Engineered Zinc Finger Proteins Methods and Protocols
Among the many types of DNA binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. In Engineered Zinc Finger Proteins: Methods and Protocols, expert researchers from some of the mos
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MO L E C U L A R BI O L O G Y
Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For other titles published in this series, go to www.springer.com/series/7651
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Engineered Zinc Finger Proteins Methods and Protocols
Edited by
Joel P. Mackay University of Sydney, Sydney, Australia
David J. Segal University of California, Davis, CA, USA
Editors Joel P. Mackay School of Molecular Bioscience University of Sydney Cnr. Butlin Ave. & Maze Cres. 2006 New South Wales Australia [email protected]
David J. Segal Department of Pharmacology & Genome Center University of California, Davis 451 E. Health Sciences Drive Davis, CA 95616 USA [email protected]
ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-60761-752-5 e-ISBN 978-1-60761-753-2 DOI 10.1007/978-1-60761-753-2 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2010930513 © Springer Science+Business Media, LLC 2010 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Cover illustration: Structural cartoons of engineered zinc fingers and their applications. Clockwise from upper right: A three-zinc finger protein (fingers 1, 2, and 3 in red, blue, and green, respectively) bound to DNA (orange), viewed along the DNA helical axis (PDB 1AAY). Zinc ions, yellow spheres. Two zinc fingers wrapping through the major groove of DNA (white surface), with DNA-contacting amino acids in positions -1, 2, 3, and 6 of each α-helix (red) shown (PDB 1AAY). Beta strands, green arrows. A model of an artificial transcription factor (ATF), composed of a six-zinc finger protein and a KRAB transcriptional repression domain (red helices at the N-terminus of the extended strand) bound to DNA (white) (based on PDB 1AAY and 1V65). Model of a heterodimeric zinc finger nuclease (ZFN), composed of two three-zinc finger proteins (purple and blue) bound to DNA in opposite orientation to juxtapose the FokI nuclease domains at their C-termini (based on PDB 1AYY and 2FOK). Models were generated by D.J.S. using INSIGHT and ICMBrowserPro. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)
Preface Among the many types of DNA-binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. Most classic
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