Rapid aggregation of gold nanoparticles induced by non-cross-linking DNA hybridization

Surface-Engineered Cancer Nanomedicine: Rational Design and Recent Progress

Cancer is highly heterogeneous in nature and characterized by abnormal, uncontrolled cells' growth. It is responsible for the second leading cause of death in the world. Nanotechnology is explored profoundly for sitespecific delivery of cancer chemotherapeutics as well as overcome multidrug-resistance (MDR) challenges in cancer. The progress in the design of various smart biocompatible materials (such as polymers, lipids and inorganic materials) has now revolutionized the area of cancer research for the rational design of nanomedicine by surface engineering with targeting ligands. The small tunable size and surface properties of nanomedicines provide the opportunity of multiple payloads and multivalent-ligand targeting to achieve drug efficacy even in MDR cancer. Furthermore, efforts are being carried out for the development of novel nano-pharmaceutical design, focusing on the delivery of therapeutic and diagnostic agents simultaneously which is called theranostics to assess the progress of therapy in cancer. This review aimed to discuss the physicochemical manipulation of cancer nanomedicine for rational design and recent progress in the area of surface engineering of nanomedicines to improve the efficacy of cancer chemotherapeutics in MDR cancer as well. Moreover, the problem of toxicity of the advanced functional materials that are used in nanomedicines and are exploited to achieve drug targeting in cancer is also addressed.

Interfacing DNA with Gold Nanoparticles for Heavy Metal Detection

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.

DNA Base Pair Stacking Assembly of Anisotropic Nanoparticles for Biosensing and Ordered Assembly

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.

Orthogonal Blue and Red Light Controlled Cell-Cell Adhesions Enable Sorting-out in Multicellular Structures

The self-assembly of different cell types into multicellular structures and their organization into spatiotemporally controlled patterns are both challenging and extremely powerful to understand how cells function within tissues and for bottom-up tissue engineering. Here, we not only independently control the self-assembly of two cell types into multicellular architectures with blue and red light, but also achieve their self-sorting into distinct assemblies. This required developing two cell types that form selective and homophilic cell–cell interactions either under blue or red light using photoswitchable proteins as artificial adhesion molecules. The interactions were individually triggerable with different colors of light, reversible in the dark, and provide noninvasive and temporal control over the cell–cell adhesions. In mixtures of the two cells, each cell type self-assembled independently upon orthogonal photoactivation, and cells sorted out into separate assemblies based on specific self-recognition. These self-sorted multicellular architectures provide us with a powerful tool for producing tissue-like structures from multiple cell types and investigate principles that govern them.

An amplification-free colorimetric test for sensitive DNA detection based on the capturing of gold nanoparticle clusters

PCR-free or amplification-free strategies for DNA detection provide an interesting alternative to classical molecular biology techniques, opening new possibilities for on-site diagnostics. In this framework, we present herein an amplification-free colorimetric test for DNA detection, based on the capture of multiple gold nanoparticle (AuNP) clusters onto the surface of magnetic microbeads, leading to an increase of the plasmonic signal and, thus, of the overall sensitivity. Noteworthy, the assay allows the detection of as low as 15 attomoles of target DNA by simple visual inspection. The AuNP-cluster capturing mechanism was investigated by UV-vis, SEM, TEM, and EDX analysis. In a case study of E. coli contamination, the colorimetric test achieves a performance comparable to the reference instrumental PCR technique, enabling the naked-eye detection of 7.5 × 10² CFU μL^-1.

Sequence-specific detection of single-stranded DNA with a gold nanoparticle-protein nanopore approach

Fast, cheap and easy to use nucleic acids detection methods are crucial to mitigate adverse impacts caused by various pathogens, and are essential in forensic investigations, food safety monitoring or evolution of infectious diseases. We report here a method based on the α-hemolysin (α-HL) nanopore, working in conjunction to unmodified citrate anion-coated gold nanoparticles (AuNPs), to detect nanomolar concentrations of short single-stranded DNA sequences (ssDNA). The core idea was to use charge neutral peptide nucleic acids (PNA) as hybridization probe for complementary target ssDNAs, and monitor at the single-particle level the PNA-induced aggregation propensity AuNPs during PNA–DNA duplexes formation, by recording ionic current blockades signature of AuNP–α-HL interactions. This approach offers advantages including: (1) a simple to operate platform, producing clear-cut readout signals based on distinct size differences of PNA-induced AuNPs aggregates, in relation to the presence in solution of complementary ssDNAs to the PNA fragments (2) sensitive and selective detection of target ssDNAs (3) specific ssDNA detection in the presence of interference DNA, without sample labeling or signal amplification. The powerful synergy of protein nanopore-based nanoparticle detection and specific PNA–DNA hybridization introduces a new strategy for nucleic acids biosensing with short detection time and label-free operation.

Cationic Magnetite Nanoparticles for Increasing siRNA Hybridization Rates

An investigation of the interaction principles of nucleic acids and nanoparticles is a priority for the development of theoretical and methodological approaches to creating bionanocomposite structures, which determines the area and boundaries of biomedical use of developed nanoscale devices. «Nucleic acid-magnetic nanoparticle» type constructs are being developed to carry out the highly efficient detection of pathogens, create express systems for genotyping and sequencing, and detect siRNA. However, the data available on the impact of nanoparticles on the behavior of siRNA are insufficient. In this work, using nanoparticles of two classical oxides of inorganic chemistry (magnetite (Fe₃O₄) and silica (SiO₂) nanoparticles), and widely used gold nanoparticles, we show their effect on the rate of siRNA hybridization. It has been determined that magnetite nanoparticles with a positive charge on the surface increase the rate of siRNA hybridization, while negatively charged magnetite and silica nanoparticles, or positively charged gold nanoparticles, do not affect hybridization rates (HR).

DNA-Programmed Bimodal 2D Assembly of Differently Sized Nanoparticles via Folding of Precursory Circular Chains

Gold nanoparticle (AuNP) assemblies in two-dimensions (2D) exhibit collective physical/chemical properties that are useful for various devices. However, technical issues still impede the efficient ordering of differently sized AuNPs on solid supports while avoiding phase separation. This paper describes a method to construct binary 2D assemblies by folding precursory circular chains composed of small and large AuNPs. The structural change is caused by a spontaneous, non-cross-linking assembly of fully matched double-stranded DNA-modified AuNPs (dsDNA-AuNPs) at a high ionic strength. Since larger dsDNA-AuNPs have a lower critical coagulation concentration of the supporting electrolyte, the spontaneous assembly of large AuNPs precedes that of small AuNPs in the precursory chain during evaporation. Transmission electron microscopy reveals that alternate-type AuNP chains are folded into a binary 2D structure in a mixed mode, whereas block-type chains are transformed into a binary 2D structure in a core-shell mode. The methodology could potentially be harnessed for the fabrication of binary AuNP arrays for various devices.

Surface potential microscopy of surfactant-controlled single gold nanoparticle

The surface potential of nanoparticles plays a key role in numerous applications, such as drug delivery and cellular uptake. The estimation of the surface potential of nanoparticles as drug carriers or contrast agents is important for the design of nanoparticle-based biomedical platforms. Herein, we report the direct measurement of the surface potential of individual gold nanorods (GNRs) via Kelvin probe force microscopy (KPFM) at the nanoscale. GNRs were capped by a surfactant, cetyltrimethylammonium bromide (CTAB), which was removed by centrifugation. CTAB removal is essential for GNR-based biomedical applications because of the cytotoxicity of CTAB. Applying KPFM analysis, we found that the mean surface potential of the GNRs became more negative as the CTAB was removed from the GNR. The results indicate that the negative charge of GNRs is covered by the electrostatic charge of the CTAB molecules. Similar trends were observed in experiments with gold nanospheres (GNS) capped by citrates. Overall, KPFM-based techniques characterize the surfactant of individual nanoparticles (i.e. GNR or GNS) with high resolution by mapping the surface potential of a single nanoparticle, which aids in designing engineered nanoparticles for biomedical applications.

Terminal-conjugated non-aggregated constraints of gold nanoparticles on lateral flow strips for mobile phone readouts of enrofloxacin

Antibiotics abuse now poses a global threat to public health. Monitoring their residual levels as well as metabolites are of great importance, still challenges remain in in situ tracing during the circulation. Herein, taking the typical antibacterial Enrofloxacin (ENR) as a subject, a paper-based aptasensor was tailored by manipulating a duo of aptameric moieties to "sandwich" the target in a lateral-flow regime. To visualize the tight-binding sandwich motif more vividly, an irregular yet robust DNA-bridged gold nanoparticles (AuNPs) proximity strategy was developed with recourse to terminal deoxynucleotidyl transferase, of which the nonaggregate constraining feature was unveiled via optical absorption and scanning probe topography. This complex performed exceptionally better in the test strip context than single-particle tags, leading to an enhanced on-chip focusing. Rather than qualitative color developing, further efforts were taken to visualize the readouts in a quantitative manner by exploiting the smartphone camera for pattern recognition along with data processing in a professional App. Overall, this prototyped contraption realized a rapid and ultrasensitive quantification of ENR down to 0.1 μg/L along with a broad linear range over 5 orders of magnitude, plus excellent selectivity and precision even for real samples. Such innovative fusion across DNA-structured nanomanufacturing and intelligent perception provides a prospective and invigorating solution to point-of-care inspection.

Accelerated non-crosslinking assembly of DNA-functionalized nanoparticles in alcoholic solvents: for application in the identification of clear liquors

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.

RNA Quantification Using Noble Metal Nanoprobes: Simultaneous Identification of Several Different mRNA Targets Using Color Multiplexing and Application to Chronic Myeloid Leukemia Diagnostics

Nanotechnology provides new tools for gene expression analysis that allow for sensitive and specific characterization of prognostic signatures related to cancer. Cancer is a complex disease where multiple gene loci contribute to the phenotype. The ability to simultaneously monitor differential expression originating from each locus allows for a more accurate indication into the degree of cancerous activity than either locus alone. Metal nanoparticles have been widely used as labels for in vitro identification and quantification of target sequences.Here we describe the synthesis of nanoparticles with different noble metal compositions in an alloy format that are then functionalized with thiol-modified ssDNA (nanoprobes). We also show how such nanoprobes are used in a non-cross-linking colorimetric method for the direct detection and quantification of specific mRNA targets, without the need for enzymatic amplification or reverse-transcription steps. The different metals in the alloy provide for distinct absorption spectra due to their characteristic plasmon resonance peaks. The color multiplexing allows for simultaneous identification of different mRNA targets involved in cancer development. A comparison of the absorption spectra of the nanoprobe mixtures taken before and after induced aggregation of metal nanoparticles allows to both identify and quantify each mRNA target. We describe the use of gold and gold-silver alloy nanoprobes for the development of the non-cross-linking method to detect a specific BCR-ABL fusion gene (e.g., e1a2 and e14a2) mRNA target associated with chronic myeloid leukemia (CML) using 10 ng/μL of unamplified total human RNA. Additionally, we demonstrate the use of this approach for the direct diagnostics of CML. This simple methodology takes less than 50 min to complete after total RNA extraction with comparable specificity and sensitivity to the more commonly used methods.

In Vivo and In Vitro Anticancer Activity of Doxorubicin-loaded DNA-AuNP Nanocarrier for the Ovarian Cancer Treatment

In this study, we have determined the anticancer activity of doxorubicin (Dox)-loaded DNA/gold nanoparticle (AuNP) nanocarrier (Dox-DNA-AuNP) for the treatment of ovarian cancer. The anticancer effect of Dox-DNA-AuNP was evaluated in vitro using the EZ-Cytox cell viability assay on three human ovarian cancer cell lines, SK-OV-3, HEY A8, and A2780. Dox-DNA-AuNP exhibited outstanding activity with good IC50 values of 4.8, 7.4, and 7.6 nM for SK-OV-3, HEY A8, and A2780, respectively. In vivo evaluation further demonstrated the superior anticancer effects of Dox-DNA-AuNP by inhibiting tumor growth compared to free Dox in an established SK-OV-3 xenograft mice model. Dox-DNA-AuNP showed about a 2.5 times higher tumor growth inhibition rate than free Dox. Furthermore, the immunohistochemical analysis of Ki67 antigen expression showed the lowest number of proliferative cells in the ovarian tumor tissue treated with Dox-DNA-AuNP. These results suggest Dox-DNA-AuNP might be a potential effective agent in ovarian cancer chemotherapy.

Colorimetric determination of carbendazim based on the specific recognition of aptamer and the poly-diallyldimethylammonium chloride aggregation of gold nanoparticles

This paper proposes the idea of establishing carbendazim (CBZ) colorimetric determination in spiked water samples by specific aptamers of unlabeled carbendazim (CBZ), gold nanoparticles (AuNPs) and cationic polymer poly-diallyldimethylammonium chloride (PDDA). In the absence of CBZ, the CBZ aptamer will react with the cationic polymer PDDA by electrostatic interaction to form a complex structure. Therefore, the gold nanoparticles will remain dispersed due to the lack of PDDA. However, when CBZ is added into the sensory system, the CBZ-specific aptamer can selectively capture CBZ to form a stable complex structure. Due to the consumption of the aptamer, PDDA is unable to interact with the aptamer and begins to induce aggregation of AuNPs, thereby causing the color of the solution to change from red to blue. Colorimetric determination of CBZ based on the specific recognition of aptamer and the PDDA-induced aggregation of AuNPs has a detection limit of 2.2 nM, a linear range (R = 0.9960) from 2.2 to 500 nM. The method has good sensitivity and specificity, and the average recovery of CBZ is 94.9-104.8% in the application of actual water samples. This colorimetric method is simple, time-saving and low requirements for equipment, therefore, it holds great potential for CBZ detection in the environmental water samples.

Au nanoparticles as label-free competitive reporters for sensitivity enhanced fiber-optic SPR heparin sensor

A label-free Au NPs-enhanced surface plasmon resonance (SPR) sensor was developed for the ultrasensitive detection of heparin based on competitive adsorption behavior of heparin and Au NPs on the poly (dimethyl-diallylammonium chloride) (PDDA)-modified optical fiber surface and the corresponding change in the resonance wavelength of SPR. Due to the high affinity between heparin and PDDA, the present senor shows good analytical performance with respect to heparin detection. Two obvious advantages of the proposed heparin sensor over other reported methods are: its much wider linear concentration range (10^-6-10^-10 g/mL) and lower limit of detection (0.0257 ng/mL). The analysis of heparin in serum demonstrated that the present sensor exhibited high sensitivity and selectivity. It should be noted that the sensing strategy takes advantage of a portable fiber-optic SPR sensing system and avoids the need for complex processes for labeled-Au NPs, and thus the present sensor promises to be a practical tool for the point-of-care monitoring of heparin.

Characterizing the non-crosslinked aggregation of DNA-modified gold nanoparticles: effects of DNA length and terminal base pair

We previously reported that fully complementary DNA duplexes formed on gold nanoparticle (GNP) surfaces aggregate at high salt concentrations. We previously reported that DNA-functionalized gold nanoparticles (GNPs) aggregate by hybridization with fully complementary DNA at high salt concentrations. Although this behavior has been applied to some precise naked-eye colorimetric analyses of DNA-related molecules, the aggregation mechanism is still unclear and comprehensive studies are needed. In this paper, we reveal the key factors that influence GNP aggregation. The effects of temperature, electrolyte concentration, probe length, and particle size, which control the stabilities of double-stranded DNAs and GNPs, were investigated. Larger GNPs aggregated more easily, and GNP aggregates were easily formed with ∼15-mer-long probes, while longer probes prevented aggregation, perhaps by preventing the formation of rigid double-stranded DNA layers, compared to shorter probes. Furthermore, GNPs with purine bases at their 5' ends aggregated more easily than those with these bases at their 3' ends. This phenomenon is different from that based on the melting-temperature trend calculated using the nearest-neighbor method.

Colorimetric-based detection of Ureaplasma urealyticum using gold nanoparticles

Ureaplasma urealyticum (uu) is one of the most common agents of urogenital infections and is associated with complications such as infertility, spontaneous abortion and other sexually transmitted diseases. Here, a DNA sensor based on oligonucleotide target-specific gold nanoparticles (AuNPs) was developed, in which the dispersed and aggregated states of oligonucleotide-functionalised AuNPs were optimised for the colorimetric detection of a polymerase chain reaction (PCR) amplicon of U. urealyticum DNA. A non-cross-linking approach utilising a single Au-nanoprobe specific of the urease gene was utilised and the effect of a PCR product concentration gradient evaluated. Results from both visual and spectral analyses showed that target-Au-nanoprobe hybrids were stable against aggregation after adding the inducer. Furthermore, when a non-target PCR product was used, the peak position shifted and salt-induced aggregation occurred. The assay's limit of detection of the assay was 10 ng with a dynamic range of 10-60 ng. This procedure provides a rapid, facile and low-cost detection format, compared to methods currently used for the identification of U. urealyticum.

Fluorescent aptasensor for carbendazim detection in aqueous samples based on gold nanoparticles quenching Rhodamine B

This paper proposes a fluorescent aptasensor for the detection of carbendazim (CBZ) in aqueous solution using CBZ-specific aptamer as sensing probe, gold nanoparticles (AuNPs) and Rhodamine B (RhoB) as indicator, respectively. In the absence of CBZ, CBZ aptamer could wrap AuNPs and maintained it dispersed in NaCl solution basically. Contrarily, the aptamer could specifically combine with CBZ and form a stable aptamer-CBZ complex, leaving AuNPs exposed to be aggregated by NaCl solution. The dispersed AuNPs could efficiently quench the fluorescence of RhoB, but those aggregated AuNPs have poor capability to impair the fluorescent indicator. Thus, the concentration of CBZ could be detected quantitatively through the distinction of the fluorescence intensity. This convenient fluorescent assay for CBZ had a wide linear range from 2.33 to 800 nM and a 2.33 nM limit of detection (LOD). Furthermore, it had high selectivity over pesticides, antibiotics, metal ions and other disrupting chemicals. As for application, the method could determine CBZ in water samples with recoveries in the range of 96.3-111.2%. This fluorescent aptasensor possessed great potential application for CBZ detection in actual aquatic environment.

Photo-switching of blunt-end stacking between DNA strands immobilized on gold nanoparticles

End-to-end stacking of DNAs on gold nanoparticles was switched by terminal base pairing/unpairing triggered by the photo-isomerization of an azobenzene moiety nearby the DNA terminal.

Using gold nanoparticles to detect single-nucleotide polymorphisms: toward liquid biopsy

The possibility of detecting genetic mutations rapidly in physiological media through liquid biopsy has attracted the attention within the materials science community. The physical properties of nanoparticles combined with robust transduction methods ensure an improved sensitivity and specificity of a given assay and its implementation into point-of-care devices for common use. Covering the last twenty years, this review gives an overview of the state-of-the-art of the research on the use of gold nanoparticles in the development of colorimetric biosensors for the detection of single-nucleotide polymorphism as cancer biomarker. We discuss the main mechanisms of the assays that either are assisted by DNA-based molecular machines or by enzymatic reactions, summarize their performance and provide an outlook towards future developments.

Chemically Fueled Plasmon Switching of Gold Nanorods by Single-Base Pairing of Surface-Grafted DNA

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 Hg²⁺ due to T-Hg-T base pairing. Inversely, the subsequent addition of cysteine (Cys) gives rise to the removal of Hg²⁺ 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.

Delivery of antisense peptide nucleic acid by gold nanoparticles for the inhibition of virus replication

Aim: We aim to use peptide nucleic acid (PNA) for antisense therapy against bovine viral diarrhea virus (BVDV), a surrogate model of human hepatitis C virus, and introduce an optimal approach for delivering PNA into the cell. Materials & methods: PNA was designed for hybridization to the 5'-untranslated region of BVDV RNA in order to form a heteroduplex structure and inhibit the translation and replication of virus. Gold nanoparticles (AuNPs) were used as a delivery system for PNA. Results: The cellular uptake of PNA-AuNPs and inhibition of BVDV infection in the middle stage of viral replication were found. Conclusion: Further research is warranted to develop AuNPs as a potential vehicle for delivering PNA in order to remove viruses from the infected cells.

Gold Nanoparticle-Based Colorimetric Strategies for Chemical and Biological Sensing Applications

Gold nanoparticles are popularly used in biological and chemical sensors and their applications owing to their fascinating chemical, optical, and catalytic properties. Particularly, the use of gold nanoparticles is widespread in colorimetric assays because of their simple, cost-effective fabrication, and ease of use. More importantly, the gold nanoparticle sensor response is a visual change in color, which allows easy interpretation of results. Therefore, many studies of gold nanoparticle-based colorimetric methods have been reported, and some review articles published over the past years. Most reviews focus exclusively on a single gold nanoparticle-based colorimetric technique for one analyte of interest. In this review, we focus on the current developments in different colorimetric assay designs for the sensing of various chemical and biological samples. We summarize and classify the sensing strategies and mechanism analyses of gold nanoparticle-based detection. Additionally, typical examples of recently developed gold nanoparticle-based colorimetric methods and their applications in the detection of various analytes are presented and discussed comprehensively.

An aptamer based aggregation assay for the neonicotinoid insecticide acetamiprid using fluorescent upconversion nanoparticles and DNA functionalized gold nanoparticles

An acetamiprid-binding aptamer (ABA), gold nanoparticles (AuNPs) and upconversion nanoparticles (UCNPs) are used in a colorimetric and fluorometric method for the ultrasensitive and selective detection of the pesticide acetamiprid. The ABA is first configured into a duplex with a complementary DNA covalently attached to AuNPs. The resulting dsDNA-functionalized AuNP probe is not stable in 0.15 M NaCl solution and aggregates. This causing the color to change from red to purple. In the presence of acetamiprid, the ABA undergoes a structural switch from a DNA duplex to an aptamer-acetamiprid complex and consequently dissociates from the AuNPs. The partially unhybridized AuNPs are stable against salt-induced aggregation and show red color. The ratio of absorbances at 524 nm (red) and 650 nm (purple blue) varies with the concentration of acetamiprid in the 0.025-10 μM concentration range. The colorimetric signal can be further amplified by introducing DNA-modified carboxylated UCNPs (silica-coated NaYF₄:Yb,Er) which display red and green fluorescence under 980 nm excitation. An inner filter effect occurs between DNA-modified UCNPs and dsDNA-modified AuNPs. The fluorometric assay is based on the measurement of the ratio of red (654 nm) and green (540 nm) fluorescence and works in the 0.025 to 1 μM acetamiprid concentration range and has a 0.36 nM detection limit (at a signal-to-noise ratio of 3). Because of the specificity of the aptamer, the assay is high selective. It was successfully used to quantify acetamiprid in contaminated real samples. Graphical abstract Schematic presentation of an upconversion fluorescent assay for acetamiprid. It involves the principle of analyte-triggered structural switch of aptamers, salt-induced AuNP aggregation, and signal amplification from UCNP.

Regioselective DNA Modification and Directed Self-Assembly of Triangular Gold Nanoplates

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.

Detection of Gold Nanoparticles Aggregation Using Light Scattering for Molecular Sensing

Gold nanoparticles (AuNPs) have been commonly used in molecular sensing, in the form of observation of the color change from red to blue of the AuNP solution, caused by target-molecule-induced AuNP aggregation. In this work, the changes in absorbance and scattering spectra caused by AuNP aggregation were studied using thrombin-induced AuNP aggregation as a model. We demonstrated for the first time that scattering spectra is more sensitive to the changes owing to AuNP aggregation than absorbance spectra. Moreover, a digital color analysis of darkfield images using dark field microscopy (DFM) facilitated a simple method for detection of AuNPs aggregation without the use of spectroscopic analysis. Furthermore, we demonstrated that DFM is useful for detecting AuNPs aggregation in a colored solution, in which the color change by AuNPs aggregation is not visible.

Target-Recycling-Amplified Colorimetric Detection of Pollen Allergen Using Non-Cross-Linking Aggregation of DNA-Modified Gold Nanoparticles

Increasing prevalence of pollen allergies has raised concerns about human health. Development of a facile and precise method to detect pollen allergens would thus be of significance for environmental assessments and medical diagnoses. Here we report a sensitive colorimetric method to detect the Japanese cedar pollen allergen, Cry j 2. The method consists of two steps: a signal amplification based on the catalytic DNA hairpin self-assembly, followed by a signal transduction using the salt-induced non-cross-linking aggregation of gold nanoparticles densely modified with short DNA. The assay exhibits a detection limit of 0.2 ng/mL, which is 130-fold greater than that of the previously reported one. Moreover, the assay enables the detection of Cry j 2 spiked in soil solutions by avoiding any interference from the contaminants. The signal amplification system includes an anti-Cry j 2 DNA aptamer, which accounts for the absence of false responses to five nontarget allergen proteins. The present method could be of general applicability to various proteins by using appropriate aptamers.

Non-Cross-Linking Aggregation of DNA-Carrying Polymer Micelles Triggered by Duplex Formation

Colloidal behaviors of particles functionalized with biomolecules are generally complicated. This study describes that colloidal behaviors of double-stranded (ds) DNA-carrying polymer micelles are well controlled by altering the molar ratio of single-stranded (ss) DNA moiety in the dsDNA shell. ssDNA-carrying micelles composed of a poly( N-isopropylacrylamide) (PNIPAAm) core surrounded by a dense shell of ssDNAs were prepared through self-assembly of PNIPAAm grafted with ssDNA by incubating its solution above the lower critical solution temperature. Spontaneous, non-cross-linking aggregation of the micelles was triggered by DNA duplex formation on the surface. Comparison of the critical coagulation concentration of NaCl among a series of the DNA-carrying micelles revealed the relationship between the helical structure of the surface-bound DNA and the colloidal stability of the micelles. The electrophoretic mobility analysis of the micelles indicated that the duplex formation reduced the structural flexibility of the surface-bound DNA, thereby decreasing the interparticle entropic repulsion. It is also suggested that the augmented rigidity of the surface-bound DNA increases the number of terminal base pairs facing the solvent, which could lead to multiple blunt-end stacking interaction among the micelles. Therefore, small DNA molecules could be considered unique surface-modifiers capable of controlling interactions between the surfaces of materials.

Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker

Epigenetic reprogramming in cancer genomes creates a distinct methylation landscape encompassing clustered methylation at regulatory regions separated by large intergenic tracks of hypomethylated regions. This methylation landscape that we referred to as Methylscape is displayed by most cancer types, thus may serve as a universal cancer biomarker. To-date most research has focused on the biological consequences of DNA Methylscape changes whereas its impact on DNA physicochemical properties remains unexplored. Herein, we examine the effect of levels and genomic distribution of methylcytosines on the physicochemical properties of DNA to detect the Methylscape biomarker. We find that DNA polymeric behaviour is strongly affected by differential patterning of methylcytosine, leading to fundamental differences in DNA solvation and DNA-gold affinity between cancerous and normal genomes. We exploit these Methylscape differences to develop simple, highly sensitive and selective electrochemical or colorimetric one-step assays for the detection of cancer. These assays are quick, i.e., analysis time ≤10 minutes, and require minimal sample preparation and small DNA input.

DNA methylation is an epigenetic modification that control genetic programs. Here, the authors found that the methylation landscape influences the physicochemical properties of DNA and that it can serve as a universal cancer biomarker, and developed a one-step assay for the detection of cancer DNA.

A competitive colorimetric chloramphenicol assay based on the non-cross-linking deaggregation of gold nanoparticles coated with a polyadenine-modified aptamer

A competitive colorimetric assay has been established to detect chloramphenicol (CAP). It is based on the use of colloidal and electrostatically stabilized aptamer-modified gold nanoparticles (GNPs). The CAP aptamer is modified by a sequence of 5 adenosine groups to anchor it on the surface of GNPs. It can competitively capture two compounds, viz. D-(-)-threo-2-amino-1-(4-nitrophenyl)-1,3-propanediol (CAP-base, with a positive charge) and CAP (which is uncharged). The capture of the positively charged CAP-base triggers the aggregation of modified GNPs in salt-containing solution, and this causes a color change from red to purple. However, in the presence of CAP and CAP-base, the capture of the uncharged CAP weakens this color change by a competing process for capture. Thus, the concentration of CAP is associated with the degree of deaggregation of GNPs and can be quantified by the ratio of absorbances at 620 nm and 520 nm. The assay has a 22 nM limit of detection in acidic solution, and the response is linear in the range of 0.20 to 3.20 μM CAP concentration. This assay was successfully applied to the determination of CAP in spiked environmental water samples. Conceivably, this method has a wide scope in that it may be applied to a wide range of analytes if respective aptamers are available. Graphical abstract Schematic presentation of a competitive non-cross linking deaggregating method for detecting chloramphenicol. The surface charge of polyA-Apt@GNPs and its aggregation degree (purple) are determined by the charge of target. (CAP-base: precursor of CAP; PolyA-Apt@GNPs: 5'-polyA-modified DNA aptamer functionalized gold nanoparticles.).

HCV Detection, Discrimination, and Genotyping Technologies

According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.

Zeptomole Biosensing of DNA with Flexible Selectivity Based on Acoustic Levitation of a Single Microsphere Binding Gold Nanoparticles by Hybridization

A novel scheme for DNA sensing at the zeptomole level is presented, based on the levitation of a single microsphere in a combined acoustic-gravitational (CAG) field. The levitation of a microsphere in the field is predominantly determined by its density. Capture and reporter probe DNAs are anchored on poly(methyl methacrylate) microsphere (PMMA) and gold nanoparticles (AuNPs), respectively, and a target DNA induces the binding of AuNPs on PMMA. This interparticle sandwich DNA-hybridization induces density increase in PMMA, which is detected as a shift in the levitation coordinate in the CAG field. The reporter DNAs are designed based on base-pair (bp) number selectivity, which is evaluated using direct interparticle hybridization between DNA-bound PMMA and complementary DNA-anchored AuNPs. Interestingly, the bp-number selectivity can be enlarged by lowering the reactant concentrations. Thus, the threshold bp, at which no density change is detected, can be adjusted by controlling the reactant concentrations. This strategy is extended to the sensing of HIV-2 DNA and single nucleotide polymorphism (SNP) detection of the KRAS gene by sandwich hybridization. In SNP detection, the present method selectively distinguishes wild-type DNA from mutant DNA differing by one nucleotide in the 21-nucleotide sequence by optimizing the lengths of probe DNAs and particle concentrations. This approach allows the detection of 1000 DNA molecules.

The sensitive detection of IVSII-1(G˃A) mutation in beta globin gene using a Nano-based ligation genotyping system

Beta-thalassemia (β-thalassemia) is a globally genetic diseases, and is most prevalent in the Middle East, particularly in Iran. Carrier detection and prenatal diagnosis are the best ways to managing it, and to prevent new community cases from emerging. We report on a simple method for rapid detection of the worst β-thalassemia point mutation in Iran (IVS-II-1 G>A), using a nano-based ligation assay, this was performed using probes with labeled magnetic nanoparticles and quantum dots. After optimizing the technique, 50 DNA samples were genotyped with this method. We found a frequency of 72% for IVSII-1 (G˃A) mutation (42% heterozygote, and 30% mutant homozygote) with a highly sensitive nano-based ligation genotyping system, offering excellent sensitivity and specificity for point mutation detection; it has been demonstrated to be inaccurate, sensitive, cost-effective, and rapid technique for single nucleotide polymorphism (SNP) genotyping.

Cross-linking gold nanoparticles aggregation method based on localised surface plasmon resonance for quantitative detection of miR-155

MiR-155 plays a critical role in the formation of cancers and other diseases. In this study, the authors aimed to design and fabricate a biosensor based on cross-linking gold nanoparticles (AuNPs) aggregation for the detection and quantification of miR-155. Also, they intended to compare this method with SYBR Green real-time polymerase chain reaction (PCR). Primers for real-time PCR, and two thiolated capture probes for biosensor, complementary with miR-155, were designed. Citrate capped AuNPs (18.7 ± 3.6 nm) were synthesised and thiolated capture probes immobilised to AuNPs. The various concentrations of synthetic miR-155 were measured by this biosensor and real-time PCR method. Colorimetric changes were studied, and the calibration curves were plotted. Results showed the detection limit of 10 nM for the fabricated biosensor and real-time PCR. Also, eye detection using colour showed the weaker detection limit (1 µM), for this biosensor. MiR-133b as the non-complementary target could not cause a change in both colour and UV-visible spectrum. The increase in hydrodynamic diameter and negative zeta potential of AuNPs after the addition of probes verified the biosensor accurately fabricated. This fabricated biosensor could detect miR-155 simpler and faster than previous methods.

A colorimetric platform for sensitively differentiating telomere DNA with different lengths, monitoring G-quadruplex and dsDNA based on silver nanoclusters and unmodified gold nanoparticles

Human telomere DNA plays a vital role in genome integrity control and carcinogenesis as an indication for extensive cell proliferation. Herein, silver nanoclusters (Ag NCs) templated by polymer and unmodified gold nanoparticles (Au NPs) are designed as a new colorimetric platform for sensitively differentiating telomere DNA with different lengths, monitoring G-quadruplex and dsDNA. Ag NCs can produce the aggregation of Au NPs, so the color of Au NPs changes to blue and the absorption peak moves to 700nm. While the telomere DNA can protect Au NPs from aggregation, the color turns to red again and the absorption band blue shift. Benefiting from the obvious color change, we can differentiate the length of telomere DNA by naked eyes. As the length of telomere DNA is longer, the variation of color becomes more noticeable. The detection limits of telomere DNA containing 10, 22, 40, 64 bases are estimated to be 1.41, 1.21, 0.23 and 0.22nM, respectively. On the other hand, when telomere DNA forms G-quadruplex in the presence of K⁺, or dsDNA with complementary sequence, both G-quadruplex and dsDNA can protect Au NPs better than the unfolded telomere DNA. Hence, a new colorimetric platform for monitoring structure conversion of DNA is established by Ag NCs-Au NPs system, and to prove this type of application, a selective K⁺ sensor is developed.