DNA Engineering. Properties and Applications. DNA Engineering. Mizoguchi Sakamoto. Kenji Mizoguchi Hirokazu Sakamoto. edited by

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Dr. Evgeni B. Starikov KIT Karlsruhe, Germany Chalmers University of Technology, Sweden DNA is one of the most known, interesting, and important materials in the world.

formation, flexibility of intercalation with flat molecules, property control with water molecules, and so on.

This book presents basic information about DNA, along with comprehensive theoretical introduction to DNA.

Further, the book describes three examples of applications: optical and electrical materials, electronic devices such as biotft memory and color-tunable lightemitting diodes, and biofuel cell

1 Dr. Evgeni B. Starikov KIT Karlsruhe, Germany Chalmers University of Technology, Sweden DNA is one of the most known, interesting, and important materials in the world. It is not only a container of hereditary information of lives but also a fascinating nanomaterial with self-organization ability with base pairing, flexibility of base sequence, π-electron band formation, flexibility of intercalation with flat molecules, property control with water molecules, and so on. DNA as a nanomaterial has the potential to open a new horizon of applications in the near future. This book presents basic information about DNA, along with comprehensive theoretical introduction to DNA. It discusses recent developments in divalent metal ion inserted M-DNA complex, which gives rise to the possibility of DNA application to electronic functionality. Further, the book describes three examples of applications: optical and electrical materials, electronic devices such as biotft memory and color-tunable lightemitting diodes, and biofuel cell application with use of proton conduction in DNA. Hirokazu Sakamoto is assistant professor at TMU since He received his PhD from the University of Tokyo in 1985 on the topic Electronic states of transition metal compounds by ultraviolet and photoemission spectroscopy. His research is focused on photoemission and ultraviolet spectroscopy of molecular crystals, semiconductors, and metals and NMR and ESR of high-tc superconductors, conducting polymers, charge transfer salts, and DNA. His current research interest is in the high-pressure ESR system being studied by Prof. Mizoguchi. V498 ISBN DNA Engineering Mizoguchi Sakamoto Kenji Mizoguchi is emeritus professor at Tokyo Metropolitan University (TMU), Japan. He joined TMU as professor in the Department of Physics in He received his PhD from TMU in 1983 on the topic NMR study on AuV and MoCo dilute magnetic alloys. Some of his prominent studies are NMR and ESR study on conducting polymers (1980), Electrosodalites, fullerides, molecular charge transfer salts (2000), and DNA and metal-dna composites (since 2002). He has published nearly 150 research papers so far. His current research interest is in the development of a high-pressure ESR system up to 10 GPa. DNA Engineering The book at hand is a marvelous collection of the high-quality reports by a number of outstanding experimenters and theorists in one of the hottest research fields of nowadays. The editors have exerted a truly great effort to demonstrate the eternal verity of R. A. Millikan s known saying, Science walks forward on two feet, namely theory and experiment, but continuous progress is only made by the use of both. This volume ought to be of clear interest not only for freshmen, but also to the colleagues truly versed in the field. Properties and Applications edited by Kenji Mizoguchi Hirokazu Sakamoto

2 DNA Engineering

4 DNA Engineering Properties and Applications edited by Kenji Mizoguchi Hirokazu Sakamoto

5 Published by Pan Stanford Publishing Pte. Ltd. Penthouse Level, Suntec Tower 3 8 Temasek Boulevard Singapore editorial@panstanford.com Web: British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. DNA Engineering: Properties and Applications Copyright c 2017 Pan Stanford Publishing Pte. Ltd. All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or mechanical, including photocopying, recording or any information storage and retrieval system now known or to be invented, without written permission from the publisher. For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not required from the publisher. ISBN (Hardcover) ISBN (ebook) PrintedintheUSA

6 To Keiko

8 Contents Preface xv PART IINTRODUCTION 1 Introduction 3 Kenji Mizoguchi 1.1 Natural DNA Structure of DNA Electronic States of DNA Examples of DNA Engineering DNA Origami Metal Ion Incorporation Into DNA 12 PARTII NATURAL DNA 2 Basic Physical Properties of Natural DNA 19 Kenji Mizoguchi and Hirokazu Sakamoto 2.1 Introduction UV/Vis Absorption of DNA Introduction Experimental Nucleotide Solution SS and DS 30mer-DNA Solution DNA Solution DNA Film Summary of UV/Vis Absorption in DNA Magnetic Property of DNA Introduction ESR Study 32

9 viii Contents Magnetic Property with SQUID Other Reports on Magnetic Property of DNA Summary of Magnetic Property in DNA 41 3 Infrared Spectral Studies on Structure and Hydration State of Dry DNA 43 Hiroshi Matsui 3.1 Introduction Infrared Spectra of Base Molecules and Nucleotides Hydration Structure of Dry Poly(dA)-Poly(dT) and Poly(dG)-Poly(dC) Summary of the Infrared Spectra in Poly(dG) Poly(dC) and Poly(dA) Poly(dT) 58 4 Proton Conduction in DNA 59 Yasumitsu Matsuo and Seiichiro Ikehata 4.1 Introduction Proton Transfer in Bio-Tissue Materials DNA Conductor Experimental Impedance Analysis Nuclear Magnetic Resonance Proton Conductivity in a DNA-H Film Sample Preparation DC Conductivity and 1 H-NMR AC Conductivity and Impedance Analysis Phase Diagram of Proton Conduction Ionic Conductivity in Deuterated DNA DNA-Na and DNA-Li Conclusions 85 5 DNA Molecules Studied by X-Ray Absorption Spectroscopy 87 Hiroki Wadati and Toshitaka Oka 5.1 Introduction ESR under X-ray Absorption X-Ray Absorption of Metal Ion Doped DNA 93

10 Contents ix 6 The Hückel Theoretical Calculation for the Electronic StructureofDNA 95 Kazumoto Iguchi 6.1 Preliminaries Introduction Quantum Chemistry for Atoms in Biology Carbon Nitrogen Oxygen Phosphorus π-electronic Configurations in Organic Molecules in Biology π-electronic configuration in benzene π-electronic configurations in A, G, C, T base molecules Electronic configurations in molecules of sugar, phosphate, and triphosphate Electronic configurations in A, G, C, and T nucleosides Electronic configurations in datp, dgtp, dctp, and dttp nucleotides Hückel Approximation Hückel Model Hückel Parameters Introduction of parameters α andβ Convenient formulas for Hückel parameters Hückel parameters for biomolecules Electronic States of Benzene C 6 H Hückel matrix for benzene C 6 H Eigenequation for benzene C 6 H Eigenvalues of Hückel matrix for benzene C 6 H Electronic States of Nucleotides Electronic States of Single Bases of A, G, C, and T Hückel matrices for A, G, C, and T 118

11 x Contents Eigenvalues and eigenvectors of secular equations Energy gaps between HOMO and LUMO of A, G, C, and T Ground state energies of A, G, C, and T Electronic States of a Single Sugar-Phosphate Group Electronic States of a Single Nucleotide with a Single Sugar-Phosphate Group Hückel matrices for nucleotide molecules of A, G, C, and T Value of β BS Energy levels of nucleotide molecules of A, G, C, and T with a single sugar-phosphate group Electronic States of DNA Decorated Ladder Models of a Single or Double Strand of DNA Geometry of a single or double strand of DNA Simple modeling of a single or double strand of DNA Tight-binding model for ladder systems Transfer matrix method Symplectic property of transfer matrix Scheme for obtaining energy bands and density of states Electronic Properties of a Single Strand of DNA π-electronic energy spectrum of decorated ladder model for a single strand of DNA Hückel matrices for a single strand of DNA with a single nucleotide base of A, G, C, and T Energy bands of π-electronic states of a single strand of DNA 146

12 Contents xi Electronic Properties of a Double Strand of DNA π-electronic energy spectrum of decorated ladder model for a double strand of DNA Electronic conduction of decorated ladder model for a double strand of DNA Energy bands of π-electronic states of a double strand of DNA Further Problems on DNA Screw Symmetry of DNA Effect of Half-Twist of DNA Aperiodicity of DNA Conclusion 165 PART III METAL ION--INCORPORATED DNA 7 Basic Properties of M-DNA 169 Kenji Mizoguchi and Hirokazu Sakamoto 7.1 Introduction UV/Vis Absorption of M-DNA Sample Preparation for UV/Vis Study M-DNA Solution Comparison with B-DNA Suppression of the inter-π-band absorption Fe-DNA Solution M-DNA Film Summary of Absorption Spectra in M-DNA Magnetic Property of M-DNA Sample Preparation for Magnetic Study M-DNA Mn-DNA ESR linewidth of Mn-ESR ESR lineshape of Mn-ESR Hyperfine structure of Mn-ESR 195

13 xii Contents Fe-DNA Electronic states of Fe Concentration dependence of (Fe 1 x Ca x )-DNA Fe-DNA under controlled condition Summary of Magnetic Property in M-DNA IR Spectral Studies on M-DNA 213 Hiroshi Matsui 8.1 Introduction Infrared Spectra in M-DNA Summary of the Infrared Spectra in M-DNA Charge Doping in Zn-DNA 221 Kenji Mizoguchi and Hirokazu Sakamoto 9.1 Introduction Freeze-Dried Zn-DNA Preparation of High-Purity Freeze-Dried Zn-DNA Magnetic Susceptibility of Freeze-Dried Zn-DNA ESR of Freeze-Dried Zn-DNA Nature of Freeze-Dried Zn-DNA Effect of Moisture on Magnetic Properties Electronic States of Freeze-Dried Zn-DNA Reported Theoretical Models for M-DNA Summary of Electronic Properties in Freeze-Dried Zn-DNA Structure of M-DNA Studied with STM 243 Kenji Mizoguchi and Hirokazu Sakamoto 10.1 Introduction Sample Preparation for STM Study STM in DNA STM in M-DNA Summary of Structure of M-DNA 252

14 Contents xiii PART IV APPLICATIONS OF DNA 11 DNA as a Material 257 Naoya Ogata 11.1 Introduction Production of High Purity DNA Production of DNA from Marine Resources Molecular Weight Control of DNA Molecular weight control by sonication Molecular weight control by fetal bovine serum Production of DNA from Onions DNA as Optical and Electrical Materials Optical Switch Laser DNA as Physiological and Medical Materials UV-Cured DNA film for Skin Wound UV-Cured DNA Film for Cell Cultivation Summary of DNA as a Material Application of DNA to Electronic Devices 277 Norihisa Kobayashi and Kazuki Nakamura 12.1 Introduction BiOTFT Memory with DNA Complex as Gate Dielectric OTFT using Bio-Related Materials and DNA-Surfactant Complexes Photo-Electrical Properties of DNA-Surfactant Complexes Fabrication of BiOTFT Devices using DNA-Surfactant Complexes Summary BiOLED with DNA Complexes Application of DNA Complexes as Charge Conductive Material Structure of Template Photopolymerized PAn/DNA Complex 291

15 xiv Contents EL Properties of Ru(bpy) Based DNA BiOLED Color Tunable OLED Based on the DNA/PAn/Ru(bpy) 2+ 3 Complex Summary Fabrication and Characteristics of DNA-Biofuel Cell 309 Yasumitsu Matsuo and Seiichiro Ikehata 13.1 Introduction Fuel Cell Construction Results and Discussion Conclusion 313 Bibliography 315 Index 341

16 Preface I (K. M.) have been interested in the development of conducting polymers since 1980s, especially by making use of magnetic resonance techniques such as nuclear magnetic resonance (NMR) and electron spin resonance (ESR). In particular, measurement of ESR by varying the frequency from 10 MHz to 24,000 MHz is highly useful to study the electronic carrier dynamics in polycrystalline samples typical of conducting polymers, through which information about the anisotropic dynamics of the electronic carriers within the local crystalline regions can be obtained. In 2001, I had an opportunity to introduce the field of conducting polymers in butsuri (meaning physics in Japanese) in praise of Japanese Nobel laureates in chemistry in 2000, Drs. Hideki Shirakawa, A. MacDiarmid, and A. J. Heeger. After that, Dr. Kazumoto Iguchi let me know the DNA research field from the viewpoint of physics, which was a start of my research on DNA in materials science. In early 2000s, many reports on the electrical properties of DNA making use of nanotechnologies appeared in the named journals, such as Nature, Science, and Physics Review Letters, with controversial conclusions, which strongly motivated us to make clear the basic physical properties of DNA. To avoid any physical contacts with DNA samples causing the controversial results, magnetic, optical, and AC measurements were mainly utilized for the purpose. This book is intended to provide the basic physical properties of DNA and the possible engineering and applications of DNA for the readers who are interested in DNA as one of the nanomaterials. Introduction to the book appears in Part I. Part II is devoted to describe the basic physical properties of DNA both experimentally and theoretically, which reconfirms that DNA has a semiconducting nature. In Part III, divalent metal ion M inserted

17 xvi Preface M-DNAs are described to introduce the charge carriers into the semiconducting DNA. Three examples of the applications of DNA to materials science, electronic devices, and fuel cell battery are demonstrated in Part IV. The double-helical struture of the synthetic oligomer DNA is expressed in two ways in this book, poly(da)-poly(dt) in Chapter 3 and Chapter 8 and poly(da-dt) in Chapter 4 and Chapter 9, which is according to the already published presentations. The chapters presented by us (K. M. and H. S.) are largely based on the contributions by many of the graduate and undergraduate students of the Tokyo Metropolitan University from 2002 to We would like to express our heartful thanks to them. We would also like to express our sincere thanks to all the contributors of this book. Finally, we would like to express our sincere thanks to Stanford Chong, the director of Pan Stanford Publishing Pte. Ltd., for inviting us to edit this book. Kenji Mizoguchi Hirokazu Sakamoto Tokyo, Japan Summer 2016

18 PART I INTRODUCTION

Hydrophobic and Superhydrophobic Organic-Inorganic Nanohybrids. Chang-Sik Ha Saravanan Nagappan

Hydrophobic and Superhydrophobic Organic-Inorganic Nanohybrids Chang-Sik Ha Saravanan Nagappan Hydrophobic and Superhydrophobic Organic-Inorganic Nanohybrids Hydrophobic and Superhydrophobic Organic-Inorganic