“Nanoscale materials, their physical and chemical properties, and even their biological effects have emerged as a new major branch of science. Interdisciplinary fields are always intriguing and exciting but also difficult to master. This book is an important contribution by an excellent group of scientists who came together to discuss the most relevant aspects of nanoscale materials from the standpoint of biophysics. It summarizes the new findings and developments in the field. The book is a valuable read for newcomers in the field, specialists in other aspects of nanomaterials, and scientists already working in nanobiophysics.” N a Prof. Károly Vékey n Research Centre for Natural Sciences, Hungary o b Nanobiophysics is a new branch of science that operates at the interface of i o physics, biology, chemistry, materials science, nanotechnology, and medicine. This book is the first to focus on nanobiophysics and introduces this field p with a focus on some selected topics related to the physics of biomolecular h nanosystems, including nucleosomal DNA and model lipid membranes, y nanobiohybrids involving DNA/RNA and single-walled carbon nanotubes, s biomolecules deposited on nanoparticles, and nanostructured surfaces. i It describes unique experimental physical methods that are used to study c nano-sized biostructures. It outlines the applied aspects of nanobiophysics, s considering the state of the art in the fabrication of two types of sensors: gas N a n o b i o p h y s i c s sensors, with a focus on breath gas detection, and nanophotonic sensors, with a focus on polycyclic aromatic hydrocarbon detection in water samples. It also covers the development of nanoscale scaffolds for the delivery of therapeutic nucleic acids to cells, which is an important example of the possible application of nanobiophysics research in nanomedicine. Fundamentals and Applications Victor A. Karachevtsev is head of the Molecular Biophysics K Department and professor of physics and mathematics at a B. Verkin Institute for Low Temperature Physics and Engineering r a of the National Academy of Sciences of Ukraine (ILTPE), Ukraine. c h He received his master’s degree in physics (1977) from the University of Kharkov, Ukraine, and PhD (1986) and DrSci ev edited by Victor A. Karachevtsev (1997) in physics and mathematics from the ILTPE. He received the State t s Award of Ukraine in Science and Technology in 2012. Prof. Karachevtsev’s e v research interests are in the functionalization of carbon nanomaterials with biopolymers, enzymes, proteins, etc., and the development of their applications in biosensing. V474 ISBN 978-981-4613-96-5 Nanobiophysics (cid:49)(cid:66)(cid:79)(cid:1)(cid:52)(cid:85)(cid:66)(cid:79)(cid:71)(cid:80)(cid:83)(cid:69)(cid:1)(cid:52)(cid:70)(cid:83)(cid:74)(cid:70)(cid:84)(cid:1)(cid:80)(cid:79)(cid:1)(cid:51)(cid:70)(cid:79)(cid:70)(cid:88)(cid:66)(cid:67)(cid:77)(cid:70)(cid:1)(cid:38)(cid:79)(cid:70)(cid:83)(cid:72)(cid:90)(cid:1)(cid:137)(cid:1)(cid:55)(cid:80)(cid:77)(cid:86)(cid:78)(cid:70)(cid:1)(cid:19) Nanobiophysics Fundamentals and Applications edited by editors Victor A. Karachevtsev PrebenMaegaard AnnaKrenz WolfgangPalz The Rise of Modern Wind Energy Wind Power for the World CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2016 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 Version Date: 20151110 International Standard Book Number-13: 978-981-4613-97-2 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. Reason- able 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 organiza- tion 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. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com Contents Preface xiii 1. Quantum-Mechanical Investigations of Noncovalent Interactions of Carbon Materials 1 Stepan G. Stepanian, Maksym V. Karachevtsev, and Ludwik Adamowicz 1.1 Introduction 2 1.2 Methods 4 1.2.1 The Hartree–Fock Method 4 1.2.2 The MP2 and Post-MP2 Methods 5 1.2.3 Density Functional Theory 6 1.2.4 Basis Sets 8 1.2.5 Surface Models 8 1.3 Physisorption of Nucleic Acid Bases on Carbon Nanotubes and Graphene 10 1.3.1 Structure and Interaction Energies 11 1.3.2 Stability Order 14 1.3.3 Base Pairs 14 p 1.4 Aromatic Amino Acids 17 1.5 -Conjugated Hydrocarbons 20 1.6 Binding of Charged Species 25 2. 1H.y7b riCdosn ocfl ussiRioNnAs with Carbon Nanotubes as RNA 26 Interference Instruments 33 Evgeny K. Apartsin, Marina Yu. Buyanova, Darya S. Novopashina, and Alya G. Venyaminova 2.1 Introduction 34 2.2 Hybrids of siRNA with Carbon Nanotubes: Formation and Properties 35 vi Contents 2.3 Cellular Uptake of CNTs and Their Hybrids in vitro with Nucleic Acids 38 in vivo 2.4 siRNA Delivery 40 2.5 siRNA Delivery 44 3. 2Si.6n gleC-oWnacllulesdio Cnasr abnodn PNearnspoetuctbiveess I nterfaced with 48 DNA/RNA 59 Maksym V. Karachevtsev and Victor A. Karachevtsev 3.1 Introduction 60 3.2 SWNT:DNA Hybrids: Structures and Energy Interaction 61 3.3 Encapsulation of DNA inside Nanotube 68 3.4 DNA Sequencing by Translocation through SWNT Nanopores 73 3.5 Recognition Ability of DNA for Carbon Nanotubes 74 3.6 Carbon Nanotube: DNA Nanoarchitectures 76 4. 3N.u7c leSousmommear ays a annd EFxuatmurpel eP roofs ap eNcatns osystem Formation: 83 Structural Dynamics of Nucleosomal DNA 95 Mariya Yu. Zhitnikova, Olena P. Boryskina, and Anna V. Shestopalova 4.1 Introduction 96 4.2 Nucleosome as the First Level of DNA Compactization 97 4.2.1 Structural Levels of DNA Compaction in Eukaryotic Cells 98 4.2.2 Nucleosome Structure: Histone Core 100 4.2.3 Interaction of Nucleosomal DNA with Histone Core 102 4.3 Nucleosome Formation 104 4.3.1 Nucleosome Stability 104 4.3.2 Nucleosome Self-Assembly 106 4.4 The Structural Features of Nucleosomal DNA 109 4.4.1 Deformation of Nucleosomal DNA 109 4.4.2 Conformational Dynamics of DNA Sugar-Phosphate Backbone 112 Contents vii 4.5 Structural Dynamics of Nucleosomal DNA Sugar-Phosphate Backbone 114 4.5.1 Data Set of Nucleosome Crystallographic Structures 114 a g 4.5.2 Frequency and Sequence-Specificity of Transitions of the / Angles to Alternative States 115 g 4.5.3 Distribution of Nucleotides with Alternative Conformations of Angle on Nucleosomal DNA 117 5. 4St.6ru cCtuornec Dluidaignngo Rsteimcsa orkf sB iorelevant Associates and 120 Complexes in Liquid Nanosystems by Small-Angle Scattering 129 Viktor Ivanovich Petrenko, Leonid Anatolievich Bulavin, Mikhail Vasilievich Avdeev, and Peter Kopcansky 5.1 Introduction 130 5.2 Small-Angle Scattering as a Powerful Method for Structure Diagnostic of Liquid Nanosystems 135 5.3 Structure and Interaction in Magnetic Fluids 137 5.3.1 Structure of Aqueous Ferrofluids 137 5.3.2 Stabilization Features of Magnetic Fluids 141 5.4 Internal Structure of Protein Amyloid Solutions 143 5.4.1 SANS on Amyloids Protofilaments 143 5.4.2 Complementary AFM Studies of Amyloids Protofilaments 145 5.5 Structure Characterization of Magnetoferritin Aqueous Systems 148 6. 5Li.q6u idC oCnryclsutasilo Onrsd ering and Nanostructuring in 153 Model Lipid Membranes 163 Longin N. Lisetski, Olga V. Vashchenko, Natalia A. Kasian, and Alina O. Krasnikova 6.1 Introduction 164 6.2 Lipid Bilayer as the Structural-Functional Base of Cell Membranes 165 viii Contents 6.3 Effects of Non-Lipid Components on the Phase State of Model Phospholipid Membranes 169 6.3.1 General Considerations 169 6.3.2 MTA of Protein Nature 172 6.3.3 Cholesterol and Other Steroids 173 6.3.4 Provitamin D 174 6.3.5 Urocanic Acid 174 6.4 Effects of Ion Medium on Liquid Crystal Phase Transitions of Phospholipid Membranes 175 6.5 Testing of the Joint Action of Drugs by Their Effects on Model Phospholipid Membranes 182 7. 6In.6te raCcotniocnluss oiof nBsi ologically Active Redox-Sensitive 187 Dyes with Nanomaterials: Mass Spectrometric Diagnostics 193 Marina V. Kosevich, Oleg A. Boryak, Vitaliy V. Chagovets, Vadim S. Shelkovsky, and Valerij A. Pokrovskiy 7.1 Introduction 194 7.2 Harnessing of Redox Properties of Dyes in Functioning of Nanomaterials and Nanodevices 195 7.3 Redox-Active Dyes 196 7.4 Mass Spectrometry in Studies of Nanomaterials 197 7.5 Observation of Reduction Reactions of Dyes under Mass Spectrometric Conditions 197 7.6 Reduction of Imidazophenzine Dyes under Mass Spectrometric Conditions 200 7.7 Interactions of Imidazophenazine Dyes Derivatives with Nanostructured Surfaces 204 7.7.1 Positive Ion Mass Spectra 205 7.7.2 Negative Ion Mass Spectra 207 7.7.3 Contribution of Field Ionization Mechanism to the LDI from the Nanostructured Graphite Surface 209 7.7.4 Intermolecular Interactions in a Nanocomposite of Methylene Blue Dye with Carbon Nanotubes 212 Contents ix 7.7.5 Interactions of Methylene Blue Dye with Mesoporous Oxide Films 219 7.7.6 Interactions of Methylene Blue with Modified Silicon Surface 221 7.8 Incorporation of Dyes into Surface Nanolayers 222 8. 7N.a9n oCsioznecdl uCsoiomnpsl exes of Bioorganic Molecules in 223 Low-Temperature Matrices 235 Alexander M. Plokhotnichenko and Victor A. Karachevtsev 8.1 Introduction 236 8.2 Matrix Isolation Method: Opportunities and Limitations 238 8.2.1 Some Experimental Details to Study Molecular Complexes by Matrix Isolation Method 242 8.2.2 Interpretation of Spectral Data 246 8.3 The Formation of Molecular Complexes in Matrix 247 p p 8.3.1 H-Bonded Complexes of Phenols 249 8.3.2 – Stacking Complexes of Flat Heterocyclic Molecules in the Low Temperature Matrices of Inert Gases 254 9. 8K.i4n etCicosn Fcrlaumsioenwso rk for Nanoscale Description of 260 Environment-Induced Transition Processes in Biomolecular Structures 267 Elmar Petrov and Victor Teslenko 9.1 Introduction 268 9.2 Master Equation for Averaged Populations 275 9.2.1 Stochastic Hamiltonian and Stochastic Equation for State Populations 276 9.2.2 Stochastically Averaged Master Equation 278 9.3 Transition Rate Constants 280 9.3.1 Temperature-Independence of Desensitization Onset of P2X3 Receptors 281