Deoxyribonucleic Acid Nanotechnology Research Articles

An Operational DNA Strand Displacement Encryption Approach.

DeoxyriboNucleic Acid (DNA) encryption is a new encryption method that appeared along with the research of DNA nanotechnology in recent years. Due to the complexity of biology in DNA nanotechnology, DNA encryption brings in an additional difficulty in deciphering and, thus, can enhance information security. As a new approach in DNA nanotechnology, DNA strand displacement has particular advantages such as being enzyme free and self-assembly. However, the existing research on DNA-strand-displacement-based encryption has mostly stayed at a theoretical or simulation stage. To this end, this paper proposes a new DNA-strand-displacement-based encryption framework. This encryption framework involves three main strategies. The first strategy was a tri-phase conversion from plaintext to DNA sequences according to a Huffman-coding-based transformation rule, which enhances the concealment of the information. The second strategy was the development of DNA strand displacement molecular modules, which produce the initial key for information encryption. The third strategy was a cyclic-shift-based operation to extend the initial key long enough, and thus increase the deciphering difficulty. The results of simulation and biological experiments demonstrated the feasibility of our scheme for encryption. The approach was further validated in terms of the key sensitivity, key space, and statistic characteristic. Our encryption framework provides a potential way to realize DNA-strand-displacement-based encryption via biological experiments and promotes the research on DNA-strand-displacement-based encryption.

Obtaining Precise Molecular Information via DNA Nanotechnology.

Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein–protein interactions, and molecular force.

Introducing Bacteria and Synthetic Biomolecules along Engineered DNA Fibers

Deoxyribonucleic acid (DNA) nanotechnology enables user-defined structures to be built with unrivalled control. The approach is currently restricted across the nanoscale, yet the ability to generate macroscopic DNA structures has enormous potential with applications spanning material, physical, and biological science. To address this need, I employed DNA nanotechnology and developed a new macromolecular nanoarchitectonic assembly method to produce DNA fibers with customizable properties. The process involves coalescing DNA nanotubes under high salt conditions to yield filament superstructures. Using this strategy, fibers over 100 microns long, with stiffnesses 10 times greater than cytoskeletal actin filaments can be fabricated. The DNA framework enables fibers to be functionalized with advanced synthetic molecules, including, aptamers, origami, nanoparticles, and vesicles. In addition, the fibers can act as bacterial extracellular scaffolds and adhere Escherichia coli cells in a controllable fashion. These results showcase the opportunities offered from DNA nanotechnology across the macroscopic scale. The new biophysical approach should find widespread use, from the generation of hybrid-fabric materials, smart analytical devices in biomedicine, and platforms to study cell-cell interactions.

Rapid Visual Authentication Based on DNA Strand Displacement.

Novel ways to track and verify items of a high value or security is an ever-present need. Taggants made from deoxyribonucleic acid (DNA) have several advantageous properties, such as high information density and robust synthesis; however, existing methods require laboratory techniques to verify, limiting applications. Here, we leverage DNA nanotechnology to create DNA taggants that can be validated in the field in seconds to minutes with a simple equipment. The system is driven by toehold-mediated strand-displacement reactions where matching oligonucleotide sequences drive the generation of a fluorescent signal through the potential energy of base pairing. By pooling different "input" oligonucleotide sequences in a taggant and spatially separating "reporter" oligonucleotide sequences on a paper ticket, unique, sequence-driven patterns emerge for different taggant formulations. Algorithmically generated oligonucleotide sequences show no crosstalk and ink-embedded taggants maintain activity for at least 99 days at 60 °C (equivalent to nearly 2 years at room temperature). The resulting fluorescent signals can be analyzed by the eye or a smartphone when paired with a UV flashlight and filtered glasses.

Constructing Large 2D Lattices Out of DNA-Tiles.

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment.

Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.

Create Nanoscale Patterns with DNA Origami.

Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.

Biomedical Applications of DNA-Based Molecular Devices.

Strict Watson-Crick base pairing and availability by automated synthesis have allowed deoxyribonucleic acid (DNA) molecules to be used as engineerable building blocks for constructing versatile nanostructures. In recent decades, with the development of DNA nanotechnology, a range of DNA-based dynamic molecular devices with sophisticated nanostructures have been designed and constructed. Featuring programmability and biocompatibility, the applications of DNA-based nanodevices have been extensively focused on the interfaces of biological systems. This review summarizes the recent progress in the design of DNA devices exhibiting programmable functions for biomedical applications. In vitro and in vivo applications of DNA-based nanodevices in cellular imaging and systemic drug delivery are highlighted. The challenges and open opportunities are also discussed.

Making Worms Glow

Deoxyribonucleic acid (DNA) is the molecule that carries genetic information in a cell. The field of DNA nanotechnology aims to use DNA as the basis for making complex nanometerscale structures. While much progress has been made in creating such nano-architectures, the use of these structures within organisms had never been attempted. Our work is focused on using a simple DNA-based pH sensor in worms to yield information about organelle activity in cells. The first of its kind, this work set up a system to use DNA as a probe in living systems.

In vitro and in vivo behavior of DNA tetrahedrons as tumor-targeting nanocarriers for doxorubicin delivery

Deoxyribonucleic acid (DNA) is a versatile material with high applicability and inherent biocompatibility. L-DNA, the perfect mirror form of the naturally occurring D-DNA, has been used in DNA nanotechnology. It has thermodynamically identical properties to D-DNA, is capable of self-assembly and bio-orthogonal base-pairing, and is resistant to nuclease activity. We previously constructed an L-DNA tetrahedron (L-Td) and found that this nanostructure has remarkably higher capacity for cell penetration than its natural counterpart (D-Td). L-Td molecules of two different sizes—one with 17-mer per side (L-Td17) and the other with 30-mer per side (L-Td30)—were prepared by assembling four L-DNA strands. In this study, cellular uptake of L-Td with different sizes was observed over time using a laser scanning confocal microscope (LSCM) equipped with a live cell chamber system. In addition, we conducted a pharmacokinetic study to examine the potential of L-Td as a carrier for in vivo tumor-targeted delivery of a low dose of doxorubicin (DOX). L-Td entered into the cells through endocytosis, and a specific DNA sequence of the L-Td ensures targeted entry into cancer cells. Compared with free DOX, DOX-loaded L-Td (DOX@L-Td) showed decreased clearance and increased initial concentration (C0), half-life, and area under the curve (AUC), indicating that DOX@L-Td circulated in the blood stream for longer than free DOX. L-Td17, in particular, had beneficial effects owing to its ability to enhance tumor accumulation of DOX and reduce the cardiotoxicity caused by it through administration of a low dose of the drug.

Advances in DNA Nanostructure-Based Smart Drug Delivery Systems

Highly specific deoxyribonucleic acid (DNA) base-pairing not only carries genetic information, but also provides the basis for self-assembly of novel nanostructures with programmable shapes and sizes. Unlike single-stranded and double-stranded DNA, DNA nanostructures exhibit good cellular permeability. They also have characteristics of uniform size, easy functionalization, precise addressability, excellent water solubility and high biocompatibility. Due to their unique properties, these tailored molecular devices are ideal nanoscale systems for targeting cells and triggering cellular responses. Recent progress in the field of DNA nanotechnology has demonstrated effectiveness and advantages of DNA nanostructures as smart and targeted drug delivery systems or imaging agents within living organisms. In this review, we summarize the recent advances in structure design, cargo loading and cellular delivery of DNA nanocarriers, and discuss their potential in therapeutic applications.

Interfacing DNA nanodevices with biology: challenges, solutions and perspectives

The cellular machinery performs millions of complex reactions with extreme precision at nanoscale. From studying these reactions, scientists have become inspired to build artificial nanosized molecular devices with programmed functions. One of the fundamental tools in designing and creating these nanodevices is molecular self-assembly. In nature, deoxyribonucleic acid (DNA) is inarguably one of the most remarkable self-assembling molecules. Governed by the Watson–Crick base-pairing rules, DNA assembles with a structural reliability and predictability based on sequence composition unlike any other complex biological polymer. This consistency has enabled rational design of hundreds of two- and three-dimensional shapes with a molecular precision and homogeneity not preceded by any other known technology at the nanometer scale.During the last two decades, DNA nanotechnology has undergone a rapid evolution pioneered by the work of Nadrian Seeman (Kallenbach et al 1983 Nature 205 829–31). Especially the introduction of the versatile DNA Origami technique by Rothemund (2006 Nature 440 297–302) led to an efflorescence of new DNA-based self-assembled nanostructures (Andersen et al 2009 Nature 459 73–6, Douglas et al 2009 Nature 459 414–8, Dietz et al 2009 Science 325 725–30, Han et al 2011 Science 332 342–6, Iinuma et al 2014 Science 344 65–9), and variations of this technique have contributed to an increasing repertoire of DNA nanostructures (Wei et al 2012 Nature 485 623–6, Ke et al 2012 Science 338 1177–83, Benson et al 2015 Nature 523 441–4, Zhang et al 2015 Nat. Nanotechnol. 10 779–84, Scheible et al 2015 Small 11 5200–5). These advances have naturally triggered the question: What can these DNA nanostructures be used for?One of the leading proposals of use for DNA nanotechnology has been in biology and biomedicine acting as a molecular ‘nanorobot’ or smart drug interacting with the cellular machinery. In this review, we will explore and examine the perspective of DNA nanotechnology for such use. We summarize which requirements DNA nanostructures must fulfil to function in cellular environments and inside living organisms. In addition, we highlight recent advances in interfacing DNA nanostructures with biology.

Prediction and simulation on DNA strand displacement for the analysis of DNA nanotechnology

The objective of this work is to study the simulation techniques to simulate the time interval between displacements of deoxyribonucleic acid (DNA) strands efficiently and predict the simulation. In this work, two algorithms are proposed. The first proposed algorithm, modified Viterbi algorithm (MVA), is used to find sequence of hidden states and predict the sequence for the hidden DNA structure. Another proposed algorithm, modified Gillespie algorithm (MGA), integrates the stochastic processes such as Gillespie algorithm (GA) and next reaction method (NRM), is used to simulate the displacement of strands efficiently. The dataset used in this work is Droshipilla melanogaster. The output is the simulation of time interval between the strands. When the time interval between the strands increases the number of molecules also increases according to the time. This work resulted the simulated time interval between the displacements of strands and obtained the efficient simulation of strand displacement for the prediction of molecular structure and interaction between molecules.

N- and p-Type doping phenomenon by artificial DNA and M-DNA on two-dimensional transition metal dichalcogenides.

Deoxyribonucleic acid (DNA) and two-dimensional (2D) transition metal dichalcogenide (TMD) nanotechnology holds great potential for the development of extremely small devices with increasingly complex functionality. However, most current research related to DNA is limited to crystal growth and synthesis. In addition, since controllable doping methods like ion implantation can cause fatal crystal damage to 2D TMD materials, it is very hard to achieve a low-level doping concentration (nondegenerate regime) on TMD in the present state of technology. Here, we report a nondegenerate doping phenomenon for TMD materials (MoS2 and WSe2, which represent n- and p-channel materials, respectively) using DNA and slightly modified DNA by metal ions (Zn(2+), Ni(2+), Co(2+), and Cu(2+)), named as M-DNA. This study is an example of interdisciplinary convergence research between DNA nanotechnology and TMD-based 2D device technology. The phosphate backbone (PO4(-)) in DNA attracts and holds hole carriers in the TMD region, n-doping the TMD films. Conversely, M-DNA nanostructures, which are functionalized by intercalating metal ions, have positive dipole moments and consequently reduce the electron carrier density of TMD materials, resulting in p-doping phenomenon. N-doping by DNA occurs at ∼6.4 × 10(10) cm(-2) on MoS2 and ∼7.3 × 10(9) cm(-2) on WSe2, which is uniform across the TMD area. p-Doping which is uniformly achieved by M-DNA occurs between 2.3 × 10(10) and 5.5 × 10(10) cm(-2) on MoS2 and between 2.4 × 10(10) and 5.0 × 10(10) cm(-2) on WSe2. These doping levels are in the nondegenerate regime, allowing for the proper design of performance parameters of TMD-based electronic and optoelectronic devices (VTH, on-/off-currents, field-effect mobility, photoresponsivity, and detectivity). In addition, by controlling the metal ions used, the p-doping level of TMD materials, which also influences their performance parameters, can be controlled. This interdisciplinary convergence research will allow for the successful integration of future layered semiconductor devices requiring extremely small and very complicated structures.

Predictive evaluation for the preparation of a synthetic Y-shaped DNA nanostructure

With the advent of deoxyribonucleic acid (DNA) nanotechnology, the Y-shaped DNA nanostructure (Y-DNA) as a basic block was first created. Due to their characteristic selectivity and specificity, Y-DNA-based materials have been utilized in a variety of scientific fields including multiplexed nanobarcoding. Basically, the tripod DNA nanostructure was prepared by simple hybridization of three different single stranded DNA (ssDNA). Before the synthetic process, the optical densities (OD) of the three ssDNAs were measured to accurately estimate the concentration. Through repeated temperature fluctuations, three ssDNAs were hybridized into a Y-shaped block with both a central junction and three blunt ended arms. After the reaction, the ODs of the synthesized DNA products were measured and compared with the theoretical OD values calculated by a MATLAB program (‘matrix laboratory’) with different molar concentrations and volumes to predict the presence of Y-DNA. Simultaneously, the product was analyzed by agarose gel electrophoresis to confirm the YDNA structure. The measured ODs of the solutions with confirmed Y-DNA structures were close to the theoretical maximum OD values. This article provides means to help understand and prepare Y-DNA by performing OD measurements. It is highly expected that this guide will be an excellent starting point for structural DNA nanotechnology.

DNA: Building Blocks of Nanotechnology

DNA : B uilding B locks of N anotechnology Alexander Powers B S J “A friend of mine suggests a very interesting possibility for relatively small machines. He says that, although it is a very wild idea, it would be interesting in surgery if you could swallow the surgeon. You put the mechanical surgeon inside the blood vessel and it goes into the heart and ‘looks’ around...it find out which valve is faulty and takes a little knife and slices it.” Richard Feynman offered this prophetic vision at his famous 1959 Caltech lecture “There’s Plenty of Room at the Bottom” – a seminal event in the history of nanotechnology. In developing nanoscale machines, Feynman suggested scientists take a hint from biology. After all, proteins zip around cells on elaborate transport systems while DNA molecules encode vast quantities of information on a molecular scale. Feynman asked innovators to, “consider the possibility that we too can make an object that maneuvers at that level”(Feynman, 1960). Little did he know that biology would be the key to making his vision a tangible reality nearly 50 years later. The burgeoning field of DNA nanotechnology -- using nucleic acids as a building material in an nonbiological context -- has recently yielded some incredible breakthroughs ranging from programmable drug delivery capsules to enzyme “spiders” and chemical logic gates. DNA nanotechnology has the potential to finally realize the nano-surgeon. Deoxyribonucleic acid (DNA) makes for an extremely effective building material at the nanoscale; afterall, nucleic acids are life’s information storage molecule of choice. Nearly everyone learns about uses four different kinds of nucleotides with different chemical structures: adenine, guanine, thymine, and cytosine. The sequence of these nucleotides describes the information available for “building” an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences. Two strands of DNA pair up according to certain rules dictated by the molecular geometry of each nucleotide. Thymine pairs with adenine and cytosine pairs with guanine. This base pairing specificity is the foundation of designing DNA nanostructures. The key to building small is encoding the assembly information into the molecules themselves rather than using external forces to arrange them. Early successes often relied on these outside forces like atomic force microscopy or scanning tunneling microscopy to build structures molecule by molecule - approaches which cannot be easily scaled up to create large, complex structures (Shankland, 2009). The main advantage of DNA as a building material is that it can spontaneously self assemble, the sequence of nucleotides can be precisely controlled and the 3D structure is well understand (in contrast to the complexity of proteins). DNA nanostructures fall into one of two categories: structural and dynamic. Static structures are fixed arrangements of DNA in specific shapes. A variety of strategies exist to do this, one of the most successful of which is DNA origami. Dynamic structures are formed similarly but are designed to move using techniques like strand displacement - this is essential for any sort of computational or mechanical functionality. “Deoxyribonucleic acid (DNA) make for an extremely effective building material at the nanoscale” DNA by the time they graduate middle school - and with good reason. Just as computers derive vast amounts of information from a simple code of 1’s and 0’s stored electronically, DNA encodes the vast complexity of life in simple chemicals. Deoxyribonucleic acids are composed of long strands of repeating subunits known as nucleotides. DNA In a 2006 Nature article, Paul Rothemund coined the fanciful term “DNA Origami” to describe his successful manipulation of DNA strands into a variety of shapes. He synthesized six different shapes including squares, triangles, and five-pointed stars consisted of flat lattices of DNA. His revolutionary technique utilized a single long “scaffold” strand of 6 • B erkeley S cientific J ournal • S ynthetics • S pring 2014 • V olume 18 • I ssue 2

EGNAS: an exhaustive DNA sequence design algorithm

BackgroundThe molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences) offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences.ResultsThe algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented.ConclusionsWe developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

A Closer Look at DNA Nanotechnology

A nanosystem in which multiple nanoscale functional components made of a variety of nanomaterials are integrated with a microelectromechanical system (MEMS) becomes increasingly important as a key device for the next generation. A deoxyribonucleic acid (DNA) nanotechnology is expected to play an important role to bridge the gap between the nanoscale components (nanocomponents) and the microscale MEMS as a complementary approach for top–down manufacturing technique and bottom–up manufacturing technique to realize nanosystems. From the design viewpoint of a system, such as large-scale integrated circuits (LSI), MEMS, and nanosystem, it should be noted that the complexity is an essence to generate its functionality. The functionality of LSI/MEMS/nanosystem, where functional components are simply arranged in a periodic order, is limited. Periodic nanostructure can be a part of a nanosystem as a nanocomponent, but it is not enough. Interaction and cooperation of multiple nanocomponents with different features make it possible to generate a unique and useful functionality of a nanosystem.

Supramolecular DNA nanotechnology

Abstract Nature uses deoxyribonucleic acid (DNA) as the main material for the storage and transmission of life’s blueprint. Today, DNA is being used as a “smart” material to help solve a number of long-standing issues facing researchers in materials science and nanotechnology. In DNA nanotechnology, DNA’s powerful base-pair molecular recognition criteria are utilized to control the final structure and function of the material being generated. A sub-area of research that our group has recently termed “supramolecular DNA nanotechnology” is emerging and is extending the limits of this molecule in nanotechnology by further fine-tuning DNA’s structural and functional potential. This review will discuss the fruition and fundamentals of supramolecular DNA nanotechnology, as well as its future as a viable science in a material world.