DNA in Supramolecular Chemistry and Nanotechnology

Eugen Stulz, Guido H. Clever, Eugen Stulz, Guido H. Clever

• Publisher: Wiley
• Year: 2015
• Print ISBN: 9781118696866
• eBook ISBN: 9781118696934
• Edition: 1
• Topic: Technology & Engineering
• Subtopic: Nanotechnology & MEMS
• Index: Technology & Engineering

This book covers the emerging topic of DNA nanotechnology and DNA supramolecular chemistry in its broader sense. By taking DNA out of its biological role, this biomolecule has become a very versatile building block in materials chemistry, supramolecular chemistry and bio-nanotechnology. Many novel structures have been realized in the past decade, which are now being used to create molecular machines, drug delivery systems, diagnosis platforms or potential electronic devices.

The book combines many aspects of DNA nanotechnology, including formation of functional structures based on covalent and non-covalent systems, DNA origami, DNA based switches, DNA machines, and alternative structures and templates. This broad coverage is very appealing since it combines both the synthesis of modified DNA as well as designer concepts to successfully plan and make DNA nanostructures.

Contributing authors have provided first a general introduction for the non-specialist reader, followed by a more in-depth analysis and presentation of their topic. In this way the book is attractive and useful for both the non-specialist who would like to have an overview of the topic, as well as the specialist reader who requires more information and inspiration to foster their own research.

Part I
(Non-) Covalently Modified DNA with Novel Functions

1.1
DNA-Based Construction of Molecular Photonic Devices

Glenn A. Burley

Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK

1.1.1 Introduction

Controlling the spatial arrangement of photonic materials reproducibly and with nanoscale precision is of fundamental importance for the development of optoelectronic devices and sensors of the future. Over the past 30 years, industry has made phenomenal progress in the fabrication of optoelectronic circuits and devices with a high level of accuracy and reproducibility. ‘Top down’ nanolithography has been the major driver in these developments, producing devices and circuits with resolution levels ranging from tens [1] to hundreds of nanometres [2]. Top down photolithographic approaches such as Extreme Ultraviolet Lithography (EUV) have been the predominant methods used to fabricate optoelectronic devices with sub-50 nm resolution levels. One of the major drawbacks in the further development of higher resolution circuits fabricated using EUV is the rising cost of the equipment required to produce smaller devices with sub-22 nm resolution [3]. The more recent development of Nanoimprint Lithography (NIL), for example, can replicate high-resolution patterns as small as 2.4 nm and is one of the leading contenders for the fabrication of sub-22 nm circuitry [1a], yet technological hurdles such as the defectivity and process variability of the resultant device platforms requires further development [4].

As a consequence of the increasing technological as well as economic challenges involved in fabricating devices through purely lithographic approaches, alternative methods and strategies of fabrication are now being investigated from both a fundamental as well as an applied perspective [5]. Building circuits and devices from functional molecular building blocks, that is, a ‘bottom up approach’, is a particularly attractive method for achieving molecular-scale precision [6]. There is increasing interest in using supramolecular assembly principles to form functional optoelectronic devices and sensors for device applications [7], yet despite a number of seminal advances in this area [8], a significant challenge still remains, that of fabricating precisely defined and error-free nanomaterials over micron-scale surface areas with complete 3D control and sub-nanometre resolution in a reproducible fashion de novo [9]. In contrast, Nature is astute at preparing micron-scale, self-assembled nanostructures via the use of a template-driven process to direct both the formation and the control of the growth of the overall nanostructure [10]. For example, the protein ferritin can be used as a template for the controlled biomineralisation of nanostructures [11]. Peptides can also be programmed to assemble in nanostructures and even act as templates for the assembly of non-natural functional materials; however, the ability to form bespoke functional materials is still restricted by our limited understanding of the rules that govern their self-assembly [10].

Of the biomacromolecules available in Nature, DNA molecules and their structural analogues have emerged as excellent templates to guide the synthesis [12] as well as the assembly of functional nanomaterials from the ‘bottom up’ (Figure 1.1.1a) [13]. By exploiting the predictable base-pairing rules of DNA and the high density of information embedded in its structure, DNA-programmed self-assembly can form sophisticated multi-dimensional assemblies ranging from 3D crystals [14], micron-scale 2D [15] and 3D [15b, 16] DNA nanostructures, as well as dynamic nanostructures [17], which can be reconfigured to release a therapeutic cargo in response to molecular cues [18].

Figure 1.1.1 (a) Watson–Crick base-pairing is used in Nature to store genetic information and in DNA nanotechnology to direct the assembly of sophisticated multi-dimensional nanostructures. DNA analogues such as Peptide Nucleic Acids (PNA) have also been used to direct the assembly of DNA nanostructures. (b) Schematic representation of DNA origami. A single-stranded DNA template is weaved in two- and three-dimensional DNA nanostructures using a variety of oligodeoxyribonucleotide (ODN) staple strands. (c) Triplex Forming Oligonucleotides (TFOs) offer an alternative directing modality through the formation of triplex structures

The principal aim of this chapter is to highlight the recent developments in the use of DNA-programmed self-assembly to guide the construction of discrete photonic nanostructures. The advantages and disadvantages of using DNA-programmed self-assembly to construct arrays of organic fluorophores and proteins will be presented. The second half of the chapter will review efforts focusing on different modes of DNA-programmed self-assembly to fabricate optoelectronic circuits and light-harvesting complexes. For specific applications of DNA-directed assembly for the construction of supramolecular photosynthetic mimics, the reader is directed to a recent review by Albinsson, Hannestad and Börjesson [19]. DNA-programmed assembly of metallic and semiconductor nanoparticles is another rapidly expanding area of DNA nanotechnology. This has been the subject of recent reports and will not be discussed herein [13a, 13c, 20].

1.1.2 Using DNA as a template to construct discrete optoelectronic nanostructures

DNA is a unique self-assembling molecular system. This uniqueness arises from the inherent programmability of Watson–Crick base-pairing of Ad...

Table of contents

• Cover
• Title Page
• Table of Contents
• Preface
• List of Contributors
• Part I: (Non-) Covalently Modified DNA with Novel Functions
• Part II: DNA Wires and Electron Transport Through DNA
• Part III: Oligonucleotides in Sensing and Diagnostic Applications
• Part IV: Conjugation of DNA with Biomolecules and Nanoparticles
• Part V: Alternative DNA Structures, Switches and Nanomachines
• Index
• End User License Agreement