Introduction to Experimental Biophysics Biological Methods for Physical Scientists, Second Edition FOUNDATIONS OF BIOCHEMISTRY AND BIOPHYSICS SERIES Introduction to Experimental Biophysics: Biological Methods for Physical Scientists, Second Edition Jay L Nadeau Introduction to Single Molecule Biophysics Yuri L Lyubchenko Biomolecular Thermodynamics: From Theory to Application Douglas Barrick Biomolecular Kinetics: A Step-by-Step Guide Clive R Bagshaw An Introduction to Biophysics: Quantitative Understanding of Biosystems, Second Edition Thomas M Nordlund and Peter M Hoffmann Introduction to Experimental Biophysics Biological Methods for Physical Scientists, Second Edition Jay L Nadeau CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2018 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S Government works Printed on acid-free paper International Standard Book Number-13: 978-1-4987-9959-1 (Paperback); 978-1-138-08815-3 (Hardback) This book contains information obtained from authentic and highly regarded sources Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint Except as permitted under U.S Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400 CCC is a not-for-profit organization that provides licenses and registration for a variety of users For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe Library of Congress Cataloging‑in‑Publication Data Names: Nadeau, Jay L., author Title: Introduction to experimental biophysics : biological methods for physical scientists / Jay L Nadeau Other titles: Experimental biophysics | Foundations of biochemistry and biophysics Description: Second edition | Boca Raton, FL : CRC Press, Taylor & Francis Group, [2017] | Series: Foundations of biochemistry and biophysics Identifiers: LCCN 2017010261| ISBN 9781138088153 (hardback) | ISBN 1138088153 (hardback) | ISBN 9781498799591 (pbk ; alk paper) | ISBN 1498799590 (pbk ; alk paper) Subjects: LCSH: Biophysics Experiments Technique Classification: LCC QH505 N247 2017 | DDC 572 dc23 LC record available at https://lccn.loc.gov/2017010261 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com v Contents Series Preface xvii Preface xix Acknowledgments xxi Author xxiii Contributors xxv Chapter Introduction and Background Chapter Basic Molecular Cloning of DNA and RNA 43 Chapter Expression of Genes in Bacteria, Yeast, and Cultured Mammalian Cells 75 Chapter Advanced Topics in Molecular Biology 129 Chapter Protein Expression Methods 157 Joshua A Maurer Chapter Protein Crystallization Oliver M Baettig and Albert M Berghuis 187 vi Contents Chapter Introduction to Biological Light Microscopy 225 Coauthored with Michael W Davidson Chapter Advanced Light Microscopy Techniques 279 Coauthored with Lina Carlini Chapter Advanced Topics in Microscopy II: Holographic Microscopy 305 Coauthored with Manuel Bedrossian Chapter 10 Quantitative Cell Culture Techniques 325 Chapter 11 Semiconductor Nanoparticles (Quantum Dots) 361 Chapter 12 Gold Nanoparticles 395 Edward S Allgeyer, Gary Craig, Sanjeev Kumar Kandpal, Jeremy Grant, and Michael D Mason Chapter 13 Advanced Topics in Gold Nanoparticles: Biomedical Applications 429 Chapter 14 Surface Functionalization Techniques 453 Chapter 15 Electrophysiology 497 Coauthored with Christian A Lindensmith and Thomas Knöpfel Chapter 16 Spectroscopy Tools and Techniques 553 Chapter 17 Introduction to Nanofabrication 623 Orad Reshef Contents Glossary 643 Appendix A: Common Solutions 683 Appendix B: Common Media 689 Appendix C: Restriction Endonucleases 693 Appendix D: Common Enzymes 721 Appendix E: Fluorescent Dyes and Quenchers 723 Appendix F: Fluorescent Proteins 729 Index 731 vii http://taylorandfrancis.com ix Detailed Contents Series Preface xvii Preface xix Acknowledgments xxi Author xxiii Contributors xxv Chapter Introduction and Background 1 1.1 BASIC BIOCHEMISTRY 1 Molecules important to molecular biophysics Making use of functional groups 1.2 ENERGIES AND POTENTIALS 8 Biologically relevant energy scales Ionic bonds Ion–dipole interactions 10 Dipole–dipole interactions 11 Hydrogen bonds 12 The (strept)avidin/biotin interaction 14 1.6 TRANSLATION AND THE GENETIC CODE 26 1.7 PROTEIN FOLDING AND TRAFFICKING 28 1.8 ALTERNATIVE GENETICS 33 1.9 WHAT IS CLONING? 34 1.10 DESIGN OF A MOLECULAR BIOLOGY EXPERIMENT AND HOW TO USE THIS BOOK 35 BACKGROUND READING 40 Chapter Basic Molecular Cloning of DNA and RNA 43 2.1 INTRODUCTION 43 2.2 OBTAINING AND STORING PLASMIDS 45 1.4 CELLS 19 2.3 SELECTION OF AN APPROPRIATE E COLI AMPLIFICATION STRAIN; TRANSFORMATION OF E COLI WITH PLASMID 47 Transformation 47 Selection 48 Transformation efficiency 49 1.5 DNA, RNA, REPLICATION, AND TRANSCRIPTION 21 The structure and function of DNA and RNA 21 Replication 23 Transcription 25 2.4 PLASMID AMPLIFICATION AND PURIFICATION 49 Amplification 49 Purification 49 Measuring concentration and purity of extracted DNA 51 1.3 PRINCIPLES OF SPECTROSCOPY 17 What can be measured 17 How transitions are measured 18 .. .Introduction to Experimental Biophysics Biological Methods for Physical Scientists, Second Edition FOUNDATIONS OF BIOCHEMISTRY AND BIOPHYSICS SERIES Introduction to Experimental Biophysics: Biological. .. An Introduction to Biophysics: Quantitative Understanding of Biosystems, Second Edition Thomas M Nordlund and Peter M Hoffmann Introduction to Experimental Biophysics Biological Methods for Physical. .. Biophysics: Biological Methods for Physical Scientists, Second Edition Jay L Nadeau Introduction to Single Molecule Biophysics Yuri L Lyubchenko Biomolecular Thermodynamics: From Theory to Application