RNA Structure Determination Methods and Protocols
This volume provides protocols and procedures for determining and modeling RNA structure. Chapters guide the reader through protocols for RNA secondary structure prediction, single sequence modeling, Crumple, RNAstructure to model conserved se
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Douglas H. Turner David H. Mathews Editors
RNA Structure Determination Methods and Protocols
METHODS
IN
MOLECULAR BIOLOGY
Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
RNA Structure Determination Methods and Protocols
Edited by
Douglas H. Turner Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, NY, USA
David H. Mathews Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
Editors Douglas H. Turner Department of Chemistry and Center for RNA Biology University of Rochester College of Arts and Sciences Rochester, NY, USA
David H. Mathews Department of Biochemistry and Biophysics and Center for RNA Biology University of Rochester Medical Center Rochester, NY, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-6431-4 ISBN 978-1-4939-6433-8 (eBook) DOI 10.1007/978-1-4939-6433-8 Library of Congress Control Number: 2016948858 © Springer Science+Business Media New York 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC New York
Preface Research in the last 30 years has revealed that an unexpectedly large fraction of genomic DNA is transcribed into RNA [1]. Moreover, many new functions of RNA are being discovered [2]. This has provided a need for ways to rapidly translate sequence into structural information. The twenty-first century witnessed many advances in modeling and determining RNA structures. Secondary structure prediction on the basis of sequences alone is increasingly accurate. New methods have been developed for experimentally probing secondary structure to identify paired and unpaired nucle
