DNA Nanotechnology

Today, DNA emerged as a fundamental and intelligent molecule to assist construction and functionalization of nanodevices in the field of nanotechnology. Besides the powerful base-pair molecular recognition property utilized to control the final structure and function of materials, the ligand-binding capability and catalytic property offered by a large number of functional nucleic acids have stimulated the enthusiasm and creativity for molecular scientists from various disciplines to construct more intelligent DNA nanostructures and nanodevices. If the double helix is the core of DNA nanotechnology, functional nucleic acids are the active surfaces which take the role of interacting with peripheral environments. In this chapter, concept and basic property of functional nucleic acids are introduced, followed by a review of the application of functional nucleic acids in DNA nanotechnology.

Since oxygen and selenium are in the same elemental family, the replacement of oxygen in nucleic acids with selenium does not significantly change the local as well as overall structures, which preserves the nucleic acid structures in a predictable manner. Furthermore, the valuable differences in chemical and electronic properties enable various functions and applications, including crystallization, phase determination, and high-resolution structure determination in X-ray crystallography, base-pair high fidelity, nanotechnology, and molecular imaging. This chapter briefly introduces the selenium-modified nucleic acids (SeNA), the selenium atom-specific mutagenesis (SAM), and their potentials in DNA nanotechnology.

Over the past two decades, DNA has become a major player in nanotechnology. A very interesting and useful method uses DNA to link various nanoparticles, where the programmable structure and molecular recognition function of DNA are coupled to the optical, electric, magnetic, and catalytic property of the nanomaterials. Compared to many inorganic nanoparticles, liposomes are self-assembled soft matters that possess surface fluidity and the potential for molecular containment. The charge, size, and phase transition properties of liposomes can be precisely tuned by varying liposome formulation. In this chapter, we describe methods for liposome preparation and DNA attachment. We also discuss the biophysical properties of DNA-functionalized liposomes and their emerging applications in DNA-directed assembly, biosensor development, and drug delivery.

Isolation and analysis of single DNA fragment are of great importance for both fundamental research and future biomedical applications. In this chapter, we introduce a technique based on atomic force microscope (AFM) to manipulate and isolate individual DNA molecules at the nanometer scale. The AFM was used to site specifically cut, push, and pick up single DNA fragments from solid surfaces. Subsequent amplification of the isolated single DNA fragments indicates that the DNA molecules keep their bioactivity after AFM manipulation. We believe that new applications will continue to be developed to further expand our repertoire of the AFM-based nanomanipulation techniques.

Mechanics is crucial for life. The single molecular mechanics of biomacromolecules lays the base of mechanical movements of organism. Here in this chapter, we will introduce the progress in single chain mechanics of DNA. The related studies are very important not only to the understanding of phenomena of life but also to the design and preparation of artificial nanomachines.

This chapter introduces the use of microfluidic tools for DNA analysis. It will cover both qualitative analysis and quantitative analysis. A microfluidic device typically implies multicomponent integration. Most reviews in scientific journals discuss microfluidics by a sequential introduction for each component. In order to present the great power of microfluidics as emerging tools for DNA research, we organized each section according to the primary function that can be achieved by a kind of microfluidic device, and emphasize the primary innovation leading to the unique function for each specific device. As microfluidic tools showed many distinct advantages over existing approaches and thus hold dramatic commercial potential, we will also discuss the problems during the commercialization process of microfluidic devices. DNA analysis we discussed herein includes amplification, detection, sequencing, counting, sizing, and weighing, and our perspective covers a wide range of related fields including chemistry, molecular biology, physics, and micro/nano-fabrication technologies, which reveals that DNA analysis on microfluidic devices is a highly interdisciplinary subject and will have lasting impact among biologists, chemists, physicians, and engineers.

DNA nanotechnology makes use of DNA strands to build highly engineerable supramolecular structures from the bottom-up. Such a research field has been experiencing a fruitful development during the past decades. In materials science, an ambitious goal is to obtain materials with designable structures and predictable functions based on a suitable synthetic strategy. The rapid growth and expansion of the area of DNA nanotechnology have provided a useful technological platform suitable to demonstrate DNA’s unique roles in nanomaterials science. Although nanoparticle-based materials have been employed for controllable DNA conjugation and DNA-programmable self-assembly, some challenges still exist. In this chapter, we try to highlight the latest developments in DNA-directed nanophase materials, including new strategies for DNA decoration of gold and carbon-based nanomaterials, DNA origami-based nanoassembly templates, and DNA-conjugated non-gold nanoparticles with specifiable bonding valences, in response to the challenges we are currently facing.

In this chaper, we decribe the structures of DNA-based assembly of inorganic nanoparticle in one, two, and three dimensions. Smart DNA linker, DNA motifs, and DNA origami were introduced to assembled nanoparticle, respectively. We also show our insights for the application of DNA-inorganic nanoparticle structures in the future.

The term “DNA origami” was proposed by Paul Rothemund in 2006 to describe his invention of a new type of DNA nanostructures. In that revolutionary work, he showed the ability of controlled folding of a long single-stranded scaffold DNA, with the help of hundreds of short staple strands, into exquisite nanopatterns. After his invention, this technique has been a constant focus in the field of DNA nanotechnology for the past few years. Great efforts have been made to build new 2D and 3D DNA origami structures, improve assembly strategy, study inherent properties, and develop new applications. In this chapter, we will summarize the structural evolution of DNA origami from Rothemund’s first invention to the latest developments in constructing more complex and larger structures, optimizing the assembly, and combining it with top-down techniques.

In this chapter, we outline the shared principles of design and fabrication of DNA nanomachines that are established and newly developed. Various functional DNA nanomachines and their applications are also discussed.

The DNA structures that act as building blocks of DNA nanomachines are introduced briefly. The molecular recognition mechanisms and dynamical properties of these building blocks are described for the elucidation of the design principles of DNA nanomachines. According to the driving mechanisms, the DNA nanomachines are divided into two categories. One category is buffer-dependent DNA nanomachines, which are triggered by changes in the environment, such as metal ions, pH, and protons. The other category is DNA strands-fueled nanomachines, in which the moving forces are generated through the hybridization of carefully designed DNA strands. A variety of DNA-based nanomachines with different functions have been constructed, such as tweezers, rotors, and walkers. Generating highly sensitive and selective response to their fuels (or stimuli), DNA nanomachines can be functionalized for various applications. The buffer-dependent DNA nanomachines have been successfully used as sensors. The specificity of DNA nanomachines is utilized for template synthesis to organize chemicals into close proximity and to control the synthesis process precisely. The switchability of DNA nanomachines is employed for carrying small molecules, nucleic strands, proteins, or even metal nanoparticles. The motions of the DNA nanomachines can also be used to control the loading and release of the nanoscale objects, as well as to transport and assemble the cargos. The immobilized DNA machines on solid phase succeed in generating signal-triggered responsive surface. Finally, we highlight some challenges and prospective.

Since the concept of structural DNA nanotechnology was laid out early in 1980s, followed by the fundamental steps in programming and engineering DNA nanostructures and later the invention of the DNA origami technique, the field of structural DNA nanotechnology has undergone tremendous development. Taking advantage of the sequence specificity and the resulting spatial addressability of DNA nanostructures, many DNA nanoarchitectures have been used for the organization of heteroelements such as proteins and nanoparticles and for the functionalization to mimic dynamic devices such as scissors and gears. Among these structures, DNA walking devices were the most complicated ones that could combine numbers of functions to realize the signal transduction. In this chapter, we would focus on the discussion of the walking style and the trigger and the functions of these differential DNA walking devices.

This chapter reviews recent progress in the development of biosensors by integrating functional DNA molecules with nanoscale science and technology. Functional DNA, a new class of DNA with functions beyond genetic information storage, can either bind to a target molecule (known as aptamers) or perform catalytic reactions (called DNAzymes). The targets of functional DNA can range from metal ions and small organic molecules to proteins, and even cells, making them a general platform for recognizing a broad range of targets. On the other hand, recent progress in nanoscale science and technology has resulted in a number of nanomaterials with interesting optical, electrical, magnetic, and catalytic properties. Inspired by functional DNA biology and nanotechnology, various methods have been developed to integrate functional DNA with these nanomaterials, such as gold nanoparticles, fluorescent nanoparticles, superparamagnetic iron oxide nanoparticles, and graphene, for designing a variety of fluorescent, colorimetric, surface-enhanced Raman scattering, and magnetic resonance imaging sensors for the detection of a broad range of analytes.

The mechanical motion of DNA nanomachine is driven by the chemical entropies that are released from the stimuli-induced structural variations of DNA nanostructures. Up to now, several stimuli have been proposed. In this chapter, we will discuss nucleic acid enzymes as a distinct stimulus to drive DNA nanomachines and its applications in biosensing are also mentioned as well.

DNA 3D nanostructures have the promising features to be the universal nanocarriers for smart or targeted drug delivery. In this chapter, we will review recent works on using DNA nanotube, DNA tetrahedron, DNA origami nanotube, and DNA origami nanorobot as drug delivery nanocarriers. Their researches showed that specially designed DNA 3D nanostructures, especially DNA tetrahedron, demonstrated great cell uptaking efficacy and are stable for both in vitro and in vivo drug delivery purpose. The exploratory works on DNA 3D nanocarriers assisted the study on cytosine-phosphate-guanine (CpG)-induced immunostimulation, and SiRNA gene silencing paved the way for DNA 3D nanostructures’ real therapeutic application.

One of the most fundamental questions in cell biology concerns how membrane proteins can perform or contribute to cell communication. Over the last few decades, we have seen major advances in understanding the structural mechanisms of membrane proteins. This chapter describes the emergence of DNA nanotechnology as a powerful tool for the structural characterization of membrane-associated protein using solution-state nuclear magnetic resonance (NMR) spectroscopy. Solution-state NMR is currently one of the best known methods for studying membrane protein structure, and a residual dipolar coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size. However, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for inducing weak alignment of membrane proteins was severely limited. Recently, in the William Shih’s group, we introduced a large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins. Nanotube-based alignment of membrane proteins represents a fine example of the productive interface between DNA nanotechnology and structural biology.

Nucleic acids are ideal for molecular computation. A full set of molecular logic gates have been constructed using deoxyribozymes, nucleic acid catalysts made of DNA. These gates have been combined to form various molecular circuits, including molecular automata which perform complex game-playing tasks. Our newest molecular automaton uses reconfigurable deoxyribozyme-based logic gates to build a multipurpose reprogrammable device that can be taught by example to play a game. Herein the design and progress on deoxyribozyme-based molecular computation is described, especially for MAYA-III, our newest molecular automaton.