and C. Betzel 5) Structure and dynamics of adenosine loops in RNA 73 bulge duplexes. RNA hydration at the bulge site L. Bielecki, T. Kulinski and R. W. Adamiak 6) The structure and function of the ribozyme RNAse P RNA 89 is dictated by magnesium(1I) ions L. Kirsebom 7) Metal ion-induced cleavages in probing of RNA structure 111 1 Ciesioika 8) Protein-DNA recognition 123 D. Rhodes 9) Specific interaction between damaged bases in DNA and 127 repair enzymes K. Morikawa vi 10) Telomeric DNA recognition 139 D. Rhodes 11) Recognition of one tRNA by two classes of aminoacyl-tRNA 143 synthetase M. Ibba, S. Bunjun, H. Losey, B. Min and D. Soli 12) Functional structures of class-I aminoacyl-tRNA synthetases 149 O. Nureki, S. Sekine, A. Shimada, T. Nakama, S. Fukai, D.G. Vassylyev, l. Sugiura, S. Kuwabare, M. Tateno, M. Nakasako, D. Moras, M. Konno and S. Yokoyama 13) Aminoacylation of tRNA induces a conformational switch on 159 the 3' -terminal ribose A. Schlosser, B. Blechschmidt, B. Nawrot and M. Sprinzl 14) Point mutants of elongation factor Tu from E: coli impaired 169 in binding aminoaycl-tRNA C.R. Knudsen, F. Mansilla, G.N. Pedersen and B.F. C. Clark 15) RNA structure and RNA-protein recognition during regulation 195 of eukaryotic gene expression G. Varani, P. Bayer, P. Cole, A. Ramos and L. Varani 16) RNA-aptamers for studying RNA protein interactions 217 M. Sprinzl, H.-P. Hoffmann, S. Brock, M. Nanninga and V. Hornung 17) Probing of ribonucleoprotein complexes with site-specifically 229 derivatized RNAs M.M. Konarska, P. Kois, M. Sha, N. Ismai1i, E.H. Gustafson and J. McCloskey 18) The IRE model for families of RNA structures: Selective recognition by binding proteins (IRPs), NMR spectroscopy and probing with metal coordination complexes 241 E. C. Theil, Y. Ke, Z. Gdaniec and H. Sierzputowska- Gracz 19) Functional analysis of RNA signals in the HIV-l genome by 249 forced evolution B. Berkhout and A. T. Das vii 20) Interaction of native RNAs with Tat peptides 277 E. Wyszko, M. Szymanski, J.P. Furste, M. Giel-Pietraszuk, M.Z. Barciszewska, P. Mucha, P. Rokowski, G. Kupryszewski, v.A. Erdmann and 1. Barciszewski 21) Biogenesis, structure and function of small nucleolar RNAs 291 W Filipowicz, P. Pelczar, V. Pogacic and F. Dragon 22) RNA structure modules with trinucleotide repeat motifs 303 W. Krzyzosiak, M. Napierala and M. Drozdz 23) Phosphorothioate oligonucleotides as aptamers of retroviral 315 reverse transcriptases M. Koziolkiewicz, A. Krakowiak, A. Owczarek and M. Boczkowska 24) Oxathiaphospholane method of the stereocontrolled synthesis 325 of phosphorothioate analogues of oligonucleotides A.Okruszek 25) Towards improved applications of cell-free protein biosynthesis 335 - the influence of mRNA structure and suppressor tRNAs on the efficiency of the system M. Gerrits, H. Merk, W. Stiege and V.A. Erdmann 26) RNA on the web 347 M. Szymanski, B.F. C. Clark and J. Barciszewski 27) How risky is direct democracy for basic science? 353 P.Mani SUBJECT INDEX 363 PREFACE This volume contains contributions from the speakers at the NATO Advanced Research Workshop on "RNA: biochemistry and biotechnology" which was held in Poznan, Poland, 10 - 17 October, 1998. RNA plays many roles in biological processes and our knowledge of its importance is expanding very rapidly. By understanding the three dimensional structure of RNA we can significantly extend our understanding of its biological functions. This can be achieved only in close cooperation among molecular biologist, chemists and biophysicists. The discovery of catalytic activity in RNAs has prompted various attempts to solve the mechanisms of their assembly into functional native states starting from linear strands. The folding of RNA was thought until now to take place in two steps. The RNA first folds into a secondary structure of stems, loops, bulges and mismatches, and in the second step a tertiary structure is formed due to long range interactions of single stranded portions of the sequence. Recently it has been shown (1. Tinoco) that RNA folding causes a secondary structure rearrangement. The growld rules for the formation of secondary structure have been derived from physical studies of oligoribonucleotides. Powerful NMR techniques and X-ray analysis have revealed more details of RNA structure including novel conformations. A wealth of information has been obtained by studying the relatively small RNA molecules (tRNA, ribozymes, aptamers). A few of these have been crystallized, enabling determination of their three dimensional structures. Independent evidence for three dimensional folding stems from high resolution proton NMR studies. Molecular dynamics calculations promise to provide us with a detailed knowledge of the atomic motions in these molecules. Details of the structures and the interaction with ligands are also derived from data obtained by a variety of spectroscopic and genetic techniques. The structural features of RNA that are important for RNA-protein specific recognition have only recently come under investigation. Several strategies for recognizing specific RNA sites can be discerned. An unsolved problem in biology is the origin and evolution oftRNA aminoacylation systems that dictate correct expression of the genetic code at the translational level. The aminoacylation of RNA structures generally is considered the starting point for the emergence of the theatre of proteins from the RNA World. Transfer RNAs and anlinoacyl-tRNA ix x synthetases are the center of attention for various biochemical, genetic and phylogenetic studies. There is, with some exceptions, one aminoacyl-tRNA synthetases for each amino acid and, because of the degeneracy of the genetic code, one or more tRNAs for each amino acid. The aminoacyl-tRNA synthetases have long been upheld as a paradigm of molecular evolution, because their products aminoacyl-tRNAs are essentially the same in all living organisms. The role of aminoacyl-tRNA synthetases is to interpret, to decode amino acids, providing the essential link between RNA and protein without which translation ofthe genetic information would be impossible. In the aminoacyl-tRNA reactions, each amino acid is joined to the tRNA that harbours the anticodon triplet of the code for that amino acid. Thus, the question of the origin of the code has to deal at some point with tRNA and aminoacyl-tRNA synthetases. Once an aminoacyl ester linkage is established with an RNA acceptor, peptide bond formation is thermodynamically favoured and such complex with elongation factor in the GTP form is transported the A-site on a ribosome. This volume contains scientific research reports covering the foregoing description of RNA biochemistry and biotechnology. The NATO Scientific Affairs Division is gratefully acknowledged for granting an award that made the organisation of the workshop and the preparation of this book possible. Jan Barciszewski Brian F. C. Clark LIST OF CONTRIBUTORS Adamiak Ryszard W., Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12,61-704 Poznan, Poland E-mail: [email protected] Barciszewska Miroslawa, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61-704 PozGan, Poland E-mail: [email protected] Barciszewski Jan, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12,61-704 Poznan, Poland E-mail: [email protected] Bayer Peter, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK Berkhout Ben, Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands E-mail: [email protected] Betzel Christian, UniversiUitskrankenhaus Eppendorf der Universit%ot Hamburg, Inst. f. Physiol. Chemie, AG Makro. Strukturaaalyse, c/o DESY, D-22603 Hamburg, Germany E-mail: [email protected] Bielecki Lukasz, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, ,61-704 Poznan, Poland E-mail: [email protected] Blechschmidt Bernd, UniversiHit Bayreuth, Lab. fUr Bioche:nie, 95440 Bayreuth, Germany Boczkowska M., Polish Academy of Sciences, Centre of Molecular and Macromolecules Stud:es, Dep<lrtment of Bborganic Chemistry, SienkiewicLa 112,90-363 Lodz, Poland Brock S., UniversiUit Bayreuth, Lab. fUr Biochemie, 95440 Bayreuth, Germany Bunjun S., Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA Ciesiolka Jerzy, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12,61-704 Poznan, Poland E-mail: [email protected] xi