DNA Nanowires Research Articles

Flow‐Enabled Self‐Assembly of Large‐Scale Aligned Nanowires

AbstractOne‐dimensional nanowires enable the realization of optical and electronic nanodevices that may find applications in energy conversion and storage systems. Herein, large‐scale aligned DNA nanowires were crafted by flow‐enabled self‐assembly (FESA). The highly oriented and continuous DNA nanowires were then capitalized on either as a template to form metallic nanowires by exposing DNA nanowires that had been preloaded with metal salts to an oxygen plasma or as a scaffold to direct the positioning and alignment of metal nanoparticles and nanorods. The FESA strategy is simple and easy to implement and thus a promising new method for the low‐cost synthesis of large‐scale one‐dimensional nanostructures for nanodevices.

An enzyme-free and label-free fluorescent biosensor for small molecules by G-quadruplex based hybridization chain reaction

An enzyme-free and label-free fluorescent biosensor is developed by G-quadruplex-based hybridization chain reaction (HCR) for small molecules, using adenosine triphosphate (ATP) as the model. Aptamer probes for the recognition of small molecules are hybridized with blocking probes. The G-quadruplex sequences are incorporated into one of the two HCR hairpin probes. In the presence of small molecules (ATP), the formation of aptamer–ATP bioaffinity complexes induces the release of blocking probes; the released blocking probes initiate HCR and numerous G-quadruplexes along DNA nanowires are self-assembled after the HCR process. Using N-methyl mesoporphyrin IX (NMM) as the fluorophore, a “turn-on” fluorescence response can be achieved and detected as low as 15μmolL−1 of ATP. This biosensor is applied to detect ATP in biologic samples with satisfactory results.

Sensitive Detection of Transcription Factor Kaiso via Self‐Assembly of DNA on an Electrode Surface

AbstractHere we report a novel method based on the assembly of DNA nanowire on an electrode surface for amplified detection of an essential transcription factor protein named Kaiso, the aberrant expression of which is involved in various kinds of tumors. This method allows efficient bioanalysis of Kaiso in three breast cancer cell lines to be conducted, thus the malignancy degree of the cell lines can be evaluated by using this method. The proposed method also shows desirable sensitivity, high selectivity, and excellent reproducibility, implying that this method may hold considerable potential for clinical diagnosis in the future.

Manganese(iii)meso-tetrakis(4-N-methylpyridyl)-porphyrin and mediator thionine co-decorated DNA nanowires for sensitive electrochemical monitoring of mercury(ii)

We developed a novel electrochemical DNA biosensor for mercury(II) ion (Hg2+) detection on the basis of manganese(III) meso-tetrakis(4-N-methylpyridyl)-porphyrin (MnTMPyP) and electron mediator thionine (Thi) co-decorated DNA nanowires for signal amplification. The T-rich capture DNA assembled on the electrode could successfully immobilize the primer DNA via specific base-pairing, which triggered the hybridization chain reaction (HCR) to form long DNA nanowires with the aim of loading abundant MnTMPyP and electron mediator Thi. In the electrolyte containing H2O2, the MnTMPyP loaded in the DNA nanowires showed superior peroxidase-like activity and electrocatalyzed the reduction of H2O2, promoting the redox reaction of Thi with a dramatically amplified electrochemical signal. However, in the presence of target Hg2+, Hg2+-mediated thymine base pairs (T–Hg2+–T) are formed between the two neighboring T-rich capture DNAs, which resulted in the release of the MnTMPyP and Thi co-decorated DNA nanowires from the electrode surface, providing a reduced readout signal for the quantitative electrochemical detection of Hg2+. The results showed that the proposed electrochemical DNA biosensor was highly sensitive to Hg2+ in the concentration of 1.0 ng L−1 to 107 ng L−1 with a detection limit of 0.5 ng L−1 (2.5 pM), and it also exhibited excellent selectivity against other interferential metal ions.

Writing and functionalisation of suspended DNA nanowires on superhydrophobic pillar arrays.

Nanowire arrays and networks with precisely controlled patterns are very interesting for innovative device concepts in mesoscopic physics. In particular, DNA templates have proven to be versatile for the fabrication of complex structures that obtained functionality via combinations with other materials, for example by functionalisation with molecules or nanoparticles, or by coating with metals. Here, the controlled motion of the a three-phase contact line (TCL) of DNA-loaded drops on superhydrophobic substrates is used to fabricate suspended nanowire arrays. In particular, the deposition of DNA wires is imaged in situ, and different patterns are obtained on hexagonal pillar arrays by controlling the TCL velocity and direction. Robust conductive wires and networks are achieved by coating the wires with a thin layer of gold, and as proof of concept conductivity measurements are performed on single suspended wires. The plastic material of the superhydrophobic pillars ensures electrical isolation from the substrate. The more general versatility of these suspended nanowire networks as functional templates is outlined by fabricating hybrid organic-metal-semiconductor nanowires by growing ZnO nanocrystals onto the metal-coated nanowires.

Target triggered self-assembly of Au nanoparticles for amplified detection of Bacillus thuringiensis transgenic sequence using SERS

The research methods for DNA detection have been widely extended since the application of nanotechnology, but it remains a challenge to detect specific DNA sequences or low abundance genes in the biological samples with accuracy and sensitivity. Here we developed a SERS biosensing platform by target DNA (tDNA) triggered self-assembly of Au nanoparticles (Au NPs) probes on DNA nanowires for signal amplification in DNA analysis. Based on the hybridization chain reactions (HCR) and surface enhanced Raman scattering (SERS) technology, the SERS intensity reveals a good linearity with tDNA ranging from 50pM to 500pM under optimal conditions. The specific detection of tDNA sequence was realized with a detection limit of 50pM (S/N=3). To demonstrate the specificity and universality of the strategy, the single-base mismatches in DNA and the Bacillus thuringiensis (Bt) transgenic sequence were successively applied in the SERS assay. The results showed that the sensitivity and accuracy of the SERS-based assay were comparable with real-time PCR. Besides, the method would provide precise and ultra-sensitive detection of tDNA but also informative supplement to the SERS biosensing platform.

Plasmonically enhanced electron escape from gold nanoparticles and their polarization-dependent excitation transfer along DNA nanowires.

Here we show plasmon mediated excitation transfer along DNA nanowires over up to one micrometer. Apparently, an electron excitation is initiated by a femtosecond laser pulse that illuminates gold nanoparticles (AuNP) on double stranded DNA (dsDNA). The dependency of this excitation on laser wavelength and polarization are investigated. Excitation of the plasmon resonance of the AuNPs via one- and two-photon absorption at 520 and 1030 nm, respectively, was explored. We demonstrate an excitation transfer along dsDNA molecules at plasmon supported four-photon excitation of AuNP cluster or at laser field driven nanoparticle electron tunneling for an alignment of the attached dsDNA to the polarization of the electric field of the laser light. These results extend the previously observed plasmonically induced three-photon excitation transfer along DNA nanowires to another nanoparticle material (gold) and the adapted irradiation wavelengths.

Programmed Self‐Assembly of a Quadruplex DNA Nanowire

The ability to produce, reproducibly and systematically, well-defined quadruplex DNA nanowires through controlled rational design is poorly understood despite potential utility in structural nanotechnology. The programmed hierarchical self-assembly of a long four-stranded DNA nanowire through cohesive self-assembly of GpC and CpG "sticky" ends is reported. The encoding of bases within the quadruplex stem allows for an uninterrupted π-stacking system with rectilinear propagation for hundreds of nanometers in length. The wire is mechanically stable and features superior nuclease resistance to double-stranded DNA. The study indicates the feasibility for programmed assembly of uninterrupted quadruplex DNA nanowires. This is fundamental to the systematic investigation of well-defined DNA nanostructures for uses in optoelectronic and electronic devices as well as other structural nanotechnology applications.

Hybridization Chain Reaction Amplification of MicroRNA Detection with a Tetrahedral DNA Nanostructure-Based Electrochemical Biosensor

There remains a great challenge in the sensitive detection of microRNA because of the short length and low abundance of microRNAs in cells. Here, we have demonstrated an ultrasensitive detection platform for microRNA by combining the tetrahedral DNA nanostructure probes and hybridization chain reaction (HCR) amplification. The detection limits for DNA and microRNA are 100 aM and 10 aM (corresponding to 600 microRNAs in a 100 μL sample), respectively. Compared to the widely used supersandwich amplification, the detection limits are improved by 3 orders of magnitude. The uncontrolled surface immobilization and consumption of target molecules that limit the amplification efficiency of supersandwich are eliminated in our platform. Taking advantage of DNA nanotechnology, we employed three-dimensional tetrahedral DNA nanostructure as the scaffold to immobilize DNA recognition probes to increase the reactivity and accessibility, while DNA nanowire tentacles are used for efficient signal amplification by capturing multiple catalytic enzymes in a highly ordered way. The synergetic effect of DNA tetrahedron and nanowire tentacles have proven to greatly improve sensitivity for both DNA and microRNA detection.

Target-Triggered Cyclic Assembly of DNA–Protein Hybrid Nanowires for Dual-Amplified Fluorescence Anisotropy Assay of Small Molecules

Aptamer-based fluorescence anisotropy (FA) assays have attracted great interest in recent years. However, a key factor that determines FA value is molar mass, thus limiting the utility of this assay for the detection of small molecules. To solve this problem, streptavidin, as a molar mass amplifier, was used in a hybridization chain reaction (HCR) to construct a target-triggered cyclic assembly of DNA-protein hybrid nanowires for highly sensitive detection of small molecules by fluorescence anisotropy. In this assay, one blocking DNA strand is released by target-aptamer recognition. The DNA then serves as an initiator to trigger enzyme-free autonomous cross-opening of hairpin probes via HCR to form a DNA nanowire for further assembly of streptavidin. Using adenosine triphosphate (ATP) as the small molecule target, this novel dual-amplified, aptamer-based FA assay affords high sensitivity with a detection limit of 100 nM. This limit of detection (LOD) is much lower than that of the disassembly approach without HCR amplification or the assembly strategy without streptavidin. In contrast to the previous turn-off disassembly approaches based on nonspecific interactions between the aptamer probe and amplification moieties, the proposed aptamer-based FA assay method exhibits a turn-on response to ATP, which can increase sensing reliability and reduce the risk of false hits. Moreover, because of its resistance to environmental interferences, this FA assay has been successfully applied for direct detection of 0.5 μM ATP in complex biological samples, including cell media, human urine, and human serum, demonstrating its practicality in real complex biological systems.

Design of a Microchannel‐Nanochannel‐Microchannel Array Based Nanoelectroporation System for Precise Gene Transfection

A micro/nano-fabrication process of a nanochannel electroporation (NEP) array and its application for precise delivery of plasmid for non-viral gene transfection is described. A dip-combing device is optimized to produce DNA nanowires across a microridge array patterned on the polydimethylsiloxane (PDMS) surface with a yield up to 95%. Molecular imprinting based on a low viscosity resin, 1,4-butanediol diacrylate (1,4-BDDA), adopted to convert the microridge-nanowire-microridge array into a microchannel-nanochannel-microchannel (MNM) array. Secondary machining by femtosecond laser ablation is applied to shorten one side of microchannels from 3000 to 50 μm to facilitate cell loading and unloading. The biochip is then sealed in a packaging case with reservoirs and microfluidic channels to enable cell and plasmid loading, and to protect the biochip from leakage and contamination. The package case can be opened for cell unloading after NEP to allow for the follow-up cell culture and analysis. These NEP cases can be placed in a spinning disc and up to ten discs can be piled together for spinning. The resulting centrifugal force can simultaneously manipulate hundreds or thousands of cells into microchannels of NEP arrays within 3 minutes. To demonstrate its application, a 13 kbp OSKM plasmid of induced pluripotent stem cell (iPSC) is injected into mouse embryonic fibroblasts cells (MEFCs). Fluorescence detection of transfected cells within the NEP biochips shows that the delivered dosage is high and much more uniform compared with similar gene transfection carried out by the conventional bulk electroporation (BEP) method.

Amplified colorimetric detection of mercuric ions through autonomous assembly of G-quadruplex DNAzyme nanowires

An amplified colorimetric detection of Hg2+ is proposed by combining T–Hg2+–T base pairs and hybridization chain reaction (HCR). Two hairpins consisting of three-fourths and one-fourth of the horseradish peroxidase (HRP)-mimicking DNAzyme in inactive configuration are used as functional elements. In the presence of Hg2+, one of the hairpins is opened by an assistant probe with the help of T–Hg2+–T base pairs and this triggers an autonomous cross-opening of the two hairpins using the strand displacement principle, resulting in the formation of DNA nanowires consisting of numerous reunited Q-quadruplex DNAzyme units. The resulting catalytically active hemin/G-quadruplex HRP-mimicking DNAzymes catalyze the oxidation of ABTS2− by H2O2 into a green-colored cationic radical ABTS•+ for the colorimetric readout. This “turn-on” sensing system enables the high sensitive and selective detection of aqueous Hg2+ with a detection limit of 9.7pM.

Photonic DNA-Chromophore Nanowire Networks: Harnessing Multiple Supramolecular Assembly Modes

Photonic DNA nanostructures are typically prepared by the assembly of multiple sequences of long DNA strands that are conjugated covalently to various dye molecules. Herein we introduce a noncovalent method for the construction of porphyrin-containing DNA nanowires and their networks that uses the programmed assembly of a single, very short, oligodeoxyribonucleotide sequence. Specifically, our strategy exploits a number of supramolecular binding modalities (including DNA base-pairing, metal-ion coordination, and β-cyclodextrin-adamantane derived host-guest interactions) for simultaneous nanowire assembly and porphyrin incorporation. Furthermore, we also show that the resultant DNA-porphyrin assembly can be further functionalized with a complementary "off-the-shelf" DNA binding dye resulting in photonic structures with broadband absorption and energy transfer capabilities.

MANUFACTURING DNA NANOWIRES WITH AIR BLOWING ASSEMBLY ON MICROPATTERNED SURFACE

Herein, we present a new flow-guided assembly approach to align and position DNA nanowires. Single or multiple drops of a λ-DNA solution were loaded from one side of template with micropad array and blown off by air flow. DNA molecules were aligned along the flow direction and well positioned under the guiding of pre-defined micropatterns. Different from other pioneering work, we focused on investigating the assembly quality, reliability and appropriateness for large-scale manufacturing. We correlated the assembly quality (alignment, patterning and the surface coverage) with the concentration of DNA in droplets and droplet evaporation and suggested appropriate process windows. With this new approach, the synthesis, alignment and patterning of nanowires may be done in a reliable and efficient manner and with high throughput.

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface.

We investigate single DNA stretching dynamics in a de-wetting flow over micropillars using Brownian dynamics simulation. The Brownian dynamics simulation is coupled with transient flow field computation through a numerical particle tracking algorithm. The droplet formation on the top of the micropillar during the de-wetting process creates a flow pattern that allows DNA to stretch across the micropillars. It is found that DNA nanowire forms if DNA molecules could extend across the stagnation point inside the connecting water filament before its breakup. It also shows that DNA locates closer to the top wall of the micropillar has higher chance to enter the flow pattern of droplet formation and thus has higher chance to be stretched across the micropillars. Our simulation tool has the potential to become a design tool for DNA manipulation in complex biomicrofluidic devices.

Macroscopic Highly Aligned DNA Nanowires Created by Controlled Evaporative Self-Assembly

By subjecting DNA aqueous solution to evaporate in a curve-on-flat geometry that was composed of either a spherical lens or a cylindrical lens situated on a flat substrate, a set of highly aligned DNA nanowires in the forms of spokes and parallel stripes over a macroscopic area (i.e., millimeter scale) were successfully created. The DNA molecules were stretched and aligned on polymer-coated substrate by the receding meniscus. The imposed curve-on-flat geometry provided a unique environment for controlling the flow within the evaporating solution by eliminating temperature gradient and possible convective instability and, thus, regulated the formation of DNA nanowires. Such controlled evaporative self-assembly is remarkably easy to implement and opens up a new avenue for crafting large-scale DNA-based nanostructures in a simple and cost-effective manner, dispensing with the need for lithography techniques.

Plasmonic Coupling and Long-Range Transfer of an Excitation along a DNA Nanowire

We demonstrate an excitation transfer along a fluorescently labeled dsDNA nanowire over a length of several micrometers. Launching of the excitation is done by exciting a localized surface plasmon mode of a 40 nm silver nanoparticle by 800 nm femtosecond laser pulses via two-photon absorption. The plasmonic mode is subsequently coupled or transformed to excitation in the nanowire in contact with the particle and propagated along it, inducing bleaching of the dyes on its way. In situ as well as ex situ fluorescence microscopy is utilized to observe the phenomenon. In addition, transfer of the excitation along the nanowire to another nanoparticle over a separation of 5.7 μm was clearly observed. The nature of the excitation coupling and transfer could not be fully resolved here, but injection of an electron into the DNA from the excited nanoparticle and subsequent coupled transfer of charge (Dexter) and delocalized exciton (Frenkel) is the most probable mechanism. However, a direct plasmonic or optical coupling and energy transfer along the nanowire cannot be totally ruled out either. By further studies the observed phenomenon could be utilized in novel molecular systems, providing a long-needed communication method between molecular devices.

2D14 ナノチャネル中での単分子DNAの金属被覆によるナノワイヤの形成(OS9-1:バイオMEMS(1))

2D14 ナノチャネル中での単分子DNAの金属被覆によるナノワイヤの形成(OS9-1:バイオMEMS(1))

Computational studies investigating the effect of sequencing and environment on the conductance of DNA nanowires

ABSTRACTUnderstanding electron transfer in molecular systems is important, especially in the context of molecular electronics. With the desire to incorporate biological molecules in molecular electronic devices, there is a need to establish the relative importance of the various factors like the environment and the molecular structure (DNA sequence) on the electrical conduction. There has been much debate about mechanisms of electron transfer in biological molecules. We have conducted a systematic study of electron conduction across DNA molecular segments using the non-equilibrium Green function (NEGF) method. The Hamiltonian matrix elements were determined within the framework of the Extended Hückel Approximation. In considering (CG) base pair sequences, we find that the conductance decreases with segment length and that the substitution of (AT) base-pairs also reduces the conductance. When the DNA segments are in aqueous solution, the conductance is found to almost double in magnitude.

Radicalized DNA Bases through Ring-Expansion Modification: An Intriguing Class of Building Blocks for the Magnetic DNA Nanowires

In the present work, cyclopentadienyl radicals are introduced to nucleobases to gain the building blocks of DNA-based molecular wires with novel electromagnetic characteristics. Calculations reveal...