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Anisotropic gold nanoparticles have attracted great interest due to their unique physicochemical properties derived from the shape anisotropy. Manipulation of their interfacial interactions, and thereby the assembling behaviors are often requisite in their applications ranging from optical sensing and diagnosis to self-assembly. Recently, the control of interfacial force based on base pair stacking of DNA terminals have offered a new avenue to surface engineering of nanostructures. In this review, we focus on the DNA base stacking-induced assembly of anisotropic gold nanoparticles, such as nanorods and nanotriangles. The fundamental aspects of anisotropic gold nanoparticles are provided, including the mechanism of the anisotropic growth, the properties arising from the anisotropic shape, and the construction of DNA-grafted anisotropic gold nanoparticles. Then, the advanced applications of their functional assemblies in biosensing and ordered assembly are summarized, followed by a comparison with gold nanospheres. Finally, conclusions and the direction of outlooks are given including future challenges and opportunities in this field.

The contamination of heavy metals (e.g., Hg, Pb, Cd and As) poses great risks to the environment and human health. Rapid and simple detection of heavy metals of considerable toxicity in low concentration levels is an important task in biological and environmental analysis. Among the many convenient detection methods for heavy metals, DNA-inspired gold nanoparticles (DNA-AuNPs) have become a well-established approach, in which assembly/disassembly of AuNPs is used for colorimetric signaling of the recognition event between DNA and target heavy metals at the AuNP interface. This review focuses on the recent efforts of employing DNA to manipulate the interfacial properties of AuNPs, as well as the major advances in the colorimetric detection of heavy metals. Beginning with the introduction of the fundamental aspects of DNA and AuNPs, three main strategies of constructing DNA-AuNPs with DNA binding-responsive interface are discussed, namely, crosslinking, electrostatic interaction and base pair stacking. Then, recent achievements in colorimetric biosensing of heavy metals based on manipulation of the interface of DNA-AuNPs are surveyed and compared. Finally, perspectives on challenges and opportunities for future research in this field are provided.

Colorimetric detection of various target molecules in aqueous solutions based on the non-crosslinking assembly of DNA-functionalized Au nanoparticles (DNA-AuNPs) has been well established in recent years. The extension of DNA-AuNPs to other solvents remains much less explored, despite the practical importance of detection in non-aqueous solutions, such as those containing an organic ingredient that is required or not removable in many contexts. However, the general consideration that DNA is easily denatured and precipitated in organic solvents has been hampering the use of DNA-AuNPs in low polar solvents. Herein, we report a more rapid non-crosslinking assembly of double-stranded (ds) DNA-AuNPs in alcoholic solvents than in aqueous solvents. When the concentration of ethanol in the disperse medium is increased from 0% to 20% (v/v), the rate of non-crosslinking assembly is distinctly increased by a factor of 5-6, whereas the rate is sharply decreased when the ethanol concentration is further increased to 40%. This biphasic kinetics trend could be attributed to the competitive balance between the enhanced intermolecular attraction between dsDNAs and the increased propensity for melting of dsDNA. Rapid naked-eye identification of clear liquors that are encoded by oligonucleotide additives has also been demonstrated by using the alcoholic non-crosslinking assembly of dsDNA-AuNPs as a proof-of-concept.

Inspired by the increasing use of plasmonic gold and silver nanoplates as probes for diverse analytes, the research community often questions which metal nanoplates should be chosen for a given application. A comparative study was performed on the performance and physicochemical properties of three types of metal nanoplates for use in plasmonic detection of Hg(II) ion. Specifically, gold, silver and Ag@Au nanoplates were studied. The established amalgamation method integrated into a detection scheme using nanoplates affords a unique yet straightforward signaling and extraction route for selective recognition of Hg(II) ion. Upon transformation of Hg(II) ion to metallic mercury, nanoplate amalgamation takes place instantly. This reshapes both the morphology and the optical characteristics of nanoplates. It is found that gold and Ag@Au nanoplates enable highly selective quantitation of Hg(II) ion by using a DNA oligomer consisting of poly-deoxycytidine (poly(C)) as a masking agent against Ag(I) ion. The silver nanoplates, in turn, display the best sensitivity owing to the chemical instability. The induced surface plasmonic shifts (of up to 250 nm and color changes from red to green) allows for determination of Hg(II) over a wide range and with a limit of detection of ~10 nM. It is recommended that the gold and Ag@Au nanoplates are used in relatively complex systems, while silver nanoplates are suited for simple matrices. Graphic abstract The amalgamation process integrated with metal (e.g., Au, Ag and Ag@Au) nanoplates affords plasmonic detection of Hg(II) ion with the aid of a poly(c) DNA sequence as the masking agent for Ag(I) ion.

The interactions between metal ions and biomolecules are crucial to various bioprocesses. Development of plasmon switching nanodevices that exploit these molecular interactions is of fundamental and technological interest. Here, we show plasmon switching based on rapid aggregation/dispersion of double-stranded DNA-modified gold nanorods (dsDNA-AuNRs) that exhibit colloidal behaviors depending on pairing/unpairing of the terminal bases. The dsDNA-AuNRs bearing a thymine-thymine (T-T) mismatch at the penultimate position undergo spontaneous non-cross-linking aggregation in the presence of Hg 2+ due to T-Hg-T base pairing. Inversely, the subsequent addition of cysteine (Cys) gives rise to the removal of Hg 2+ from the T-Hg-T base pair to reproduce the T-T mismatch, resulting in stable dispersion of the dsDNA-AuNRs. The chemical-responsive plasmon switch allows for the rapid and repeatable cycles at room temperature. The validity of the present method is further exemplified by developing another plasmon switch fueled by Ag + and Cys by installing the Ag + -binding DNA sequence in the dsDNA-AuNR.

A technique for tuning interparticle distance in plasmonic gold nanoparticle (AuNP) assemblies has shown great potential for the development of optoelectronic nanodevices. However, it still remains a challenge to reversibly alter the distance in a facile manner. DNA-templated AuNP assemblies are among the mostly investigated plasmonic nanomaterials. In previous work, salt-induced structural shrinkage of DNA-templated AuNP (5 nm in diameter) dimers/trimers is demonstrated only by electron microscopic analyses. In the present study, interparticle distance is modulated in larger AuNP (15 nm or 20 nm in diameter) dimers that exhibit strong surface plasmon resonance (SPR). The reversible SPR shift is achieved by using the temperature-dependent shrinkage/extension of the DNA-templated AuNP dimers. The present proof-of-concept study suggests a potential application of the reversible structural change to optical switching., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Directed assemblies of anisotropic metal nanoparticles exhibit attractive physical and chemical properties. However, an effective methodology to prepare differently directed assemblies from the same anisotropic nanoparticles is not yet available. Gold nanorods (AuNRs) region-selectively modified with different DNA strands can form side-by-side (SBS) and end-to-end (ETE) assemblies in a non-crosslinking manner. When the complementary DNA is hybridized to the surface-bound DNA, stacking interaction between the blunt ends takes place in the designated regions. Such AuNRs assemble into highly ordered structures, assisted by capillary forces emerging on the substrate surface. Moreover, insertion of a mercury(II)-mediated thymine-thymine base pair into the periphery of the DNA layer allows selective formation of the SBS or ETE assemblies from the strictly identical AuNRs with or without mercury(II)., (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Gold nanoparticles modified with DNA duplexes are rapidly and spontaneously aggregated at high ionic strength. In contrast, this aggregation is greatly suppressed when the DNA duplex has a single-base mismatch or a single-nucleotide overhang located at the outermost surface of the particle. These colloidal features emerge irrespective of the size and composition of the particle core; however, the effects of the shape remain unexplored. Using gold nanorods and nanotriangles (nanoplatelets), we show herein that both remarkable rapidity in colloidal aggregation and extreme susceptibility to DNA structural perturbations are preserved, regardless of the shape and aspect ratio of the core. It is also demonstrated that the DNA-modified gold nanorods and nanotriangles are applicable to naked-eye detection of a single-base difference in a gene model. The current study corroborates the generality of the unique colloidal properties of DNA-functionalized nanoparticles, and thus enhances the feasibility of their practical use., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Solution-phase synthesis and post-synthetic bio-modification have continued to play a dominant role in preparation of nanostructured biomaterials. Heterogeneous nucleation and growth that occur much more often in nature, however, remain rarely explored in nano-biomaterials research. We have newly developed a DNA-modulated photoconversion approach to uniform silver nanoparticles that afford DNA-directed recognition and multi-mode imaging. The present study was aimed at understanding the rapid heterogeneous nucleation and growth of AgNPs at the solid-liquid interface with the aid of DNA. Dynamic changes in absorbance, size and morphology of silver nanostructures were monitored and analyzed to clarify the growth kinetics, which indicated a synthetic route involving synchronous growth of silver nanostructures and the fragmentation and consumption of AgCl. Various stabilizers, including polymer and amino acids, were assessed and compared with respect to the efficacy in photoconversion of AgCl. DNA was found to offer the best monodispersity and the smallest diameter for the resultant AgNPs, due to its strong interactions to silver species as well as excellent charge dispersion ability. By controlling the physicochemical property of DNA through choice of pH and ionic strength, we have demonstrated tunable structure and composition of the nanoparticles., (Copyright © 2015 Elsevier Inc. All rights reserved.)

We demonstrate a facile approach for converting AgCl to functional silver nanoparticles (AgNPs) via photoreduction in the presence of DNA. The resulting AgNPs are biofunctionalized, and exhibit photostable luminescence and DNA-specific Raman signatures, showing high potential for use in DNA-directed recognition and advanced bioimaging., (This journal is © The Royal Society of Chemistry 2011)

The currently established DNA nanoprobes for the detection of mycotoxin from beverages have been limited by complicated sample pretreatment and uncontrollable nanoparticle flocculation in complex systems. We develop a rapid colorimetric approach for ochratoxin A (OTA) detection in Baijiu in a sample-in/"yes" or "no" answer-out fashion through target-modulated base pair stacking assembly of DNA-functionalized gold nanoparticles (DNA–AuNPs). The colorimetric signification of OTA relies on the competition of OTA with the AuNP surface-grafted DNA in binding with an OTA-targeted aptamer. The specific recognition of OTA by the aptamer prevents DNA duplex formation on the AuNP surface, thereby inhibiting the base pair stacking assembly of the DNA–AuNPs and giving rise to a "turn-on" color. By further suppressing DNA hybridization using a bulged loop design and an alcohol solution, the DNA–AuNPs exhibit an improved reproducibility for OTA sensing while maintaining excellent susceptivity to OTA. A detection limit of 88 nM was achieved along with high specificity towards OTA, which is lower than the maximum tolerated level of OTA in foodstuffs defined by countries worldwide. The entire reaction time, avoiding sample pretreatment, is less than 17 min. The DNA–AuNPs with anti-interference features and sensitive "turn-on" performance promise convenient on-site detection of mycotoxin from daily beverages. [ABSTRACT FROM AUTHOR]

Circular single‐stranded DNA (c‐ssDNA) has significant applications in DNA detection, the development of nucleic acid medicine, and DNA nanotechnology because it shows highly unique features in mobility, dynamics, and topology. However, in most cases, the efficiency of c‐ssDNA preparation is very low because polymeric byproducts are easily formed due to intermolecular reaction. Herein, we report a one‐pot ligation method to efficiently prepare large c‐ssDNA. By ligating several short fragments of linear single‐stranded DNA (l‐ssDNA) in one‐pot by using T4 DNA ligase, longer l‐ssDNAs intermediates are formed and then rapidly consumed by the cyclization. Since the intramolecular cyclization reaction is much faster than intermolecular polymerization, the formation of polymeric products is suppressed and the dominance of intramolecular cyclization is promoted. With this simple approach, large‐sized single‐stranded c‐ssDNAs (e.g. 200‐nt) were successfully synthesized in high selectivity and yield. [ABSTRACT FROM AUTHOR]

Abstract: Nanoparticle (NP) arrays exhibit collective physical and chemical properties, which are potentially applicable to various nanodevices, such as data storage media and biosensors. In this Communication, a spontaneous method of constructing the 2D NP arrays from precursory 1D chains of DNA‐modified NPs is described. The single‐stranded (ss) DNA‐modified gold NPs are hybridized to a long repetitive ssDNA synthesized with rolling circle amplification to produce the precursory NP chains. Transmission electron microscopy reveals that the chains of fully matched double‐stranded (ds) DNA‐modified NPs undergo shrinkage and folding during evaporation to afford the 2D NP arrays. In particular, the chains of long dsDNA‐modified NPs with short interparticle spacing form the NP arrays with anisotropic interparticle spacing. The present approach could be useful for readily aligning NPs on the substrate surface. [ABSTRACT FROM AUTHOR]

Canine distemper virus (CDV) is the causative agent of canine distemper (CD) that is a highly contagious, lethal, multisystemic viral disease of receptive carnivores. The prevalence of CDV is a major concern in susceptible animals. Presently, it is unclear whether intragenic recombination can contribute to gene mutations and segment reassortment in the virus. In this study, 25 full-length CDV genome sequences were subjected to phylogenetic and recombinational analyses. The results of phylogenetic analysis, intragenic recombination, and nucleotide selection pressure indicated that mutation and recombination occurred in the six individual genes segment (H, F, P, N, L, M) of the CDV genome. The analysis also revealed pronounced genetic diversity in the CDV genome according to the geographically distinct lineages (genotypes), namely Asia-1, Asia-2, Asia-3, Europe, America-1, and America-2. The six recombination events were detected using SimPlot and RDP programs. The analysis of selection pressure demonstrated that a majority of the nucleotides in the CDV individual gene were under negative selection. Collectively, these data suggested that homologous recombination acts as a key force driving the genetic diversity and evolution of canine distemper virus. [ABSTRACT FROM AUTHOR]

Abstract: Involvement of single‐nucleotide polymorphism (SNP) genotyping in healthcare should allow for more effective use of pharmacogenomics. However, user‐friendly assays without the requirement of a special instrument still remain unavailable. This study describes naked‐eye SNP discrimination in exon 5 of the human cytochrome P450 2C19 monooxygenase gene, CYP2C19*1 (the wild‐type allele) and CYP2C19*2 (the variant allele with G681A point mutation). The present assay is composed of allele‐specific single‐base primer extension and salt‐induced aggregation of DNA‐modified gold nanoparticles (DNA–AuNPs). Genetic samples extracted from human hair roots are subjected to this assay. The results are verified by direct sequencing. This study should promise the prospective use of DNA–AuNPs in gene diagnosis. [ABSTRACT FROM AUTHOR]

Gold nanoparticles modified with DNA duplexes are rapidly and spontaneously aggregated at high ionic strength. In contrast, this aggregation is greatly suppressed when the DNA duplex has a single-base mismatch or a single-nucleotide overhang located at the outermost surface of the particle. These colloidal features emerge irrespective of the size and composition of the particle core; however, the effects of the shape remain unexplored. Using gold nanorods and nanotriangles (nanoplatelets), we show herein that both remarkable rapidity in colloidal aggregation and extreme susceptibility to DNA structural perturbations are preserved, regardless of the shape and aspect ratio of the core. It is also demonstrated that the DNA-modified gold nanorods and nanotriangles are applicable to naked-eye detection of a single-base difference in a gene model. The current study corroborates the generality of the unique colloidal properties of DNA-functionalized nanoparticles, and thus enhances the feasibility of their practical use. [ABSTRACT FROM AUTHOR]

As a class of emerging nanoparticles, gold nanotriangles (AuNTs) are characterized by unique structural anisotropy and plasmonic properties. The organization of AuNTs into well-defined architecture potentially promises collective properties that are difficult to produce by individual AuNTs. To date, however, the orientation-controlled self-assembly of AuNTs has been achieved with limited success. Here, we describe an effective and straightforward approach to induce directed self-assembly of AuNTs. By taking advantage of the uneven chemical reactivity of AuNT surfaces, we implement regioselective modification of the edges and the top/bottom surfaces with two different double-stranded DNA (dsDNA) sequences. By means of terminal single base pairing/unpairing, controlled assembly of the dsDNA-modified AuNTs evolves in a face-to-face or edge-to-edge manner based on blunt-end stacking interaction on an intentional region of the AuNTs, along with entropic repulsion by unpaired terminal nucleobases on the other region. This approach could be useful for achieving directed self-assembly of other anisotropic nanoparticles. [ABSTRACT FROM AUTHOR]

Abstract: We developed a micro-nanofluidic bioreactor-detector system for isothermal DNA amplification and sensitive real-time detection of the amplified products for sequence-specific molecular identification. Aluminum (Al) chips with a range of volumes from 7.07μL to 39nL and an associated real-time confocal optical detector are described. The detector provided highly sensitive fluorescence detection and low background noise. One of the important aspects of the system was the development of a surface processing technique that afforded chips with an inert surface to improve amplification stability in micro-nanoliter reaction assays. The micro-nanofluidic system exhibited more sensitive exponential DNA amplification characteristics than a standard PCR tube amplification system with a volume of 25μL, the response time was clearly reduced at the same DNA template concentration, and the sensitivity in the number of copies of the DNA template was improved by >600-fold. Efficient amplification of nucleic acid was achieved with as few as three copies of the DNA template. This system may be useful for the development of novel lab-on-a-chip devices and shows promise for single-molecule amplification in droplet assays, with potential applications in nanobiotechnology, nanomedicine, and clinical molecular diagnostics. [Copyright &y& Elsevier]