Table Of Content

Enzymes of Molecular Biology Methods in Molecular Biology John M. Walker, ES SER ROtiDE 16. Enzymes of Molecular Biology, edited by Michael M. Burrell, 1993 15. PCR Protocols: Current Methods and Applications, edited by Bruce A. White, 1993 14. Glycoprotein Analysis in Biomedicine, edited by Elizabeth F. Hounsell, 1993 13. Protocols in Molecular Neurobiology, edited by Alan Longstaff and Patricia Revest, 1992 12. Pulsed-Field Gel Electrophoresis: Protocols, Methods, and Theories, edited by Margit Burmeister and Levy Ulanovsky, 1992 11. Practical Protein Chromatography, edited by Andrew Kenney and Susan Fowell, 1992 10. Immunochemical Protocols, edited by Margaret M. Manson, 1992 9. Protocols in Human Molecular Genetics, edited by Christopher G. Mathew, 1991 8. Practical Molecular Virology, edited by Mary I~ L. Collins, 1991 7. Gene Transfer and Expression Protocols, edited by Edward J. Murray, 1991 6. Plant Cell and Tissue Culture, edited by Jeffrey W. Pollard and John M. Walker, 1990 5. Animal Cell Culture, edited by Jeffrey W. Pollard and John M. Walker, 1990 4. New Nucleic Acid Techniques, edited by John M. Walker, 1988 3. New Protein Techniques, edited by John M. Walker, 1988 .2 Nucleic Acids, edited by John M. Walker, 1984 .1 Proteins, edited by John M. Walker, 1984 r • Methods in Molecular Biology • 16 E n z y m e s of Molecular Biology Edited by M i c h a e l M. B u r r e l l Advanced Technologies (Cambridge) Limited, Cambridge, UK Humana Press ~ Totowa, New Jersey © 1993 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any formo r by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Photocopy Authorization Policy: Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by The Humana Press Inc., provided that the base fee of US $3.00 per copy, plus US $00.20 per page is paid directly to the Copyright Clearance Center at 27 Congress Street, Salem, MA 01970. For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to The Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [0-89603-234-5/93 $3.00 + $00.20]. Printed in the United States of America. Library of Congress Cataloging in Publication Data Main entry under title: Methods in molecular biology. Enzymes of molecular biology / edited by Michael M. Burrell. p. cm. -- (Methods in molecular biology ; 16) Includes index. ISBN 0-89603-234-5 .1 Enzymology. 2. Molecular biology. .1 Burrell, Michael M. II. Series: Methods in molecular biology (Totowa, NJ) ; 16. QP601.E567 1993 574.19'25~c20 92-45040 CIP Preface The scientist' s understanding of the cell at the molecular level has advanced rapidly over the last twenty years. This improved understanding has led to the development of many new laboratory methods that increasingly allow old problems to be tackled in new ways. Thus the modern scientist cannot specialize in just one field of knowledge, but must be aware of many disciplines. To aid the process of investigation, the Methods ni Molecular Biology series has brought together many protocols and has highlighted the useful variations and the pitfalls of the different methods. However, protocols frequently cannot be simply taken from the shelf. Thus the starting sample for a chosen protocol may be unavailable in the correct state or form, or the products of the procedure require a different sort of processing. Therefore the scientist needs more detailed information on the nature and requirements of the enzymes being used. This information, though usually available in the literature, is often widely dispersed and frequently occurs in older volumes of journals; not everyone has comprehensive library facilities available. Also many scientists searching out such information are nott rained enzymologists and may be unaware of some of the parameters that are important in a specific enzyme reaction. The present book, Enzymes of Molecular Biology, provides a companion volume to the Methods ni Molecular Biology series--a ref- erence text designed to minimize the time scientists must spend searching the literature to discover how best to make their reactions work effi- ciently. The intention is to provide sufficient information for even a nonenzymologist to design an experiment, and we have therefore brought together information about a broad range of enzymes commonly used as tools in molecular biology. Within the constraints of producing a sensi- bly sized volume, enzymes have been chosen that modify both nucleic acids and proteins. The chapters have been arranged to provide some background information on each selected enzyme and those parameters and properties important in its use. Each chapter starts with a description of both the source and use of the enzyme under discussion, and then vi Preface provides details on the size and structure of the protein. This is followed by a discussion of those specific parameters--such as pH, ionic strength, activators, inhibitors, K, and substrate concentration--that must be satisfied to achieve an optimized reaction. The chapters then each con- clude with exemplary practical procedures and protocols that put the previous discussion in context. Enzymes of Molecular Biology will be useful to graduates and undergraduates coming to a topic for the first time and to every investi- gator working in a new system or area. The intention is to provide a good starting point for further inquiry Michael M. Burrell Contents Preface ....................................................................................................................... v Contributors ............................................................................................................ ix .HC .1 Nucleases: An Overview, A. Fred Weir ....................................................................................... 1 .HC 2. Deoxyribonuclease I (EC 3.1.21.1) and II (EC 3.1.22.1), A. Fred Weir ....................................................................................... 7 .HC 3. DNA Polymerases (EC 2.7.7.7), Martin J. Maunders ......................................................................... 17 .HC 4. Taq Polymerase (EC 2.7.7.7): With Particular Emphasis on Its Use in PCR Protocols, Axel Landgraf and Heiner Wolfes .................................................. 31 CH. 5. Eukaryotic Nuclear RNA Polymerases (EC 2.7.7.6), Deborah A. Cook and Robert J. Slater ........................................... 59 .HC 6. Reverse Transcriptase (EC 2.7.7.49): The Use of Cloned Moloney Murine Leukemia Virus Reverse Transcriptase to Synthesize DNA from RNA, Gary F. Gerard and James M. D'Alessio ....................................... 73 .HC 7. Terminal Deoxyribonucleotidyl Transferase (EC 2.7.7.31), Frank Grosse and Andreas Manns ................................................. 95 CH. 8. Restriction Enzymes, Alfred Pingoud, Jiirgen Alves, and Robert Geiger ...................... 107 .HC 9. DNA Methyltransferases (EC 2.1.1.72 and EC 2.1.1.73), David P. Hornby ............................................................................. 201 .HC .01 DNA and RNA Ligases (EC 6.5.1.1, EC 6.5.1.2, and EC 6.5.1.3), Martin J. Maunders ....................................................................... 213 CH. 11. The BAL 13 Nucleases (EC 3.1.11), Horace B. Gray, Jr. and Tao Lu ................................................... 231 CH. 12. Mung-Bean Nuclease 1 (EC 3.1.30.1), Andrew J. Sharp and Robert J. Slater .......................................... 253 .HC .31 RNase A (EC 3.1.27.5), Michael M. BurreU ........................................................................ 263 C,. .41 Pronase (EC 3.4.24.4), Patricia J. Sweeney and John M. Walker .................................... 271 vii viii Contents Crt. .51 Proteolytic Enzymes forP eptide Production, Patricia J. Sweeney and John M. Walker .................................... 277 .HC .61 Proteinase K (EC 3.4.21.14), Patricia J. Sweeney and John M. Walker .................................... 305 .HC .71 Carboxypeptidase Y (EC 3.4.16.1), Julia S. Winder and John M. Walker ........................................... 313 .HC .81 Aminopeptidases: Aminopeptidase M (EC 3.4.11.2), Pyroglutamate Aminopeptidase (EC 3.4.19.3), and Prolidase (EC 3.4.13.9), Patricia J. Sweeney and John M. Walker .................................... 319 .HC .91 Alkaline Phosphatase (EC 3.1.3. I), Martin J. Maunders ....................................................................... 331 .HC 20. Polynucleotide Kinase (EC 2.7.1.78), Martin J. Maunders ....................................................................... 343 Index ...................................................................................................................... 357 Contributors JORGEN ALVES ° ehcsinizideM eluhcshcoH ,revonnaH murtneZ ,eimehcoiB Abteilung ehcsilakisyhpoiB ,eimehC ,revonnaH ynamreG MICHAEL M. BURRELL ° decnavdA seigolonhceT )egdirbmaC( ,.dtL ,egdirbmaC KU DEBORAH A. Cook ° School of larutaN ,secneicS ehT ytisrevinU of ,erihsdroftreH ,dleiftaH KU (Present address: uD Pont, ,KU ,eganevetS )KU JAMES M. D'ALESSIO ° Molecular hcraeseR ygoloiB dna ,tnempoleveD adsehteB Research ,seirotarobaL Life ,seigolonhceT ,.cnI ,grubsrehtiaG DM ROBERT GEIGER • ehcsinizideM eluhcshcoH ,revonnaH murtneZ ,eimehcoiB Abteilung ehcsilakisyhpoiB ,eimehC ,revonnaH ynamreG GARY F. GERARD ° Molecular ygoloiB hcraeseR dna ,tnempoleveD adsehteB Research ,seirotarobaL Life ,seigolonhceT ,.cnI ,grubsrehtiaG DM HORACE B. GRAY, JR. ° tnemtrapeD of lacimehcoiB dna lacisyhpoiB ,secneicS ytisrevinU of ,notsuoH XT FRANK GROSSE tutitsnI-kcnalP-xaM fur elletnemirepxE ,nizideM ° gnulietbA ,negnittoG ,eimehC ynamreG (Present address: hcirnieH Institut Pette fur elletnemirepxE ,eigoloriV gnulietbA ,eigoIorivromuT ,grubmaH )ynamreG DAVID P. HORNBY ° Krebs ,etutitsnI Sheffield ,ytisrevinU ,dleiffehS KU AXEL LAND~RAF ° ehcsinizideM eluhcshcoH ,revonnaH murtneZ ,eimehcoiB Abteilung ehcsilakisyhpoiB ,eimehC ,revonnaH ynamreG TAO Lu ° tnemtrapeD of lacimehcoiB dna lacisyhpoiB ,secneicS ytisrevinU of ,notsuoH TX ANDRBAS MANNS tutitsnI-kcnalP-xaM fur elletnemirepxE ,nizideM ° gnulietbA ,negnittoG ,eimehC ynamreG ix