Chapter 1

Introduction

Although the detailed structure of deoxyribonucleic acid (DNA) was revealed by Watson and Crick [1] back in 1953, stunning and useful new structural modes are still being discovered even today for this versatile macromolecule. Taking lessons from its in vivo role and aided by technological advances, nanoengineers have begun to explore novel and creative uses for DNA including: molecular detection [2], therapeutic regimens [3], complex nanodevices [4], nanomechanical actuators and motors [5], directed organic synthesis [6], and molecular computation [6]. Owing to its unique Watson-Crick hydrogen-bonding nature, DNA ensures the specificity and precision required by biosensors and programmable nanoassemblies [7]. Nucleic acid has been recognized as an attractive scaffolding material because of its very long linear structure and its mechanical rigidity over short distances [8].

The synthesis of nanomaterials using DNA templates is attracting substantial interest in current nanoscience research due to their enormous potential for applications in industrial and medical fields. Utilization of the biochemical functionalities of DNA has been exploited to fabricate and organize nanomaterials. The DNA-based approaches have several advantages over conventional chemical methods when preparing structured nanoscaled materials. These benefits derive from the unique functionalities of biological substances. The numerous active functional moieties of DNA can be conjugated with other organic and inorganic substances. The charged and chemically reactive moieties on the biomolecules, such as amine and carboxyl groups, can be exploited to attract and react with other chemical molecules. Furthermore, their natural substrate-specific affinity makes it possible to assemble and align the biomolecule in a specific pattern. For example, the specific affinities of base pairs of nucleotides have been used to assemble substances in a programmed position, to align small structured materials in a designer pattern, and to conjugate biomolecular substances with each other.

A variety of biomolecules possessing single or multiple functionalities have been used for the preparation of nanoscaled materials. Nucleotides are biomolecules which are commonly used in bionanotechnology due to their hybridizing functions and ease of preparation in the laboratory [9-11]. Moreover, their topological structures are tunable with proper sequence design. Reconfigurable structures of the ribbon, supercoil ring, or triangle can be made from the designed DNA strands [12,13].

Noble metal nanoparticles are fascinating materials with great nanotechnological potential due to their unique and strongly size-dependent electronic, optical, physical, and chemical properties [14,15]. In general, the particulate matter is categorized into particles = 10 µm, = 2.5 µm, and > 0.1 µm in diameter. The latter ones are also referred to as ultrafine particles or nanoparticles (NPs). They are classified into metal-based (e.g., metal and metal oxides, quantum dots [QDs]), carbon-based (e.g., single- and multiwalled carbon nanotubes [SWCNT and MWCNTs], fullerenes), polymer-based and lipid-based (e.g., liposomes) subgroups. Depending on their basic material, nanoparticles are expected to affect biological systems in different ways. However, they share the common characteristic that they exhibit a large surface-to-mass ratio and, therefore, are considered to be biologically more reactive than larger particles of identical material and form. Additionally, the surfaces of nanoparticles can be easily functionalized with various organic and biomolecular ligands, among which the molecules with a sulfur headgroup have been attracting considerable interest [16]. Simple thiol chemistry or electrostatic attachment can bind DNA to gold nanostructures. When attached to gold nanostructures DNA has an increased half-life from minutes to hours [17] against attack by large nucleases due to the increased steric hindrance caused by attachment to the gold surface [17]. Additionally, polyvalent cations near the gold nanoparticle surface electrostatically repel dications located within the nucleases, also increasing oligonucleotide stability [18]. The strong affinity of sulfur to gold has been exploited to form molecular contacts, to link other species to the gold surface, or to form well-ordered self-assembled monolayers (SAMs) [19] for applications like surface patterning [20] and molecular electronics [21]. Several strategies [22] have employed alkanethiol-capped DNA oligonucleotides to link gold nanoparticle building blocks to form periodic functional assemblies, in addition to serving as efficient DNA detection schemes.

DNA represents an ideal scaffold for the generation of ordered nanostructures with noble metal nanoparticles. Over the past decade, researchers have developed many uses for oligonucleotides-noble metal nanoparticle(s) (DNAs-gold nanoparticle(s)) conjugates [23]. These nanostructures, which consist of a nanoparticle core (typically 2-200 nm in size) and many oligonucleotide strands covalently attached to their surface [24], exhibit several unusual properties that make them attractive for nanoconjugate applications and particle stabilizations [25]. These properties include cooperative binding and enhanced affinities for complementary nucleic acids [26] that can be used for signal amplification [27], unusual distance-dependent plasmonic properties [28], and the ability to enter cells without the use of auxiliary transfection agents [29]. They also exhibit an extraordinary intracellular stability that makes them useful for antisense studies, drug delivery, and intracellular molecular diagnostics [30]. Indeed, nucleic acid stability is a key property of any system that aims to use such structures for intracellular regulatory or diagnostic events. The problem is that Nature has evolved an arsenal of enzymes, known as nucleases, to degrade foreign nucleic acids that enter cells [31]. DNAs-gold nanoparticle(s) conjugate might suppress the enzymatic degradation of DNA.

The colloidal stability of gold nanoparticles and their bioconjugates is a complex function of amphiphilic molecules, ligands and biomolecules. Amphiphilic molecules are very popular in nanotechnology due to their self-assembly properties. Most common surface active compounds do not carry a strong charge in the polar headgroup and, therefore, do not interact strongly enough to induce the compaction of negative DNA or its oligomers. In fact, it is the surface active agent self-assembly process itself that, while facilitated by the presence of the DNA molecule, induces compaction of the DNA. Since the self-assembly of the surfactants is relatively easy to control, it is in principle possible to control the compaction of DNA. In fact, this concept has been used with other positively charged agents to improve their efficiency and control. This self-assembly of the surface active compounds and gold nanoparticles was also ascribed to the hydrophobic interactions [32].

The conjugation of a limited number of thiolated DNA strands on the surface of gold nanoparticles is performed following several ligand exchange steps [33]. In order to minimize nonspecific interactions between the negatively charged DNA strands and the metal surface and to optimize colloidal stability, gold nanoparticles are prepared with a negatively charged shell. This labile ligand can be displaced by thiolated DNA strands in the presence of charge screening cations (typically Na+). However, colloidal stability of larger stabilized gold nanoparticles (AuNPs) (> 30 nm in diameter) is only optimum for lower NaCl concentrations lower (< 50 mM). In order to further stabilize the AuNP-DNA conjugates, the gold surface can be passivated by adding a large excess of short thiolated poly(ethylene glycol) (PEG) oligomers [34].

A bottom-up strategy has been adopted for the hierarchical structuring of atoms or molecules to nanometer-scale bioconjugates. Over the past decade, by using the self-assembling nature of artificially designed molecules, chemists have succeeded in constructing many kinds of nanometer-scale molecular assemblies, e.g., molecular recognition-directed molecular assemblies [35], surfactant bilayer membranes [36-38], self-assembled monolayers [39] and alternatively deposited polyelectrolyte multilayers [40]. Nanometer-scale molecular self-assembling is the first step of the biomimetic approach of the bottom-up strategy for materials fabrication. The second step of the bottom-up strategy is to organize the nanometer-scale molecular assemblies into larger supramolecular systems in the mesoscopic scale of nanometer [41] to the submicrometer range [42]. Self-assembly is one of the few practical strategies for making ensembles of nanostructures and will therefore be an essential part of nanotechnology [43]. In order to generate complex structures through self-assembly, it is essential to develop methods by which different components in solution can come together in an ordered fashion. One approach to achieve ordered self-assembly on the nanoscale is to use biomolecules as scaffolds for directed assembly because of the specificity and versatility they provide [44]. The nanoparticle networks or superstructures assembled on various DNA substrates are expected to produce systems with interesting electronic and optical properties [45].

DNA-functionalized colloidal gold nanoparticles (AuNP@DNAs) hold promise for applications in bionanotechnology [46]. Following the pioneering work of Mirkin and coworkers, these modified nanoparticles can act as useful building blocks to form spatially well-defined superstructures, including nanocrystals [47], binary [48] and multilayered [49]...