Introduction to Bionanotechnology 9811512922, 9789811512926

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Young-Chul Lee · Ju-Young Moon

Introduction to Bionanotechnology

Introduction to Bionanotechnology

Young-Chul Lee • Ju-Young Moon

Introduction to Bionanotechnology

Young-Chul Lee Department of BioNano Technology Gachon University Seongnam-si, Republic of Korea

Ju-Young Moon Department of Beauty Design Management Hansung University Seoul, Republic of Korea

ISBN 978-981-15-1292-6    ISBN 978-981-15-1293-3 (eBook) https://doi.org/10.1007/978-981-15-1293-3 © Springer Nature Singapore Pte Ltd. 2020 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, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore

Preface

In recent decades, nanotechnology and biotechnology are the emerging areas that attracted researchers around the world. While nanotechnology is all about the design, development, and applications of materials that have at least one dimension at the nanoscale (< 100 nm), biotechnology is developed based on knowledge about living systems and how to manipulate it for human purpose. It should be noticed that matters such as DNA and RNA in living systems could be considered as one type of nanobiomaterials. The association between nanotechnology and biotechnology opens a new door for hybrid technology with unique features. In this book, we tried to bring a concept of bionanotechnology, its applications as well as its limitations and future direction to the readers. It has also been tried to keep the writing style of the book as simple as possible while its academic contents are still preserved. We hope that students, experts, and everyone who works and is interested in this research area will find this book useful. I would like to thank our family, friends, colleagues, and experts in this research field for their support and advice to complete this work. Seongnam-si, Republic of Korea Seoul, Republic of Korea 

Young-Chul Lee Ju-Young Moon

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Contents

1 Introduction to Nanotechnology and Bionanotechnology��������������������    1 1.1 The Era of Nanotechnology��������������������������������������������������������������    1 1.1.1 Nanotechnology: A Historical Perspective ��������������������������    1 1.1.2 Powerful Assistant for Nanotechnology: Scanning Probe Microscopes (SPMs)��������������������������������������������������    3 1.2 Biotechnology and Nanotechnology Meet at Intersection����������������    5 1.2.1 Background and Definition of Nanotechnology and Bionanotechnology ��������������������������������������������������������������    5 1.2.2 Notable Prospects of Bionanotechnology����������������������������   10 1.3 Summary ������������������������������������������������������������������������������������������   11 References��������������������������������������������������������������������������������������������������   14 2 Fundamental of Biological Systems and Bionanotechnology��������������   15 2.1 Nucleic Acid in Bionanotechnology ������������������������������������������������   15 2.1.1 DNA as a Biomaterial in Bionanotechnology����������������������   15 2.1.2 Structural DNA Nanotechnology������������������������������������������   17 2.2 Peptides and Proteins in Bionanotechnology������������������������������������   19 2.2.1 The Supramolecular Structure of Peptides and Proteins��������������������������������������������������������   19 2.2.2 Sensors Based Peptides and Proteins������������������������������������   20 2.3 The Biological System of the Elements (BSE)��������������������������������   22 2.3.1 Interelemental Correlations��������������������������������������������������   23 2.3.2 The Biological Function of Elements ����������������������������������   23 2.4 Information Flows in Biological Systems����������������������������������������   26 2.4.1 Transcription: DNA to RNA ������������������������������������������������   27 2.4.2 Translation: RNA to Protein ������������������������������������������������   27 2.5 Summary and Outlooks��������������������������������������������������������������������   28 References��������������������������������������������������������������������������������������������������   30 3 Bionanomaterials Production ����������������������������������������������������������������   33 3.1 Introduction��������������������������������������������������������������������������������������   33 3.2 Microorganism-Based Synthesis of NPs������������������������������������������   34 vii

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3.2.1 Synthesis of NPs by Bacteria������������������������������������������������   34 3.2.2 NPs Synthesized by Fungi����������������������������������������������������   43 3.2.3 NPs Synthesized by Yeast ����������������������������������������������������   45 3.3 Plant Extracts-Based Synthesis of NPs��������������������������������������������   46 3.3.1 Synthesis of NPs Using Leaf Extracts����������������������������������   46 3.3.2 Synthesis of NPs Using Seed Extracts����������������������������������   47 3.3.3 Synthesis of NPs Using Fruit Extracts����������������������������������   47 3.3.4 Synthesis of NPs Using Root Extracts����������������������������������   48 3.3.5 Synthesis of NPs Using Flower Extracts������������������������������   48 3.4 Polysaccharide-Based Synthesis of NPs������������������������������������������   49 3.4.1 Synthesis of NPs from Alginate��������������������������������������������   49 3.4.2 Synthesis of NPs from Chitosan ������������������������������������������   50 3.4.3 Synthesis of NPs from Dextran��������������������������������������������   51 3.5 Genetically Engineered Escherichia coli������������������������������������������   51 3.6 Conclusions��������������������������������������������������������������������������������������   52 References��������������������������������������������������������������������������������������������������   55 4 Interaction of Nanomaterials with Biological Systems������������������������   61 4.1 Introduction��������������������������������������������������������������������������������������   61 4.2 Interaction of Nanomaterials with Biological Systems��������������������   62 4.2.1 Protein Binding ��������������������������������������������������������������������   62 4.2.2 Ligand-Mediated Interactions����������������������������������������������   63 4.2.3 Interactions during Intracellular Processing ������������������������   64 4.3 Applications��������������������������������������������������������������������������������������   66 4.3.1 Bio-Barcodes Assay��������������������������������������������������������������   66 4.3.2 Contrast Agents for Cell Imaging ����������������������������������������   68 4.3.3 Theranostic Nanoparticles (NPs)������������������������������������������   69 4.3.4 Targeted Therapies����������������������������������������������������������������   69 4.3.5 Combined Drug Therapies����������������������������������������������������   71 4.4 Conclusion����������������������������������������������������������������������������������������   72 References��������������������������������������������������������������������������������������������������   75 5 Bionanotechnology: Biological Self-Assembly��������������������������������������   79 5.1 Biological Self-Assembly ����������������������������������������������������������������   79 5.2 Self-Assembly of Proteins and Peptides ������������������������������������������   83 5.3 Self-Assembly of Surface (S)-Layer Structure ��������������������������������   84 5.4 Self-Assembly of Phospholipids Membranes����������������������������������   85 5.5 Self-Assembly of Viruses������������������������������������������������������������������   87 5.6 Summary ������������������������������������������������������������������������������������������   88 References��������������������������������������������������������������������������������������������������   90 6 Bio-Nanorobotics: Mimicking Life at the Nanoscale����������������������������   93 6.1 Introduction��������������������������������������������������������������������������������������   93 6.2 Bio-Nanorobotic Systems ����������������������������������������������������������������   95 6.2.1 Overview������������������������������������������������������������������������������   95 6.2.2 Bionanomolecular Machines������������������������������������������������   95

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6.3 Design and Control for Bio-Nanorobotic Systems ��������������������������  100 6.3.1 The Pathways of Construction����������������������������������������������  101 6.3.2 Design Architecture for the Bio-Nano Robotic Systems ������������������������������������������������������������������  105 6.3.3 Control Architecture for the Bio-Nanorobotic Systems ��������������������������������������������������������������������������������  107 6.4 Conclusion����������������������������������������������������������������������������������������  107 References��������������������������������������������������������������������������������������������������  111 7 Bioanalytical Techniques for Bionanotechnology ��������������������������������  115 7.1 Introduction��������������������������������������������������������������������������������������  115 7.2 Fudamentals of Using Biomolecular as Sensors in Bionanotechnology ����������������������������������������������������������������������  115 7.3 Commonly-Applied Bioanalytical Techniques in Bionanotechnology ����������������������������������������������������������������������  117 7.3.1 X-Ray Crystallography Provides Atomic Structures������������  117 7.3.2 NMR Spectroscopy May be Used to Derive Atomic Structures ����������������������������������������������������������������  119 7.3.3 Electron Microscopy Reveals Molecular Morphology��������������������������������������������������������������������������  121 7.3.4 Atomic Force Microscopy Probes the Surface of Biomolecules ������������������������������������������������  123 7.4 Conclusion����������������������������������������������������������������������������������������  124 References��������������������������������������������������������������������������������������������������  128 8 Bionanotechnology in Medicine��������������������������������������������������������������  129 8.1 Introduction��������������������������������������������������������������������������������������  129 8.2 Applications of Bionanotechnology in Diagnostics ������������������������  130 8.2.1 Nanostructures and Nanosystems in Diagnostics ����������������  131 8.2.2 Nanoparticles (NPs) in Diagnostics��������������������������������������  135 8.2.3 Biosensors in Diagnostics ����������������������������������������������������  137 8.3 Applications of Bionanotechnology in Therapeutics������������������������  138 8.3.1 Nano Self-Assembled Systems in Delivery of Therapeutic Agents ����������������������������������������������������������  139 8.3.2 Other Nanostructures and Nanosystems in Medical Applications��������������������������������������������������������  141 8.3.3 Nanoparticles (NPs) in Molecular/Therapeutic Imaging ��������������������������������������������������������������������������������  141 8.4 Conclusions��������������������������������������������������������������������������������������  143 References��������������������������������������������������������������������������������������������������  146 9 Bionanotechnology in Pharmaceuticals ������������������������������������������������  149 9.1 Dendrimers����������������������������������������������������������������������������������������  149 9.1.1 Dendrimers in Biosensors ����������������������������������������������������  150 9.1.2 Gene delivery������������������������������������������������������������������������  151 9.2 Micelles��������������������������������������������������������������������������������������������  153

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9.2.1 Micelles in Drug Delivery����������������������������������������������������  153 9.2.2 DNA Micelles ����������������������������������������������������������������������  154 9.3 Liposomes ����������������������������������������������������������������������������������������  156 9.3.1 Liposomes in Clinical Applications��������������������������������������  156 9.3.2 Liposomes for Delivery of Protein and Peptides������������������  159 9.4 Lipid Particles ����������������������������������������������������������������������������������  160 9.5 Carbon Nanotubes (CNTs) ��������������������������������������������������������������  162 9.5.1 Functionalization of CNTs����������������������������������������������������  162 9.6 Future Outlooks��������������������������������������������������������������������������������  164 References��������������������������������������������������������������������������������������������������  167 10 Bionanotechnology in Biotechnology ����������������������������������������������������  171 10.1 Introduction������������������������������������������������������������������������������������  171 10.2 Bionanotechnology in Molecular Biology��������������������������������������  171 10.2.1 Detection of Proteins����������������������������������������������������������  172 10.2.2 Separation and Purification of Biological Molecules����������������������������������������������������������������������������  174 10.2.3 Detection Pathogens������������������������������������������������������������  175 10.2.4 Lab-on-a-Chip for Biomolecule Application����������������������  179 10.3 Bionanotechnology in Biomedical Engineering ����������������������������  181 10.3.1 Tissue Engineering��������������������������������������������������������������  181 10.3.2 Genetic Engineering�����������������������������������������������������������  183 10.3.3 Biomechanics Engineering ������������������������������������������������  184 10.4 Bionanotechnology in Bioimaging ������������������������������������������������  185 10.4.1 Hollow Nanocapsules in Biomedical Imaging Applications������������������������������������������������������������������������  185 10.4.2 NPs as Contrast Agents for Optoacoustic (OA) Imaging ������������������������������������������������������������������������������  187 10.4.3 Radio-Labeled NPs for Biomedical Imaging����������������������  188 10.5 Conclusions������������������������������������������������������������������������������������  190 References��������������������������������������������������������������������������������������������������  193 11 Bionanotechnology in Agriculture, Food, Cosmetic and Cosmeceutical ����������������������������������������������������������������������������������  199 11.1 Bionanotechnology in Agriculture��������������������������������������������������  199 11.1.1 Bionano-Pesticides��������������������������������������������������������������  199 11.1.2 Bionano-Fertilizers ������������������������������������������������������������  202 11.2 Bionanotechnology in Food������������������������������������������������������������  203 11.2.1 Food Safety ������������������������������������������������������������������������  203 11.2.2 Food Packaging������������������������������������������������������������������  205 11.3 Bionanotechnology in Cosmetic and Cosmeceutical����������������������  208 11.3.1 Organic Nanoparticles (NPs)����������������������������������������������  208 11.3.2 Inorganic Nanoparticles (NPs)��������������������������������������������  211 11.4 Summary ����������������������������������������������������������������������������������������  212 References��������������������������������������������������������������������������������������������������  214

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12 Bionanotechnology in Environment ������������������������������������������������������  219 12.1 Introduction������������������������������������������������������������������������������������  219 12.2 Plastic Replacement������������������������������������������������������������������������  220 12.2.1 Polylactic Acid (PLA)��������������������������������������������������������  220 12.2.2 Polylactic Acid (PLA) Composite for Plastics Replacement����������������������������������������������������  221 12.3 Wastewater Treatment��������������������������������������������������������������������  223 12.3.1 Elastin-Like Polypeptides (ELP)����������������������������������������  223 12.3.2 Graphene Oxide (GO) Gels������������������������������������������������  224 12.3.3 Chitosan������������������������������������������������������������������������������  224 12.3.4 Biopolymers from Plant Extracts����������������������������������������  226 12.3.5 Cellulose Nanomaterials ����������������������������������������������������  227 12.4 Conclusion��������������������������������������������������������������������������������������  228 References��������������������������������������������������������������������������������������������������  231

About the Authors

Young-Chul  Lee  received his master’s and PhD degree in Chemical and Biomolecular Engineering from Korea Advanced Institute of Science and Technology (KAIST), Daejeon, in February 2006 and 2011, after obtaining his bachelor’s degree in Polymer Science and Engineering from Pusan University in 2004. From 2011 to 2013, he was a postdoctoral researcher in the Department of Chemical and Biochemical Engineering, Chosun University and the Department of Civil and Environmental Engineering, KAIST, Korea. From March 2013 to March 2014, he worked as a research professor at Research Institute of Industrial Science and Technology, Inha University. He joined as an assistant professor in the Department of BioNano Technology, Gachon University from April 2014. Dr. Lee’s research interests are inorganic–organic (nano)particles for biological and environmental applications using unique nanoparticles such as carbon dots, aminoclays, and photocatalysts entrapped in hydrogels and 2D layered materials, etc. Ju-Young Moon  is currently working as a director at the International Association of Beauty Arts Education, who has earned a bachelor’s degree in Beauty Art at Wonkwang University and a master’s degree at the Graduate School of Integrated Medicine, CHA University. Her research focus is on cosmeceuticals, especially on cosmetic products with bioactive ingredients in medically effective plant phenolics.

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Chapter 1

Introduction to Nanotechnology and Bionanotechnology

1.1  The Era of Nanotechnology Nanotechnology emerged as a novel and powerful tool to manipulate matters at a “nano-scale” and enable the evolution of many aspects, including biotechnology, medicine, pharmaceuticals, agriculture, food, cosmetics, environment protection, electronics, information technology, construction, military, energy industry, space industry, and consumer products among others. It extended the ability of people beyond the limited border that had not been broken for many decades and opened a window to the tiny universe of minuscule functional machines and specific-­behavior-­ particles as well. Back to 50 years ago, a portable seawater desalination device was solely an imagination of human beings. Prior to the advent of nanotechnology, people might not think that they would have a high-capacity hydrogen warehouse within a nano-scale system. People even could not imagine that they would be able to monitor their health status by a wearable on-skin chip embedded on their skin or a minuscule robot moving in their blood vessels. These are no longer fictional scenarios in movies, but a reality today. It can be said that nanotechnology, as a reliable foundation, has supported human to fulfill our dreams and imagination, resulting in dramatical change of our life. Particularly, nanomaterials, as the child of nanotechnology, have led us to the era of miniature structures.

1.1.1  Nanotechnology: A Historical Perspective The ideas and concepts of nanotechnology were first introduced by physicist Richard Feynman in a talk entitled “There’s Plenty of Room at the Bottom” in 1959. He speculated the inconceivable possibilities and potentials in the very small world. Arguing that there is an abundant number of atoms building up the ordinary matter, he expected that there is plenty of space within the matter [1]. A possibility of © Springer Nature Singapore Pte Ltd. 2020 Y.-C. Lee, J.-Y. Moon, Introduction to Bionanotechnology, https://doi.org/10.1007/978-981-15-1293-3_1

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1  Introduction to Nanotechnology and Bionanotechnology

n­ ano-­level matter manipulation, for instance, using of atomic blocks to assemble at a molecular level, was discussed in the talk [2]. The authentic coining of the term “nanotechnology” is attributed to the Japanese scientist called Norio Taniguchi, who first mentioned it in a 1974 conference to describe semiconductor processes occurring on the order of a nanometer [3]. He defined the term “nanotechnology” as follows: “Nano-technology mainly consists of the processing of separation, consolidation, and deformation of materials by one atom or one molecule”. The term, however, was not used again until 1981 when K. Eric Drexler published his first paper on nanotechnology, in which he described how protein assemblies can serve as functional units such as pumps, motors, and cables at the nano-scale [4]. The 1980s witnessed the beginning of nanotechnology’s golden era with the contribution of Richard E. Smalley’s research team and K. Eric Drexler. A new form of carbon, so-called “bulky-balls” or “fullerenes” or “buckminsterfullerenes” (Fig. 1.1), was discovered in 1985 by Richard E. Smalley along with Robert Curl and Sir Harold W. Kroto. This tremendous discovery helped the scientists won 1996 Nobel Prize in Chemistry. Each bulky-ball cluster is in the form of closed, convex, and spheroidal cage molecule formed by the arrangement of 60 carbon atoms in pentagonal and hexagonal faces [4]. In 1986, K. Eric Drexler published a book entitled “Engines of Creation: The Coming Era of Nanotechnology”, which is a true milestone and a crucial reference for the field on nanotechnology [4]. He offered the idea of a nano-scale “assembler”

Fig. 1.1  Schematic representation of fullerene. (Picture is drawn by ChemDoodle3D Version 3.0.0). Note: Buckminsterfullerene is named after the architect R. Buckminster Fuller owing to the resemblance between the carbon structure and Fuller’s geodesic domes. The popular name for the buckminsterfullerene is “bucky-ball” because this caged cluster is resembling a soccer ball where hexagon atom facets are arranged to form ordered closed structure pentagon atom facets serving as vertexes [4].

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being able to construct a copy of itself and of other arbitrarily complex items. His vision of nanotechnology, nowadays, is frequently called “molecular nanotechnology” [3]. In 1992, the scientist continued providing more technical and comprehensive description of the foundations and promising applications of nanotechnology in his book “Nanosystems: Molecular Machinery, Manufacturing, and Computation” [4]. K. Eric Drexler appreciably contributed to the driving force making nanotechnology a major scientific field, thus being often described as “the founding father of nanotechnology”. Also, in the early 1990s, carbon nanotubes were discovered by Sumio Iijima, another Japanese scientist, in 1991. These nano-scale structures, in their single-shell form (so-called single-walled nanotubes—SWNTs) are considered as the lengthened variants of the fullerenes mentioned above (Fig. 1.2) [4]. The innovative emergence of bionanotechnology branch was primarily attributed by Chad A. Mirkin’s research work which focused on self-assembled monolayers, design of new ligand, molecule-based electronic devices, nanoparticles, nanolithography, and DNA-directed materials synthesis. As a pioneer in chemical modifications of nanosystems, Chad A.  Mirkin provided the fundamental basis for bionanotechnology development in a number of varied application aspects and the motivation to learn how natural systems manipulate atoms in attempt to make new material generations [2].

1.1.2  P  owerful Assistant for Nanotechnology: Scanning Probe Microscopes (SPMs) The speculation of miniaturized devices was risen in the middle of the twentieth century, but it took some decades for such devices to appear. Chemists were already creating molecules atom-by-atom at the time that Feynman gave his talk, and chemistry nowadays is an enabling method for building molecules with dozens of atoms.

Fig. 1.2 Schematic representation of (10) carbon nanotube. (Picture is drawn by ChemDoodle3D Version 3.0.0). Note: Carbon nanotubes look like graphite sheets wrapped around into elongated cylinders with opened or cap closed ends [4]. The tube presented here is single-walled, although there are also double-­ walled and multi-walled carbon nanotubes.

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Since that talk, biology and physics fields have also created additional methods for engineering materials at the atomic scale [1]. Currently, a plentiful variety of methods are available for manipulating things at nano level. One of the most essential and powerful assistants for nanotechnology is the Scanning Probe Microscopes (SPMs), of which the introduction and development have impressively contributed to the opening and progression of nanotechnology era. The major milestone of nanotechnology’s history was invention of the Scanning Tunneling Microscope (STM) belonging to the SPM family in the 1980s by Gerd Binnig and Heinrich Rohrer, who won the 1986 Nobel prize in Physics for it. It was the first time that a microscope instrument like the STM could provide the ability to image small molecules and individual atoms, and the STM is still commonly used, especially to study the physics of semiconductors and metals [5]. It is able to directly obtain atomic-resolution three-dimensional (3-D) images of solid surfaces [6]. Much of the STM operation is conducted in ultra-high vacuum (UHV) and at low temperatures. The major downside of the STM is the requirement of conductive samples, thus ruling out most of its possible applications in important fields [5]. The invention of the STM was followed a few years later by the born of the Atomic Force Microscope (AFM) or Scanning Force Microscope (SFM) (Fig. 1.3). The AFM is the most popular type of SPM family because, different from the STM, it can be utilized with non-conductive samples, and so has extensive applicability. A drawback of the AFM is that the soft nature and stickiness of the biological samples can interfere with the tip, so atomic resolution could not be reached. A noteworthy improvement in the study of biological as well as other soft materials is made by the creation of tapping-mode AFM, in which the probe or the tip oscillates at a resonant frequency and at amplitude setpoint whilst scanning across sample surface. This type of AFM allows reconstructing a topographic image [4]. The SPM helps us open a direct window into the nano-scale world. This microscope family is one of the foremost tools that are making possible the current evolution of nanoscience and nanoengineering. Today, many other types of SPMs are

Fig. 1.3  Diagram of an atomic force microscope (AFM)

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invented, for example, Noncontact Atomic Force Microscope (NC-AFM), Low Temperature Scanning Probe Microscopy, Dynamic Force Microscope (dynamic AFM), and Molecular Recognition Force Microscope. All of them scan a surface with an ultrafine tip, placed very close to the surface (sometimes at distances equal approximately 1  nm), and measure tip-surface interactions such as the tunneling current between tip and sample in the case of STMs, and the interatomic forces in the case of AFMs [5]. Efforts have been made to create next generations of SPMs with greatly improved features.

1.2  Biotechnology and Nanotechnology Meet at Intersection 1.2.1  B  ackground and Definition of Nanotechnology and Bionanotechnology The fact is that biotechnology, nanotechnology and bionanotechnology are virtually novel concepts. Up to now, there is no consensus on the definition and scopes of these fields. To some extent, many new nanotechnological discoveries cross existing conceptual border of biotechnology and vice versa. It is not redundant to remark some fundamental definition in an effort to determine the scope or definition of bionanotechnology. 1.2.1.1  Nanotechnology A common definition of the term is a speculative field proposing to build a tiny machinery with components at nanometer (10−9 m) scale utilizing various principles of macroscopic engineering [7]. The term “nanotechnology” is defined by the National Nanotechnology Initiative (NNI, in the USA) as follows: “Nanotechnology is the understanding and control of matter at dimensions between approximately 1 and 100 nanometers, where unique phenomena enable novel applications. Encompassing nano-scale science, engineering, and technology, nanotechnology involves imaging, measuring, modelling, and manipulating matter at this length scale” [8]. Occasionally, the term “molecular nanotechnology” mentioned above can be used interchangeably with the term “nanotechnology”. Nanotechnology can be defined by another approach as a field that involves the manufacturing and engineering at nanometer scales, with atomic precision [2]. In his books, K. Eric Drexler has introduced his compelling idea of the design and computer modeling of various machines, in which nano-scale manipulators are used to build objects atom-by-atom such as structures built of diamond-like lattices of carbon and minute computers with moving parts whose size is within atomic scale. In a major revolution of nanotechnology, molecular nanotechnology presents human’s ambition of modifying

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matter one atom at a time. Scientists purchase such precision that every structure and action can be controlled at the level of individual atoms, and devices can perform with minimum size to reduce necessary resource as much as possible [7]. It is sometimes confusing whether structures smaller than 1 μm and larger than 100 nm are true nanostructures or not. Additionally, what if novel phenomena are originated by structures at this size range? In this case, they can be regarded as nanotechnology enabled materials, and thus they belong to nanotechnology study [2]. The behavior of a material of the nano-scale differs in primary ways—for instance, physical or chemical aspects—from that of the macro- and the micro-­ scales, which qualifies that material as a nano-scale material. Dimensions, together with structure and composition, impacts material properties in the miniature materials. The property transition predominantly results from at least two factors, including nanometer dimensions and the very large surface-to-volume ratio. The later means that atom is closed to an interface and that chemical bonds and interatomic forces dominate [9]. Prediction of alteration in material properties was also given by Richard Feynman. He noted that as we go down in size, problems would arise from the varying magnitude of various physical phenomena. In the molecular world, for instance, gravity would become less appreciable, Van der Waals attractions and surface tension would become more considerable [4]. On one hand, we may have to deal with various problems of engineering materials at such small scale. On the other hand, fortunately, several alterations in material behaviors, such as the distinctive molecule–solid and interface interactions at nanostructure surfaces and the large surface areas of nanostructures, inspire scientists and provide the foundation of research at an intersection of nanotechnology and biotechnology [9]. The specific binding of antibody molecules and antigens is an example of nano-scale behaviors where interfacial orientations play a key role. Two approaches for nanostructure fabrications involve top-down and bottom-up techniques. In top-down approach, objects are built down from the large to the small. Top-down methods include micro/nanomachining methods, lithography-­ based methods, and nonlithographic miniaturization. In bottom-up approach, objects are built up from the small to the large [6]. This bottom-up process is the one whereby systems and devices are assembled from molecular or atomic scaled elemental constituents into larger and progressively complex structures–as is usually used by nature to construct biological systems from proteins and other macromolecules. In practice, several combinations of top-down and bottom-up techniques are probably necessary to efficiently manufacture and integrate nano-scale systems [9]. 1.2.1.2  Biotechnology There are several ways to define the term “biotechnology”. Biotechnology can be simply defined as the commercialization of cell and molecular biology. The American Chemical Society defines biotechnology as the application of biological

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organisms, systems, or processes by various industries to learning about the science of life and the improvement of the value of materials and organisms such as pharmaceuticals, crops, and livestock [10]. Biotechnology can be described as the use of either living material or biological products to create new products applied in various fields with the ultimate goal to benefit humanity [11]. United States National Science Academy gives the definition of biotechnology as the “Controlled use of biological agents like cells or cellular components for beneficial use”. This definition covers both classical and modern biotechnology. More generally, biotechnology can be defined as “The use of living organisms, cells or cellular components for the production of compounds or precise genetic improvement of living things for the benefit of man” [12]. Despite the long history of ancient and classical biotechnology, biotechnology has just really exploded in the twentieth century, along with the explosion of numerous science branches—from chemistry, physics, engineering to computer application and information technology [12]. The so-called modern biotechnology was born. Biotechnology, especially modern biotechnology, arose from the use of natural enzymes to manipulate the genetic material or genetic code, which was then exploited to modify whole organisms. Biotechnology or recombinant DNA technology is the most recent stage in plant breeding development. Biotechnology can be applied as a process of selective breeding involving identification of one or more known genes responsible for a certain trait and to exactly delete, insert, or modify them in plants. This widens the range of traits and enables desired specific genes to be expressed in crop plants without the uptake of unwanted traits [13]. The applications of biotechnology in some fields, is still the subject of public controversy. For example, genetically modified crops, which are created by biotechnology, are used as key to reduce hunger while they are considered a further risk to food security by several people [14]. Gene mounting and genetic engineering have been upgraded in the enhancement of industrial fermentation. As a result, biotechnology become a novel approach for manufacturing commercial products using living organisms. Moreover, knowledge of bioprocesses has been exploited to deliver good-quality products. The application of biological sciences in industrial processes is known as bioprocess. Currently, most pharmaceutical and biological products are manufactured in well-defined industrial bioprocesses [15]. The atomic details were not prerequisite to achieve the end goal of biotechnology. Today, we are capable of work on objects at a much finer level, and we have the tools to fabricate biological machines atom-by-atom according to our own designs [1]. It is speculated that more and more innovative breakthroughs will be achieved as biotechnology has overlapped with nanotechnology—another authoritative technology.

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1.2.1.3  Bionanotechnology Human’s history has recorded a variety of scientific and technological achievements inspired or guided by the nature world around us. Two interesting examples includes the airplane inspired by the bird and the submarine inspired by the fish. Until now, specialists still make many efforts to improve the design and performance of airframe based on what they have learned from the bird and the bat. Nature has taught us enormous lessons, expanding our reachable frontiers to the very high sky and very low seabed. The subset of nanotechnology inspired by nature, especially by biological world, has also helped us go into the nano-micro world. Biotechnology is described as an interdisciplinary area governing the application of chemistry and biology in engineering sciences. In the past decades, the application of biotechnology focuses only on horticulture, plant cell technology, and animal biotechnology. Today, the development of biotechnology, however, has moved beyond the borders. The knowledge has grown in many engineering fields as well as in biomaterial and nano-biotechnology products [15]. Bionanotechnology “debuted” as a young subdiscipline of nanotechnology in which the biological systems act as an inspiring factor. In this subdiscipline, nanotechnology looks to biological world for starting the research and manufacture. It is described as the use of natural biological building blocks—such as carbohydrates, lipids, proteins, and nucleic acids—and biological activity and specificity for the development of technology at the nano-scale [4]. In some literatures, bionanotechnology can be defined as the subset of nanotechnology where biological world involves in either the inspiration or the ultimate goal. A number of authors define bionanotechnology as atom-level manufacturing and engineering that use biological systems for guidance or nanotechnology for applications in biomedical or biological fields [2]. This definition is overlapped with another term “nanobiotechnology”—a term relating to the application of nano-scale principles and tools to biology [4]. In fact, according to several authors, there is an interchangeable use of “bionanotechnology” and “nanobiotechnology” terms. Throughout this book, nevertheless, the term “bionanotechnology” will be used to describe the use of biological principles such as recognition and assembly for applications in nanotechnology. In other words, nanotechnology hereby is inspired and guided by biosystems—or biological systems, unlike nanobiotechnology that uses nanotechnological tools and principles for study of biological world. This definition does not limit the scope of this field, since the discoveries assisted by bionanotechnology have hugely contributed to the progress of numerous fields, including biology-­related ones. This fascinating thing will be further discussed in later chapters of this book. Despite the diversity of bionanotechnology areas, all areas share a central concept: the ability to design molecular machineries with a precision or specification at atomic scale [1]. Indeed, working examples of these machines exist today within

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living cells. Nano-sized manipulators for building biomolecules have been present in the earliest cells. An abundance of molecular machines, structures and processes have been perfected by living organisms through modification and evolution over trillions of generations [7]. The structures of living organisms—from a simple system of prokaryote to a very complicated system like our bodies—are virtually the inexhaustible inspiration sources for the study and discoveries in bionanotechnology. 1.2.1.4  Natural Biological Assembly at the Nano-Scale When studying bionanotechnology, you should take a look on the concept of “self-­ assembly”, which is the essential theme driving the assembly of numerous complex molecules and structures in biological systems. Our usual cognition about the macroscopic world may mislead us about the self-assembly of biomolecules because the forces involved in macroscopic structures are different from those in biomolecular structures and interactions. Unlike engineering in our macroscopic world, which is mainly based on gravity effect on solid objects, the dominated phenomenon in the molecular world is the effect of thermal motion on the intramolecular and intermolecular atomic interactions. In the molecular world, kinetic energy is proportional to the temperature and which manifests itself as vibrational, rotational, and translational motions. The forces assembling molecules together are constantly fighting against these motions and are frequently outweighed by them [7]. Perhaps this is one of the most difficult limitations to overcome when we attempt to create self-­ assembling objects. When building and manipulating objects in cellular environment, the unusual cellular environment itself is another problem that we should concern. Take proteins as an example. After synthesized in cells, proteins diffuse to their ultimate sites of function where untold competitors of target molecules are present. Thus, a typical protein is required to be able to recognize its unique target among many competitors. The build of a structure is more simply in the macroscopic world, where an engineer can selectively handle assemble of its parts. However, for a proper binding of molecules, each molecule is obligatorily designed with a specific recognition to its target [7]. Plentiful artificial self-assembling systems imitating natural self-assembly of molecules are constructed. Building blocks of complex polymer molecules are snapped easily and economically on wires, tubes, beads, flat supports, in suspensions, and liposomes. These self-assembled structures can possess genetically introduced bio-functionality in order that general molecules are prevented from fusing with cell membrane layers. DNA, peptides, protein foldings, ATP synthase, and lipid bilayers are promising candidates for self-assembly [2]. Chapter 5 of this book will discuss in more detail about biological self-assembly and its applications.

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1.2.2  Notable Prospects of Bionanotechnology 1.2.2.1  Why Bionanotechnology? We nowadays cannot deny the importance of bionanotechnogy in our life. Bionanotechnology has the ability to surpass limits, and it has undoubtedly improved health care as well as our quality of life. Fundamental knowledge achieved in bionanotechnology has been translated to productsor devices that will more and more impact many aspects of life in the near future. For instance, advanced biotechnology with nanomaterials was found to be able to enhance the bioremediation efficiency of contaminated soils [16]. Nanopesticides and nanofertilizers have been created for application in agriculture. Additionally, biosensors applied in diagnostics or food safety become attractive topics. Liposomes have emerged and considered as a potential nanocarrier allowing the delivery of active substances or therapeutic agents to targeted sites. New discoveries in this bionanotechnology are believed to surprise us and change our vision as well as our ability to handle different arenas, including material manufacture, medicine, pharmacy, biotechnology, agriculture, environment, food and cosmetic production along with others. Throughout this book, we will let you—the reader—to travel into the world of bionanotechnology with its appealing and up-to-­ date outcomes. 1.2.2.2  How Does Bionanotechnology Inspire Other Disciplines? As mentioned before, bionanotechnology adds to biotechology a prominent ability which is the ability to design and modify atomic-scale elements of the objects. Atomic-specific bionanomachineries can be designed using bionanotechnology. These machines perform an explicit three-dimensional molecular task, and in some excellent applications, individual control mechanisms can be embedded in bionanomachineries’ structures [4]. Biotechnology, which is itself a potent discipline, has been revolutionized through bionanotechnological research and development. For instance, the surface functionalization at nano-levels is a crucial bionanotechnological aspect that many biotechnology companies have harnessed [2]. Bionano entities can be functionalized by polymers, viruses, nucleic acids, anti-­ bodies or other proteins to aid diagnostic and therapeutic application [2]. Early diagnosis and treatment have been much enabled by bionanotechnological development. This is indeed meaningful because lots of lives of patients with fatal conditions and diseases can be saved if physicians can timely detect diseases. Bio-imaging and drug delivery become a dominant part of bionanotechnology industry, and targeted bio-imaging and drug-delivery are of high interest today. Bio-­ imaging has been improved not only to enhance imaging in techniques such as ultrasound, magnetic resonance imaging (MRI), in-vitro cell imaging but also to

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advance imaging technologies such as transmission electron microscopy (TEM), atomic force microscope (AFM), environmental scanning electron microscope (ESEM), and near-field scanning optical microscopy (NSOM). Supported by surface functionalization techniques, nano-vectors are endowed with several features for drug delivery such as escaping the reticuloendothelial system (RES), crossing the blood–brain barrier (BBB), avoiding toxicity and overdose, automatic-­ identification of tumor sites along with others [2]. Bionanotechnology practice apparently has much wider scope beyond the bother of biological applications. For example, bionanotechnology could be applied to fabricate metal nanowires, interconnects or other physical elements at the nano-level using DNA oligomers, protein fibrils, or peptide nanotubes [4]. An developing branch of bionanotechnology is the adaptation of biocatalytic proteins or enzymes to the synthesis of nanomaterials since this approach requires the mild conditions for the biological catalysis and thus makes the manufacturing procedure more environmentally benign, and/or less side product generating [17]. Undoubtedly, bionanotechnology somehow makes a fairly pronounced contribution to environment and ecosystem protection. When working on tiny entities, it is still, however, necessary to be aware of their influences on surrounding environment and use bionanotechnology wisely. In the end, we deploy bionanotechnology to prevent and treat pollution, not to cause another pollution issue. Devise environmentally conscious solutions are definitely encouraged to let bionanotechnology benefit the most in the long term. Our goals in this book are to let the reader approach the essential concepts, key achievements and prime examples of the field to enable beyond study of bionanotechnology as well as let them appreciate the innovative approaches and meaningful discoveries of the field.

1.3  Summary The coining of the term “nanotechnology” was first mentioned in a 1974, but it took nearly one decade for its birth when K. Eric Drexler talked about it in 1981. Scanning probe microscopes (SPMs) family is one of the most essential and powerful assistants contributing to the opening and progression of nanotechnology era. The development of nanotechnology inspires more and more innovative ideas and achievements in a diversity of fields. Additionally, biotechnology, another attractive and powerful discipline, really exploded in the twentieth century with the birth of modern biotechnology. It can be considered that bionanotechnology is the intersection where nanotechnology and biotechnology meet with novel nanotechnological discoveries cross existing conceptual border of biotechnology and vice versa. Bionanotechnology is simply defined as a young subdiscipline of nanotechnology, in which the biological systems act as an inspiring factor. There is speculation that more and more breakthroughs will be achieved as nanotechnology has overlapped with biotechnology.

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Key Definition Atomic force microscope is a technique among scanning probe microscope family that is used to measure topography on nonconducting surfaces as well as atomic and molecular resolution on surfaces. This technique measures Van der Waals and electrostatic forces between cantilever tip and surface and can be utilized with non-­ conductive samples. Bionanotechnology is defined as the subset of nanotechnology where biological world involves in either the inspiration or the ultimate goal. Biotechnology is described as the application of biological organisms, systems, or processes by various industries to learning about the science of life and the improvement of the value of materials and organisms such as pharmaceuticals, crops, and livestock. Nanotechnology is the understanding and control of matter at dimensions between approximately 1 and 100 nm, where unique phenomena enable novel applications. Scanning probe microscope is a family of techniques that use a probe or sharp tip to create an image of a sample by scanning its surface and recording the resulting interaction. These microscopes are used to measure surface electronic structure and/ or atomic structure. Scanning tunneling microscope is a technique among scanning probe microscope family that probes both surface electronic and atomic structure by measuring tunneling current from the probe tip to sample surface across a narrow vacuum (dielectric) gap. Abbreviations Abbreviation 3-D AFM ATP BBB DNA ESEM MRI NC-AFM NNI NSOM RES SFM SPMs STM SWNTs TEM UHV

Full name Three-dimensional Atomic force microscope Adenosine triphosphate Blood–brain barrier Deoxyribonucleic acid Environmental scanning electron microscope Magnetic resonance imaging Noncontact atomic force microscope National Nanotechnology Initiative Near-field scanning optical microscopy Reticuloendothelial system Scanning force microscope Scanning probe microscopes Scanning tunneling microscope Single-walled nanotubes Transmission electron microscopy Ultra-high vacuum

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Problem Sets 1.1. What are the two nano-scale carbon structures that were discovered in the beginning of nanotechnology’s era? 1.2. What is a drawback of Atomic Force Microscope (AFM)? 1.3. True/False questions: (a) Engineering materials at nano-scale may have both advantages and disadvantages. (b) The specific binding of antibodies and antigens is an example of macro-­ scale behaviors where interfacial orientations play a key role. (c) Biotechnology can be defined as “The use of living and non-living organisms, cells or cellular components for the production of compounds or precise genetic improvement of living and non-living things for the benefit of man”. (d) The term “bionanotechnology” hereby is described as nanotechnology that is inspired and guided or biological systems, unlike nanobiotechnology that uses nanotechnological tools and principles for study of biological world. 1.4. Fill in the blanks below: (a) The major milestone of nanotechnology’s history was invention of ______ belonging to the SPM family in the 1980s. (b) The probe of ______ AFM oscillates at a resonant frequency and at amplitude setpoint while ______ across sample surface. This type of AFM allows reconstructing a topographic image. (c) Bionano entities can be functionalized by ______ to aid diagnostic and therapeutic application. Answers 1.1. Fullerenes and carbon nanotubes (CNTs). 1.2. The soft nature and stickiness of the biological samples can interfere with the tip, so atomic resolution could not be reached. 1.3. True; b) False; c) False; d) True. 1.4. (a) The major milestone of nanotechnology’s history was invention of Scanning Tunneling Microscope (or STM) belonging to the SPM family in the 1980s. (b) The probe of tapping-mode AFM oscillates at a resonant frequency and at amplitude setpoint while scanning across sample surface. This type of AFM allows reconstructing a topographic image. (c) Bionano entities can be functionalized by polymers, viruses, nucleic acids, anti-bodies or other proteins to aid diagnostic and therapeutic application.

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References 1. Goodsell DS. Bionanotechnology: lessons from nature. Wiley; 2004. 2. Papazoglou ES, Parthasarathy A. Bionanotechnology. Morgan & Claypool; 2007. 3. Hulla JE, Sahu SC, Hayes AW.  Nanotechnology: history and future. Hum Exp Toxicol. 2015;34:1318–21. https://doi.org/10.1177/0960327115603588. 4. Gazit E.  Plenty of room for biology at the bottom: an introduction to bionanotechnology. Imperial College Press; 2007. 5. Schmid G. Nanotechnology. Wiley; 2008. 6. Bhushan B. Springer handbook of nanotechnology. Berlin: Springer; 2004. 7. Goodsell DS.  Biomolecules and nanotechnology. Am Sci. 2000;88:230–7. https://doi. org/10.1511/2000.3.230. 8. National Science and Technology Council. National nanotechnology initiative strategic plan; 2014. https://www.nano.gov/sites/default/files/pub_resource/2014_nni_strategic_plan.pdf. Accessed 26 Aug 2018. 9. National Research Council. Implications of emerging micro and nanotechnology. The National Academies Press; 2002. 10. Koltuniewicz AB. Sustainable process engineering: prospects and opportunities. De Gruyter; 2014. 11. Verma A, Agrahari S, Rastogi S, Singh A.  Biotechnology in the realm of history. J  Pharm Bioall Sci. 2011;3:321–3. https://doi.org/10.4103/0975-7406.84430. 12. Nair AJ. Introduction to biotechnology and genetic engineering. Infinity Science Press; 2008. 13. Harriman RW, Bolar JP, Smith FD.  Importance of biotechnology to the horticultural plant industry. J Crop Improv. 2006;17:1–26. https://doi.org/10.1300/J411v17n01_01. 14. Qaim M, Kouser S. Genetically modified crops and food security. PLoS One. 2013;8:e64879. https://doi.org/10.1371/journal.pone.0064879. 15. Najafpour G. Biochemical engineering and biotechnology. Elsevier Science; 2015. 16. Gong X, et al. Remediation of contaminated soils by biotechnology with nanomaterials: bio-­ behavior, applications, and perspectives. Crit Rev Biotechnol. 2018;38:455–68. https://doi.org /10.1080/07388551.2017.1368446. 17. Bhushan B. Encyclopedia of nanotechnology. Amsterdam: Springer; 2012.

Chapter 2

Fundamental of Biological Systems and Bionanotechnology

2.1  Nucleic Acid in Bionanotechnology Nucleic acids including DNA and RNA have exhibited a wide range of biochemical functions, such as the storage and transfer of genetic information, molecular recognition, the regulation of gene expression and catalysis. Nucleic acid engineering in bionanotechnology is one of the most key DNA nanotechnologies including DNA origami, aptamers, and ribozymes. The base-pairing and self-assembly are basic templates for nucleic acid engineering in bionanotechnology [1–3].

2.1.1  DNA as a Biomaterial in Bionanotechnology DNA is a double helix where two long chains are wound around a common axis in a helical fashion to yield double stranded DNA (dsDNA), which is known as the carrier of genetic information. Each the double helix is mainly formed by repeating nucleotides consisted polymers, in which a single nucleotide composes three components including a sugar molecule, a phosphodiester group and a nitrogenous base or nucleobase. Generally, four classes of nucleobases including Adenine (A), Cytosine (C), Guanine (G) and Thymine (T) are primarily responsible for constructing DNA and the sequence of these four bases that encodes the information. While T and C are pyrimidines, A and G are purines that consist of a pyrimidine fused to an imidazole ring [1, 4]. Many studies indicated DNA have a potential material for designing n and constructing nanostructures and devices. Also, it is known as the basic building block of life and the genetic material of most organisms and organelles. Moreover, due to the double stranded helical structure, DNA is regarded as an most important material in self-assembly applications [5]. In recent years, DNA has been applied with various roles, not only limiting in the role of genetic molecule in biological systems but also regarding as a generic © Springer Nature Singapore Pte Ltd. 2020 Y.-C. Lee, J.-Y. Moon, Introduction to Bionanotechnology, https://doi.org/10.1007/978-981-15-1293-3_2

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­ aterial for nanoscale engineering. Due to possessing exceptional properties such m as biological function, biocompatibility, molecular recognition ability, and nanoscale controllability, various DNA materials have been created with potential properties in both the biological functions and the structural characteristics of DNA molecules. A natural bridge linking nanotechnology and biotechnology has been built due to the DNA materials, which leads to far-ranging real-world applications. In bionanotechnology, DNA material have been classified into two classes: substrate and linker based on the DNA role in the construction (Fig. 2.1) [6]. As a linker, DNA can be used to interface with other functional moieties such as gold nanoparticles (AuNPs) [7, 8], clay minerals [9], proteins [10], and lipids [11] to form hybrid materials with desired properties. For illustration, due to the presence of linker DNA, AuNPs may be easily functionalized with thiol-modified DNA and polymerized to form large aggregates (Fig. 2.2), which will change the color of AuNPs from red to blue because of the coupling of gold surface plasmon when AuNPs are close to each other [12]. Due to this color change, AuNPs-DNA can be used to construct colorimetric sensors for detection of nucleic acids, metal ions, small molecules, and even cells [13]. In contract, DNA can also act as a substrate which may interface with enzymes in biochemical reactions [6]. DNA materials in various formats, i.e. branched nanostructures and hydrogels were generated based the interface between DNA substrate and specific enzymes [14]. For example, employing DNA as a substrate, a bulk hydrogel made entirely of DNA is successfully synthesized by using enzymatic ligation. By using this DNA hydrogel as a structural scaffold, a protein-producing DNA hydrogel was fabricated by linking plasmid DNA on the hydrogel matrix due to enzymatic ligation. In addition, taking the advantages of both DNA materials and polymerase chain reaction (PCR), a thermostable branched DNA remaining intact even under denaturing conditions was formed. Moreover, via enzymatic polymerization, it was demonstrated that a

Fig. 2.1  DNA materials in bionanotechnology. Reprinted with permission from [6], Copyright © 2014 American Chemical Society

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Fig. 2.2  Schematic representation of DNA directed assembly and melting of DNA-functionalized AuNPs. Reprinted with permission from [13]. Copyright © 2011 American Chemical Society

p­ hysical DNA hydrogel possessing unique internal structure and several mechanical properties was recently constructed. In the construction of DNA materials, DNA has showed great potential as both substrate and linker, but it is still in the initial stages to become a well-established and widely applied material. Therefore, several important challenges to develop the applications of DNA includes the ease of design and fabrication, minimizing cost, and scaling-up. It is expected that DNA materials will continuously bridge the gap of nanotechnology and biotechnology and it will be a potential material to be employed for many real-world applications.

2.1.2  Structural DNA Nanotechnology 2.1.2.1  DNA Origami The term origami comes from the Japanese folk art which is a folding paper into a special shape [15]. In 2006, the “DNA origami” method was first introduced by Paul W. K. Rothemund [16]. According to the method, the formation of a DNA origami can be conducted in five stages, in which the first two was performed by hand and the last three aided by computer. In the first step, a geometric model of a DNA structure will be created with the desired shape that is 33 nm wide and 35 nm tall. The parallel double helices are cut to fit the shape in sequential pairs and are constrained to be an integer number of turns in length. The second step is conducted to incorporate a periodic array of crossovers between helices [17]. Crossovers represent positions at which a strand of DNA following along one ring switches to an adjacent ring, bridging the interhelical gap. In next step, the design of a set of ‘staple strands’ that provide Watson–Crick complements for the scaffold and create the periodic crossovers. At these crossovers, staples reverse direction; thus crossovers are antiparallel and a stable configuration well characterized in DNA nanostructures [18]. To minimize and balance twist strain between crossovers, the non-integer number of base pairs per half-turn and the asymmetric nature of the helix was used. Therefore, to balance the strain created by representing 1.5 turns with 16 bp, the arrangement

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of periodic crossovers in a glide symmetry, namely that the minor groove faces alternating directions in alternating columns of periodic crossovers [19]. But this approach makes scaffold crossovers not balance. Thus the change of the position of the twist of scaffold crossovers is conducted to minimize strain; staple sequences are recomputed accordingly in the fourth step. Along seams and some edges the minor groove angle (1508) places scaffold crossovers in tension with adjacent periodic crossovers; such situations are left unchanged. In the final step, to give the staples larger binding domains with the scaffold (in order to achieve higher binding specificity and higher binding energy which results in higher melting temperatures), pairs of adjacent staples are merged across nicks to yield fewer, longer, staples. To strengthen a seam, an additional pattern of breaks and merges may be used to produce staples that cross the seam and a seam that is spanned by staples is termed ‘bridged’. Because a long strand of DNA will be folded to form a desired structure due to the support of smaller staple strands, this method is called DNA origami [15]. DNA allows the programmed self-assembly of two dimensional (2D) and three dimension (3D) with shapes and patterns at nanoscale. Particularly, DNA origami has proven useful for organizing nanoscale objects, such as biomolecules, nanoelectronic or photonic, small molecules and moving DNA machines. In addition, a single origami is able to perform as a template that contains up to 200 small devices, however only a single multi-component electronic or optical device is constructed. It would be desirable to organize origami into periodic arrays in many technological applications such as wiring of electronic devices together, creating cooperative optical effects as seen in optical meta-surfaces, and creating DNA ‘etch masks’or enabling easier extraction of single-molecule biophysical data [20, 21]. In 2009, there are a lots of invented 3D DNA origami structures, in which four independent hollow 3D DNA origami structures (two boxes, one tetrahedron, and prisms) which consist of planar faces were reported and the multilayer, honeycomb-lattice DNA origami design is also introduced [22]. Among these four structures, the two DNA origami boxes have been designed to attain opening and closing mechanisms and thus can also be considered pioneering nanomechanical DNA origami devices. In addition, DNA origami structures have been recently utilized to decorate solid-state nanopores or to open nanopores in lipid bilayers. 2.1.2.2  DNA Origami Devices Recently, DNA nanotechnology has enabled us to create various DNA nanodevices with rotating parts. Numerous useful nanomechanical DNA devices have been developed due to the structure of DNA origami, in which the long single-stranded will be folded into the designed structures with the assistance of short staple strands [23]. “DNA origami pliers”, the first developed nanomechanical DNA origami device, can be regarded as “single-molecule beacons” or function as pinching devices for the detection of biomolecules [24]. The use ‘DNA origami forceps’ and ‘DNA

2.2  Peptides and Proteins in Bionanotechnology

19

o­ rigami pliers’, which consist of two levers ~170 nm long that is connected at a fulcrum, variety of single-molecule inorganic and organic targets that ranges from metal ions to proteins is able to visually detected by using AFM (atomic force microscopy) with a shape transition of the origami devices. Pinching, zipping or unzipping are often chosen in any detection mechanism of interests and they are suitable for using orthogonally with various shape of origami devices. Pinching is defined as a process detecting single-target molecules binding to multiple ligands each. For this purpose, each of the staple strands will attach two ligands placed in the concavities, and these ligands cooperatively capture a single-target molecule between the jaws. Although selective pinching and detection of a target molecule was successful using protein–ligand bindings, single-molecule pinching of other targets binding more weakly is very difficult among the strongest of all biological interaction. Second detection mechanism that is available from the present nanomechanical DNA origami devices and is appropriate for such targets is a zipping that involves multiple binding events. Multiple elements binding together in the presence of the target are introduced to each of the levers and cooperatively triggering selective closure of the origami devices. While unzipping is a reverse process compared with the zipping mechanism and it is the third detection mechanism of the present nanomechanical DNA origami devices. DNA can also be used to construct devices that perform robotic tasks such as sensing, computation, and actuation [25]. By using cadnano, a computer-aided design tool for DNA origami, a novel DNA nanorobot with a practical function directly linked to its movement was developed [26]. Basically, the devices were designed as a hexagonal barrel that consists of two domains covalently attached in the rear by single-stranded scaffold hinges, or noncovalently fastened in the front by staples modified with DNA aptamer–based locks. Initial self-assembly proceeds in a one-pot reaction in which 196 oligonucleotide staple strands direct a 7308-base filamentous phage–derived scaffold strand into its target shape during a thermal annealing ramp of rapid heating followed by slow cooling.

2.2  Peptides and Proteins in Bionanotechnology Generally, DNA molecules have usually gained more attention than peptides for its application in bionanotechnology. Due to the following features, however, peptides and proteins are able to be practical candidates for new material synthesis and device fabrications [27].

2.2.1  The Supramolecular Structure of Peptides and Proteins Small peptides are made up of short amino acid sequences that have less complicated functionality than proteins. While compared to proteins the oligomeric polymers may not perform highly specialized tasks. They are likely to be easily

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synthesized with desired amino acid sequences by establishing the chemical and genetic engineering procedures, and therefore they are versatile components of the bionanotechnology toolbox [28]. Normally, in protein construction, we can use 20 different standard L-α-amino acids. However, we are only likely to synthesize only 10 types of amino acids in 20 amino acids required for synthesis of proteins found in humans. Therefore, we must obtain the rest of 10 amino acids, called essential amino acids, in the diet. Moreover, the amino acid sequence of a protein will be encoded in DNA. Normally proteins are synthesized through a series of steps of transcription and translation, which will be discussed in detail in next sections [29]. Proteins are known as macromolecules that have four different levels of structure including primary, secondary, tertiary and quaternary (Fig  2.3). The primary structure will be built by the combination of amino acid sequences. In secondary structure, depending on hydrogen bonding, stretches or strands of proteins will possess distinct characteristic local structural conformations. The right-handed coiled strand (α-helix) and the sheet conformation consisting of pairs of strands lying side-by-side (the ß-sheet) are two main types of secondary structure. The tertiary structure of proteins is overall three dimension (3D) shape of entirely protein molecules. Protein subunits is a special protein made up of multiple polypeptide chains and the quaternary structure is a larger aggregate protein complex through refers interact these proteins subunits [29]. Proteins are actively involved in the following functions: (i) enzymatic reactions for inorganic synthesis; (ii) controlled nucleation, growth, and morphogenesis; (iii) transport of raw materials [28]. In biology, among the major building blocks, proteins are central to the assembly of biological materials that have highly controlled nanostructures and functions. Generally, biological hard tissues will be assembled in aqueous environments under the mild physiological conditions using biomacromolecules: mainly proteins but also carbohydrates and lipids through the genetic control of organisms [28].

2.2.2  Sensors Based Peptides and Proteins Recently, peptides and proteins have been developed with active roles as useful building blocks in the design of sensors. For illustration, nanosensor based protein nanopores is one of the most common devices that was designed for applications of proteins in bionanotechnology [30]. In this type of sensor, ionic current blockade occurs as a single molecule is translocated though the channel protein, and this ionic current blockade contains information about the identity, structure, concentration and dynamics of the target molecule. It has been shown that ss-DNA could be detected label-free in a sequence-specific manner via translocation in nanopores, and this approach shows great promise for the development of new sensors [27, 30]. Also, self-assembly of peptides can be used to trigger an optical signal for biosensing [27]. Ghadiali and Stevens generated nanoparticle enzyme sensors by immobilizing a peptide sequence on the substrate of an enzyme on gold nanoparti-

2.2  Peptides and Proteins in Bionanotechnology

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Fig. 2.3  Levels of protein structure. (a) Primary; (b) Secondary; (c) Tertiary; (d) Quaternary

cles, and the enzyme activity induces the assembly or the disassembly of the nanoparticles, thus resulting in a variation in the gold plasmon resonance that yields a color change of the solution [31]. It was demonstrated that nanoparticle-based sensor systems containing biotinylated ATP molecules may detect target peptides as the kinase reaction induced by the peptide could drive the crosslinking of gold nanoparticles functionalized with the peptide substrate and streptavidin [32]. Similarly, Some recent studies functionalized gold nanoparticles by peptides with high affinity for development of novel sensors to detect heavy metals, because it is the presence of the metal ions that could aggregate these nanoparticles to create changes in the intensity and position of the plasmon absorbance peak, depending on the types of ions [33]. Recently, the most popular system in biomolecular sensor applications is the integration of peptides and proteins with optical probes, and a new emerging sensor format is the integration of peptides and their derivatives in electrochemical sensors [27]. For instance, Yemini et al. designed and built a highly sensitive amperometric enzyme biosensor based on immobilizing self-assembled peptide nanotubes that is

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attached to a gold electrode surface [34]. This biosensor enables a sensitive detection of glucose base on monitoring the hydrogen peroxide which is produced by an enzymatic reaction between a glucose and the glucose oxidases attached onto the peptide nanotubes. In addition, based on using ethanol dehydrogenase and NAD+, a sensitive detection of ethanol may be conducted by the marked electrocatalytic activity toward NADH.  In another approach, non-conductive peptide nanotubes were modified with antibodies to develop sensitive sensors for viruses (Fig  2.4) [35]. The sensor chip used the peptide nanotubes that were prepared by self-­ assembly from bollaamphiphilic peptide monomers and then coated with antibodies in a simple incubation process. These peptide nanotubes were assembled onto the device platform and headed to the gap between a pair of electrodes due to positive dielectrophoresis. Pathogen detection was happened through the difference in the dielectric properties of viral particles and water molecules.

2.3  The Biological System of the Elements (BSE) At the molecular level, biological processes are based on physical and chemical conditions whose fundamental chemical systematics in the Periodic System of the Elements (PSE) were introduced by Mendeleyer and Meyer in 1869. However, these physical and chemical regularities are frequently modified in biological systems to adapt all organismic life to the aqueous environment. Because the position and classification of the chemical elements in PSE does not permit any statement to be offered about their functional essentiality, acute, or chronic toxicity for living organisms, Biological System of the Elements (BSE) has been developed (Fig 2.5a,b) [36]. BSE primarily considers aspects of basic biochemical and physiological research which includes: (a) the expression as a linear correlation coefficient of the interelement relations between single elements, (b) uptake forms of single elements and their compounds into the living organism, (c) the physiological function of individual elements relating to evolutionary development of organic life in the inorganic environment. Virus Antibody for virus Au

Peptide nanotube

Au

SiO2 n-Si

Fig. 2.4  Design of the pathogen-sensor platform assembled from peptide nanotubes. The peptide nanotube incorporates virus-recognition elements on the surface

2.3  The Biological System of the Elements (BSE)

23

2.3.1  Interelemental Correlations The high interelemental correlations of the elements Ca, P, N, K and Mg for 54 species growing in the field was introduced by Garten based on correlations between concentrations of elements in plants [37]. It was indicated that the high correlation coefficients for N and P is due to the high association of these two elements, especially in protein biosynthesis and for Ca and Mg, this is because of the basis of common enzyme activators during various metabolic processes. The result of analyses of multielement correlations conducted the 1980s is shown in Fig. 2.5a [36]. The correlation data represented an important criterion in compiling the BSE. According to the correlation data, it is clear that for the alkaline metals, the element potassium (K) and the alkaline-earth metals (Ca and Mg), and to a certain extent also Sr, they have both high correlations to each other and also to the macronutrients N and P. In addition, the correlation has a significantly decreasing tendency in the sequence Ca, Mg, Sr and Ba although the ionic radii of the hydrated elements do not display any great differences (Ca2+: 0.6 nm; Mg2+: 0.8 nm; Sr2+: 0.5 nm; Ba2+: 0.5 nm). Potassium is likely to form high positive correlations with almost macroelements (K/Ca: 0.7545; K/N: 0.8370; K/Mg: 0.7928; K/P: 0.7768) and halogens (K/Br: 0.8684; K/CI: 0.6904), which makes it has an outstanding role as an electrolytic element in plant metabolism. Generally, the alkaline metals rarely tend to form towards complex structures, while the alkaline-earth metals have a moderate tendency and the transition metals have a strong tendency [36]. The form of these elements transported in the plant organism may be determined due to this property. According to their function, Na+ and K+ ions will basically function as transporters of charges, Mg2+ and Ca2+ ion as stabilizers of organic structures and information transmitters, and the transition metals, in combination with proteins, as catalysts. With a rule is greater than r = +0.9 the elements Al, Fe, Sc and La have a high correlation tendency, which can be attributed to the trivalent charge state of the cations of these elements and the very similar radius of the hydrated ions Al3+, Fe3+ and La3+ of 0.9 nm. Also, this can be regarded as the reason for the correlations between the lanthanide elements or with Al, Fe and Sc. Boron can be regarded as an essential element for plant due to its high correlations with P (r = + 0.7917) and N (r = +0.8121). The high correlation of P and N at r = +0.8352 confirms the high degree of association which the two elements display, especially during protein biosynthesis [37].

2.3.2  The Biological Function of Elements In the living organism, the importance of an element is not evaluated based on the amount contained in the organism, therefore a systematic division of their roles according to physiological and biochemical aspects is necessary. Normally, there

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Fig. 2.5 (a) Basic biological system of the elements; (b) The biological system of the elements with correlation data from linear regression analysis. Reprinted with permission from [36]. Copyright 1994, Elsevier

2.3  The Biological System of the Elements (BSE)

25

are the 30 essential elements classified into the six bulk or structural elements, five macrominerals, and 19 trace elements (Table 2.1) [38]. C, H, O, N, P, S, Si and Ca are essential elements in the constitution of the functional molecular structural elements of the cell metabolism (proteins, lipids, carbohydrates, nucleic acids, etc.) and they are regarded as structural elements. Nitrogen and sulphur are biochemically integrated into the carbon chain by being firmly bound to the organic substance after reducing their generally high oxidation stage. Whereas, phosphorus, boron and silicon rather tend towards ester formation with OH groups of the most varied molecules, particularly the sugars and are not reduced. All structural elements in the top left of the BSE (Fig 2.5b) seem to be the elements which during evolution have developed via the photochemical process from a silicon dioxide matrix towards the basic organic matrix as the 'building blocks ' of life. Therefore, Si is known as the former structure-forming element on Earth and it is present as a structural element totally (e.g. diatoms) or partially (e.g. Sphenopsida) in lower plants [36]. The H atom represents an exception within the structural elements and also in the chemical system of the elements: (i) provides the reduction equivalents in many redox processes; (ii) responsible for the pH value conditions in the cell body in the form of the H3O+ ion. The elements K, Na, Ca, Cl and Mg are called as electrolytic elements because they are needed for the constitution of specific physiological potentials and are necessary for maintaining defined osmolyric conditions in cell metabolism. In the BSE, the electrolytic elements and the structural elements stay next to each other. The element Ca may occur simultaneously as a structural element and an electrolytic element. The growth and survival of cells and organisms must need to the presence of trace elements, which are called essential ultratrace elements. Normally, they ­usually occur and function in cells at extremely low concentrations, usually far less than 1 μM and as low as 10−8–10−9 M [38]. Moreover, the biochemical criteria for an essential element includes: (1) present in tissues of different animals at comparable concentrations; (2) similar physiological or structural abnormalities will occur by its absence regardless of species; (3) reverses or prevents these abnormalities through its presence; and (4) specific biochemical changes caused by abnormalities can be remedied with its presence [39]. The specific functions and deficiency signs of the essential ultratrace metals is shown in Table 2.2.

Table 2.1  Classification of the essential elements [38]   1.  Bulk structure elements  2.  Macrominerals   3.  Trace elements    Ultratrace elements     Nonmetals     Metals

H, C, N, O, P, S Na, K, Mg, Ca, Cl, PO4, SO4 Fe, Zn, Cu F, I, Se, Si, As, B. Mn, Mo, Co, V, Ni, Cd, Sn, Pb, [Li]

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2.4  Information Flows in Biological Systems Information flow in biological system is one of the important contents in bionanotechnology that has recently been studied in molecular biology and it is also known as a signal transduction in biochemistry. The central dogma of molecular biology which has been built to express the flows of genetic information from DNA sequences to protein is regarded as a main information flow in biological systems [40].

Table 2.2  Properties of the essential ultratrace metals [38] Elements Manganese

Deficiency Signs Growth depression; bone deformities; membrane abnormalities connective tissue defects Molybdenum Growth depression Cobalt Chromium

Anemia; growth retardation Insulin resistance

Vanadium

Growth depression

Nickel

Growth depression Reduced N utilization Reduced Fe metabolism Growth depression; Reduced reproduction Growth depression Growth depression; anemia Growth depression Reduced reproduction Growth depression; dental caries.

Cadmium Tin Lead Lithium Fluorine Iodine Selenium

Silicon Arsenic Boron

Specific function Carbohydrate metabolism; superoxide dismutase; pyruvate carboxylase; etc

Oxidase: aldehyde, sulfite, xanthine. Molybdopterin. Constituent of vitamin B12 Potentiation of insulin action on carbohydrates and lipids; active as a biooarganic chromium complex Control sodium pump; inhibition ATPase, p-transferases Constituent of ureases; reduced hemopoiesis Stimulates elongation factors in ribosomes Interaction with riboflavin Many enzyme effects Control sodium pump

Structure of teeth and bones; replace OH, inhibits enolase, pyrophosphatase Goiter; reduced thyroid function. Constituent of thyroid hormones T3, T4 Muscle and pancreas degeneration Constituent of glutathione peroxidase and hemolysis. other enzymes. Protection against oxidation of erythrocytes Growth depression; bone and matrix Structure role in connective tissue and deformities. osteogenic cells Impairment of growth, reproduction, Increased arginine, metabolism of methyl heart function compounds Growth of angiosperms; impaired Control of membrane function; nucleic nitrogen-fixation acid biosynthesis; lignin biosynthesis

2.4  Information Flows in Biological Systems

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2.4.1  Transcription: DNA to RNA Transcription is defined as a process which a double strand of DNA will transport information flows to a new molecule of messenger RNA (mRNA) and it is also first step in gene expression process. DNA safely and stably stores genetic material in the nuclei of cells as a reference, or template. The mRNA is not a totally identical duplicate of the DNA sequence due to its complementary to the template of DNA. However, the mRNA still contains the same information with DNA Generally, transcription will be carried out through the action of an enzyme, transcription factors (RNA polymerase and a number of accessory proteins). The RNA polymerase enzyme plays a role as a primer to begin the transcription process when it attaches onto the template DNA strand and then catalyze production of complementary RNA also starts. In transcription process, to recruit RNA polymerase to a suit transcription site, a specific DNA sequences (enhancer and promoter sequences) will bind with transcription factors (RNA polymerase and proteins). Normally, a transcription process will go through 4 stages including transcription initiation, strand elongation, transcription termination. Transcript initiation is first step in transcription process, it starts when RNA polymerase enzyme binds to a promoter, the DNA upstream (5’) of the gene. Promoters in bacteria commonly consist three sequence elements, while there are about 7 elements in eukaryotes. In prokaryotes, most genes often possess a sequence with consensus sequence TATAT, namely Pribnow box, which is positioned about 10 bases. Once transcription is initiated, RNA polymerase begins reading the template strand due to the unwinding of DNA double helix, then adding nucleotides into the 3’ end of the growing chain. In the temperature condition of 37 °C, nucleotides will be added with a high speed of 42–54 nculeotides/s in bacteria, whereas it is much lower pace, about 22–25 nucleotides/s in eukaryotes. At the end of noncoding sequence, we may find terminator sequences which two types of these sequences were found in bacteria. Generally, depending upon the exactly utilized polymerase, termination of transcription occurs in eukaryotes through different processes. With polymerase I genes, a termination will stop the transcription through a similar mechanism with rho-dependent termination in bacteria, but with polymerase III genes, the transcription will end as soon as a ­termination sequence is transcribed due to a mechanism resembling rho-independent prokaryotic termination. However, the transcription termination of polymerase II transcripts is very complex, in which the transcription of polymerate II genes may be conducted continuously for hundreds or even thousands of nucleotides.

2.4.2  Translation: RNA to Protein Translation is the process by which mRNA is decoded and translated to produce a polypeptide sequence, otherwise known as a protein. This method of synthesizing proteins is directed by the mRNA and accomplished with the help of a ribosome, a

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large complex of ribosomal RNAs (rRNAs) and proteins. In translation, a cell decodes the mRNA’s genetic message and assembles the brand-new polypeptide chain. Transfer RNA, or tRNA, translates the sequence of codons on the mRNA strand. The main function of tRNA is to transfer a free amino acid from the cytoplasm to a ribosome, where it is attached to the growing polypeptide chain. tRNAs continue to add amino acids to the growing end of the polypeptide chain until they reach a stop codon on the mRNA. The ribosome then releases the completed protein into the cell.

2.5  Summary and Outlooks DNA is a storing and transmitting molecule of genetic information in biological systems. Therefore, the DNA nanotechnology has recently used the information of this molecule to assemble structural motifs as well as connect them together. This technology has showed a significant impact on nanotechnology and nanoscience. Especially, with development of DNA origami, a plenty of aesthetically beautiful DNA nanostructures have been designed and developed. However, in the near future DNA nanotechnology will move from structure and design to focus on function. For example, 2D DNA origami structures will start to be utilized as a platform for a wide variety of fascinating single-molecule, especially by high-speed atomic force microscopy. In addition, the application of DNA tubes for membrane protein enables to be a potential approach to create DNA nanostructures with highly useful function and modify these DNA nanostructures with other materials, i.e. organic molecules (folate and cholesterol), proteins (antibodies), siRNA, aptamers, and carbon nanotubes. Key Definition Polymerase chain reaction (PCR) is a revolutionary method to synthesize new strand of DNA complementary to the offered template strand based on using the ability of DNA polymerase, which was developed by Kary Mullis in the 1980s. Periodic System of the Elements (PSE) is a table organized all the chemical elements in order of increasing atomic number. DNA is a double helix where two long chains are wound around a common axis in a helical fashion to yield double stranded DNA. Transcription is defined as a process which a double strand of DNA will transport information flows to a new molecule of messenger RNA (mRNA). Translation is the process by which mRNA is decoded and translated to produce a polypeptide sequence, otherwise known as a protein.

2.5  Summary and Outlooks

29

Abbreviations Abbreviation AuNPs PCR 3D PSE BSE A C G T

Full name Gold nanoparticles Polymerase chain reaction Three dimension Periodic system of the elements Biological system of the elements Adenine Cytosine Guanine Thymine

The Key Points and Questions 1. Name four types of nucleobase involved in the structure of DNA? 2. What is a main role of nucleic acids in the biological system? (a) The storage and transfer of genetic information (b) Molecular recognition (c) The regulation of gene expression and catalysis (d) None of them 3 . What is the difference between nucleobases in the structure? 4. What is the DNA origami method? Name five stages of the DNA origami method? 5. What is the definition of a transcription? (a) A process which a double strand of DNA transport information flows to a new molecule of messenger RNA (mRNA) (b) The first step in gene expression process (c) Transcription is carried out through the action of an enzyme, RNA polymerase and accessory proteins (d) All of them 6 . What is the main difference of a transcription and a translation process? 7. What are crucial aspects considered in the BSE system? Answers 1. Four classes of nucleobases including Adenine (A), Cytosine (C), Guanine (G) and Thymine (T) 2. (a). 3. While T and C are pyrimidines, A and G are purines that consist of a pyrimidine fused to an imidazole ring 4. DNA origami, first introduced by Paul W.  K. Rothemund, was defined as an assembly technique which folds single-stranded DNA template molecules into target structures.

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Five stages of the DNA origami method, including: + Step 1: a geometric model of a DNA structure will be created with the desired shape + Step 2: incorporating a periodic array of crossovers between helices + Step 3: the design of a set of ‘staple strands’ + Step 4: staple sequences are recomputed to minimize strain; + Step 5: pairs of adjacent staples are merged across nicks to yield fewer, longer, staples 5. (d). 6. Translation is the decoding and translating process of mRNA to produce a polypeptide sequence. Whereas, transcription is transportation of information flows to a new molecule of messenger RNA by a double strand of DNA. 7. Aspects of basic biochemical and physiological research which includes: (a) the expression as a linear correlation coefficient of the interelement relations between single elements, (b) uptake forms of single elements and their compounds into the living organism, (c) the physiological function of individual elements relating to evolutionary development of organic life in the inorganic environment.

References 1. Seeman NC. Nanomaterials based on DNA. Annu Rev Biochem. 2010;79:65–87. 2. Pinheiro AV, Han D, Shih WM, Yan H. Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol. 2011;6:763–72. 3. Guo P. The emerging field of RNA nanotechnology. Nat Nanotechnol. 2010;5:833–42. https:// doi.org/10.1038/NNANO.2010.231. 4. Samanta A, Medintz IL. Nanoparticles and DNA—a powerful and growing functional combination in bionanotechnology. Nanoscale. 2016;8:9037–95. 5. Abu-Salah KM, Ansari AA, Alrokayan SA. DNA-based applications in nanobiotechnology. J Biomed Biotechnol. 2010;2010:715295. https://doi.org/10.1155/2010/715295. 6. Yang D, et al. DNA materials: bridging nanotechnology and biotechnology. Acc Chem Res. 2014;47:1902–11. 7. Hinman SS, McKeating KS, Cheng Q. DNA linkers and diluents for ultrastable gold nanoparticle bioconjugates in multiplexed assay development. Anal Chem. 2017;89:4272–9. 8. Lytton-Jean AKR, et  al. Highly cooperative behavior of peptide nucleic acid-linked DNA-­ modified gold-nanoparticle and comb-polymer aggregates. Adv Mater. 2009;21:706–9. 9. Cai P, Huang Q-Y, Zhang X-W.  Interactions of DNA with clay minerals and soil colloidal particles and protection against degradation by Dnase. Environ Sci Technol. 2006;40:2971–6. https://doi.org/10.1021/es0522985. 10. Schneider B, et al. Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Res. 2014;42:3381–94. 11. Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP.  DNA and lipid bilayers: self-­ assembly and insertion. J R Soc Interface. 2008;5:S241–50.

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12. Storhoff JJ, et al. What controls the optical properties of DNA-linked gold nanoparticle assemblies? J Am Chem Soc. 2000;112:4640–50. https://doi.org/10.1021/ja993825l. 13. Smith BD, Dave N, Huang P-JJ, Liu J. Assembly of DNA-functionalized gold nanoparticles with gaps and overhangs in linker DNA. J Phys Chem C. 2011;115:7851–7. 14. Um SH, et al. Enzyme-catalysed assembly of DNA hydrogel. Nat Mater. 2006;5:797–801. 15. Zadegan RM, Norton ML. Structural DNA nanotechnology: from design to applications. Int J Mol Sci. 2012;13:7149–62. https://doi.org/10.3390/ijms13067149. 16. Rothemund PWK.  Folding DNA to create nanoscale shapes and patterns. Nature. 2006;440:297–302. 17. Han D, et  al. DNA origami with complex curvatures in three-dimensional space. Science. 2011;332:342–6. 18. Fu T-J, Seeman NC. DNA double-crossover molecules. Biochemistry. 1993;32:3211–20. 19. Rothemund PWK, et al. Design and characterization of programmable DNA nanotubes. J Am Chem Soc. 2004;126:16344–52. 20. Woo S, Rothemund PWK.  Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion. Nat Commun. 2014;5:4889. 21. Nangreave J, Han D, Liu Y, Yan H. DNA origami: a history and current perspective. Curr Opin Chem Biol. 2010;14:608–15. https://doi.org/10.1016/j.cbpa.2010.06.182. 22. Kuzuy A, Ohya Y. Nanomechanical molecular devices made of DNA origami. Acc Chem Res. 2014;47:1742–9. 23. Högberg B. Remote control of nanoscale devices. Science. 2018;359:279. 24. Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Komiyama M. Nanomechanical DNA origami ‘single-­ molecule beacons’ directly imaged by atomic force microscopy. Nat Commun. 2011;2:449. 25. Andersen ES, et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature. 2009;459:73–7. 26. Douglas SM, Bachelet I, Church GM. A logic-gated nanorobot for targeted transport of molecular payloads. Science. 2012;335:831–4. 27. Rica R d l, Matsui H. Applications of peptide and protein-based materials in bionanotechnology. Chem Soc Rev. 2010;39:3499–509. 28. Tamerler C, Sarikaya M. Genetically designed peptide-based molecular materials. ACS Nano. 2009;3:1606–15. 29. Protein Structure. Technical brief 2009. Particle Sciences—Drug Development Services 8 (2009). 30. Branton D, et  al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26:1146–53. 31. Ghadiali JE, Stevens MM.  Enzyme-responsive nanoparticle systems. Adv Mater. 2008;20:4359–63. 32. Wang Z, Levy R, Fernig DG, Brust M. Kinase-catalyzed modification of gold nanoparticles: a new approach to colorimetric kinase activity screening. J Am Chem Soc. 2006;128:2214–5. 33. Slocik JM, Zabinski JS, Phillips D, Naik RR. Colorimetric response of peptide-functionalized gold nanoparticles to metal ions. Small. 2008;4:548–51. 34. Yemini M, Reches M, Gazit E, Rishpon J. Peptide nanotube-modified electrodes for enzyme-­ biosensor applications. Anal Chem. 2005;77:5155–9. 35. Rica R d l, Mendoza E, Lechuga LM, Matsui H. Label-free pathogen detection with sensor chips assembled from peptide nanotubes. Angew Chem Int Ed. 2008;47:9752–5. 36. Markert B. The biological system of the elements (BSE) for terrestrial plants (glycophytes). Sci Total Environ. 1994;155:221–8. 37. Garten CT. Correlations between concentrations of elements in plants. Nature. 1976;261:686–8. 38. Frieden E. New perspectives on the essential trace elements. J Chem Educ. 1985;62:917–23. 39. Cotzias GC. in Proceedings First Annual Conference Trace Substances in Environmental Health. (ed D. H. Hemphill) 5–19 (MO). 40. Yamato I, Murata T, Khrennikov A.  Energy and information flows in biological systems: Bioenergy transduction of V1-ATPase rotary motor and dynamics of thermodynamic entropy in information flows. Prog Biophys Mol Biol. 2017;130:33–8.

Chapter 3

Bionanomaterials Production

3.1  Introduction Generally, nanoparticles (NPs) have been synthesized and manufactured using physical and chemical methods (ion sputtering, solvothermal synthesis, reduction and sol-gel technique based on two basic approaches: bottom-up and top-­down. However, the traditional methods might release hazard substances to environments so that the potential for human exposure to NPs would increase [1, 2]. Therefore, scientists have attempted to reduce the risks by using new eco-­friendly agents (e.g., microbial enzymes or plant phytochemicals) instead of chemical agents [1, 3, 4]. So, a non-toxic way of synthesizing NPs can be achieved by using a “green” method called biological method, this is a kind of bottom-up approach that scientist used microorganisms and plant extracts to synthesize NPs [5], then the products are namely as “bionanoparticles”. Many bacterial, fungal, and plants have shown their advantages on synthesis and manufacturing NPs as well as their biological NPs potential use in biomedical applications. For instance, silver NPs are well-known as an anti-microbial agent, and it can be achieved by biological methods, such as Premasudha et al. investigated that silver (Ag) NPs using Eclipta alba leaf extract showed antimicrobial [6] and Gandhi and co-workers successfully synthesized Ag NPs by Escherichia coli showing a great anti-bacterial activity [7]. According to the crucial issues, for developing a safely environmental and inexpensive way for synthesis and manufacturing of NPs, this chapter will focus on providing an overview of synthesis of NPs based on biological as reducing and capping agents (Fig. 3.1 and Table 3.1).

© Springer Nature Singapore Pte Ltd. 2020 Y.-C. Lee, J.-Y. Moon, Introduction to Bionanotechnology, https://doi.org/10.1007/978-981-15-1293-3_3

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34

3  Bionanomaterials Production

Fig. 3.1  Schematic representation of method and mechanism for synthesis of bionanoparticles

3.2  Microorganism-Based Synthesis of NPs 3.2.1  Synthesis of NPs by Bacteria Among the microorganisms, bacteria are one of the most abundant organisms and their ability to survive under extreme conditions, so it has attracted the attention of most scientists in the field of biosynthesis of NPs. Besides, the bacterial-based synthesis is easier and cheaper than other methods because they are fast-growing, inex-

3.2 Microorganism-Based Synthesis of NPs

35

Fig. 3.2  Schematic representation of possible mechanism for the synthesis of gold NPs using bacteria [12]

pensive to cultivate, and especially easy to control their growth conditions such as pH, growth medium, and temperature [4, 8, 9]. NPs are synthesized by microbes have been widely used in many biological applications (e.g., bioremediation, biomineralization, bioleaching, and bio-corrosion) [10]. Biosynthesis method including biological and enzymatic reactions plays a major role in creating NPs. Although exact mechanism has not been investigated because different bacteria have different mechanisms for the synthesis, this mechanism may include efflux system, changing redox potential of metal ions to less toxic metal salts or zero-valent metals, extra-cellular combination, and reducing the membrane permeability. Finally metal NPs are usually produced either intra or extra-cellular with exquisite morphology [1, 2, 9, 11, 12]. Moreover these mechanisms also involve to detoxification pathway as well as are dependent on efflux energy from the cell by membrane protein that is produced by either as ATPase or as chemo-osmotic or proton anti-transporters so that bacteria can survive and grow in a high concentration of toxic metals, particularly, nicotinamide adenine dinucleotide (NADH) and NADH-dependent nitrate reductase plays an important role in this mechanism [8, 12]. The scheme below represents one of the synthesis Au NPs process by biological agents (Fig. 3.2): 3.2.1.1  Silver Nanoparticles (ag NPs) In 1970, Ag NPs were successfully synthesized by extracellular synthesis using cell-free supernatant of five psychrophilic bacteria (Pseudomonas antarctica, Pseudomonas proteolytica, Pseudomonas meridiana, Arthrobacter kerguelensis and Arthrobacter gangotriensis) [13]. The synthetic Ag NPs (6–13 nm) were stable for 8 months in the dark and the stability depended on the temperature, pH, and the

36

3  Bionanomaterials Production

Interaction between fungal cell wall and nanoparticles

Fungal cell wall burst due to nanoparticles

Fig. 3.3  Possible mechanism behind fungus and nanoparticles interaction [35]

species of bacteria (P. antarctica or A. kerguelensis). This study provides first-time data on the production of Ag NPs by cell-free culture supernatant of psychrophilic bacteria. There are two groups that used Pseudomonas stutzeri AG259 as a microorganism agent to synthesize Ag NPs based on biological method [14, 15]. It is reported that Ag+ ions were isolated from a silver mine and resistant onto bacterial strain lead to form Ag NPs, after that Ag NPs intracellularly accumulated with some silver sulfide diameters ranging from 35 to 46 nm [15], whilst, Klaus et al. successfully synthesized larger Ag NPs (~ 200  nm) at high concentrations of Ag ions during P. stutzeri AG259 culture [14]. According to the Klaus et al. report, Ag+ ions were detoxified by P. stutzeri AG259 through precipitation in the periplasmic space, which then reduced to elemental Ag with many crystal phenotypes including equilateral triangles and hexagons (e.g., crystalline silver, monoclinic silver sulfide acanthite (Ag2S), and a further undetermined structure). Gandhi et al. successfully synthesized Ag NPs by E. coli in which Ag ions exposure culture supernatant of E. coli, resulting in the extracellular reduction of the Ag+ ions and formation of silver NPs [7]. They also evaluated antibacterial activity of the NPs, enhancing the antibacterial effect for Bacitracin against E. coli, Ampicillin against Corynebacterium diphtheria, for Gentamycin against Pseudomonas aeruginosa, and Kanamycin against Klebsiella pneumoniae.

3.2 Microorganism-Based Synthesis of NPs

37

Ag+

OH

Ag0

2H+

O

OH

OH OH

OH

COCH3

OH3C

OH3C

O

COCH3 OH

REDUCTASE

NO2–

2H2O

NO3–

2H+ NADP+

NADPH

Fig. 3.4  Hypothetical mechanism for the synthesis of Ag NPs using Fusarium oxysporum [36]

Shewanella oneidensis MR-1 can react with AgNO3 solution to produce extracellular Ag NPs in the form of nanocrystallites with well-defined homogeneous compositions [16]. The crystals consisted of small and monodispersed spheres (average diameter 4 ± 1.5 nm) and these NPs showed a higher toxicity than other chemically synthesized Ag NPs (colloidal-Ag and oleate-Ag) based on Gram-negative (S. oneidensis and E. coli) and Gram-positive (B. subtilis) bacteria assays. Wei et al. reported that the combination of solar irradiation of cell-free Bacillus amyloliquefaciens extract where AgNO3 can obtain Ag NPs [17]. Under optimized conditions (e.g. light intensity, extract concentration, and NaCl), Ag NPs (average diameter of 14.6 nm) were obtained over a fast period of time in the circular and triangular crystalline structure and it also displayed antimicrobial activity against B. subtilis and E. coli in liquid and solid medium. Particularly, they expressed that the formation of Ag NPs under irradiation might not be involved in enzymatic reactions, otherwise protein and sunlight were responsible for the formation of Ag NPs. The effects of visible light irradiation and culture supernatant of bacteria on biological synthesis NPs were also demonstrated [18]. AgNO3 was combined with culture supernatant Klebsiella pneumonia under the visible light emission and successfully synthesized dispersed uniform Ag NPs in their size and shape (average

Mechanism

Advantages

Disadvantages

 –  Clean, non-toxic, biocompatible and ecofriendly  –  Culturing of microorganisms is – Enzymes and Conventional Microorganism-   method for synthesis of NPs time-consuming proteins of methods based synthesis microorganisms as  –  Cost effective, safe, and sustainable of NPs  –  Difficult to control over size, shape, reducing agents and crystallinity for the synthesis of  –  Bacteria are easy to handle and can be easily  –  Particles are not mono-dispersed. NPs manipulated   – Low productivity  –  Eco-friendly, non-toxic, and cost-effectiveness  –  Plants cannot be manipulated as the   – Metabolite Plant choice of nanoparticles through optimized compounds of extract-based synthesis through genetic engineering plant extract as synthesis of reducing and nanoparticles  –  Easily scaled up for mass production of NPs  –  Plant produces low protein yield, stabilizing agents leading to decreases the synthesis yield  –  More advantages than using microorganisms with less complex culture maintenance process.  –  Low production yield. – Biocompatibility, biodegradable, – Polysaccharide   Polysaccharide-   biometabolizability, non-toxicity, non-antigenicity, as reducing and based synthesis and cost-effectiveness stabilizer agents of nanoparticles for the synthesis of  –  Gelation ability and mucoadhesive  –  Large molecules lead to difficult in NPs based on controlling the size of synthetic gelation nanoparticles mechanism  –  Excellent control the release of encapsulated agents on drug delivery system application  –  Prolonged residence time at the absorbing position based on its mucoadhesive nature  –  May decrease uptake by the mononuclear phagocyte system  –  Its manipulation and the availability of  –  Culturing of genetic engineered E.coli   – Genetic Advanced Genetic well-established genetic tools is time-consuming engineered of methods engineered E.coli as reducing  –  Easy maintenance and fast growing time E.coli   – Low production agent

Approaches

Table 3.1  Comparison between conventional and advanced green methods for biosynthesis nanoparticles Refs.

38 3  Bionanomaterials Production

3.2 Microorganism-Based Synthesis of NPs

39

Fig. 3.5  Possible chemical constituent of plant extract responsible for the bioreduction of metal ions [53]

size of 3 nm). It is indicated that hypothetical mechanism of light (redox properties of agent released by Enterobacteria that could act as electron shuttles in metal reductions) responsible for the synthesis of Ag NPs from K. pneumoniae under visible irradiation. Kalishwaralal et al. investigated that Ag NPs could be synthesized by extracellular biosynthesis using the culture supernatant of Bacillus licheniformis, the highly stable Ag NPs of about 50 nm formed when silver nitrate (AgNO3) was added to the bacteria [19]. Moreover, B. licheniformis is a non-pathogenic bacterium, so this method has greater advantages than other methods of using other pathogenic bacteria. Saifuddin et al. have been described a rapid biosynthesis of Ag NPs using culture supernatant of B. subtilis with microwave irradiation [20]. They reported that the B. subtilis has a potential for monodispersed extracellular synthesis and it can combine with microwave irradiation to form Ag NPs in the range of 5–50 nm. Besides, the studied also demonstrated that extracellular synthesis has a great advantage (e.g., achieving better NPs size as well as reducing the accumulation of NPs) over an intracellular process.

40

3  Bionanomaterials Production COOH O OH

O

HO

OH

OH

COOH

O

m

O

O

n

Fig. 3.6  Chemical structure of alginate

3.2.1.2  Gold Nanoparticles (au NPs) Regarding to the report of Ahmad et al. [21] has been described that monodisperse Au NPs could be synthesized by extracellular biosynthesis using a novel extremophilic actinomycete, Thermomonospora sp. Particle sizes in range of 8–10 nm and complex morphologies due to differences in strength interaction of different protein with Au3+ ions lead to different crystallographic faces of Au NPs. Furthermore, Lactobacillus strains have been reported to be capable of interacting with Au ions to form Au NPs within the bacterial cells [22]. The reaction occurred on the surface of cell through the intracellular reduction of Au3+ ions in the cell which is then transported into the cell and aggregated to larger-sized particles. This research also suggested that synthesizing nanomaterials by recovering metal ions using biological agent is useful for medical applications. Lengke et  al. synthesized and controlled morphology of gold NPs using Plectonema boryanum UTEX 485 [23]. Cubic gold NPs (