Assembly-disassembly of DNAs and gold nanoparticles: a strategy of intervention based on oligonucleotides and restriction enzymes

A smartphone-based electrochemical POCT for CEA based on signal amplification of Zr6MOFs

Carcinoembryonic antigen (CEA) is a biomarker of high expression in cancer cells. Highly sensitive and selective detection of CEA holds significant clinical value in the diagnosis, monitoring and efficacy evaluation of malignant tumors. In this work, a smartphone-based electrochemical point-of-care testing (POCT) platform for the detection of CEA was developed based on a Zr6MOF signal amplification strategy. Ferrocene labeled DNA strands (Fc-DNA) were immobilized on Zr6MOFs to form a Fc-DNA/Zr6MOF signal probe. Double-stranded DNA (dsDNA) formed by complementary DNA (cDNA) and CEA aptamer was assembled on a screen-printed electrode via an Au-S bond. When CEA was added, the aptamer specifically bound with CEA, resulting in the exposure of cDNA. Then, Fc-DNA/Zr6MOF signal probes were introduced on the electrode surface through hybridization between Fc-DNA and cDNA. The detection of CEA was realized by measuring the electrochemical response of Fc. The POCT device was made by connecting a modified electrode with a smartphone through a Sensit Smart USB flash disk. Due to the signal amplification of Zr6MOFs, this POCT platform exhibited high sensitivity, wide linear range, and low detection limit for CEA detection. The developed POCT platform has been used for the detection of CEA in actual human serum samples with satisfactory results.

K+-Responsive Crown Ether-Based Amphiphilic Copolymer: Synthesis and Application in the Release of Drugs and Au Nanoparticles

Due to unique chelating and macrocyclic effects, crown ether compounds exhibit wide application prospects. They could be introduced into amphiphilic copolymers to provide new trigger mode for drug delivery. In this work, new amphiphilic random polymers of poly(lipoic acid-methacrylate-co-poly(ethylene glycol) methyl ether methacrylate-co-N-isopropylacrylamide-co-benzo-18-crown-6-methacrylamide (abbrev. PLENB) containing a crown ether ring and disulphide bond were synthesized via RAFT polymerization. Using the solvent evaporation method, the PLENB micelles were formed and then used to load substances, such as doxorubicin hydrochloride (DOX) and gold nanoparticles. The results showed that PLENB exhibited a variety of lowest critical solution temperature (LCST) in response to the presence of different ions, such as K+, Na+ and Mg2+. In particular, the addition of 150 mM K+ increased the LCST of PLENB from 31 to 37 °C and induced the release of DOX from the PLENB@DOX assemblies with a release rate of 99.84% within 12 h under 37 °C. However, Na+ and Mg2+ ions could not initiate the same response. Furthermore, K+ ions drove the disassembly of gold aggregates from the PLENB-SH@Au assemblies to achieve the transport of Au NPs, which is helpful to construct a K+-triggered carrier system.

Assessing Plasmonic Nanoprobes in Electromagnetic Field Enhancement for SERS Detection of Biomarkers

The exploration of the plasmonic field enhancement of nanoprobes consisting of gold and magnetic core@gold shell nanoparticles has found increasing application for the development of surface-enhanced Raman spectroscopy (SERS)-based biosensors. The understanding of factors controlling the electromagnetic field enhancement, as a result of the plasmonic field enhancement of the nanoprobes in SERS biosensing applications, is critical for the design and preparation of the optimal nanoprobes. This report describes findings from theoretical calculations of the electromagnetic field intensity of dimer models of gold and magnetic core@gold shell nanoparticles in immunoassay SERS detection of biomarkers. The electromagnetic field intensities for a series of dimeric nanoprobes with antibody–antigen–antibody binding defined interparticle distances were examined in terms of nanoparticle sizes, core–shell sizes, and interparticle spacing. The results reveal that the electromagnetic field enhancement not only depended on the nanoparticle size and the relative core size and shell thicknesses of the magnetic core@shell nanoparticles but also strongly on the interparticle spacing. Some of the dependencies are also compared with experimental data from SERS detection of selected cancer biomarkers, showing good agreement. The findings have implications for the design and optimization of functional nanoprobes for SERS-based biosensors.

Disulfide-induced self-assembled targets: A novel strategy for the label free colorimetric detection of DNAs/RNAs via unmodified gold nanoparticles

A modified non-cross-linking gold-nanoparticles (Au-NPs) aggregation strategy has been developed for the label free colorimetric detection of DNAs/RNAs based on self-assembling target species in the presence of thiolated probes. Two complementary thiol- modified probes, each of which specifically binds at one half of the target introduced SH groups at both ends of dsDNA. Continuous disulfide bond formation at 3' and 5' terminals of targets leads to the self-assembly of dsDNAs into the sulfur- rich and flexible products with different lengths. These products have a high affinity for the surface of Au-NPs and efficiently protect the surface from salt induced aggregation. To evaluate the assay efficacy, a small part of the citrus tristeza virus (CTV) genome was targeted, leading to a detection limit of about 5 × 10-9 mol.L-1 over a linear ranged from 20 × 10-9 to 10 × 10-7 mol.L-1. This approach also exhibits good reproducibility and recovery levels in the presence of plant total RNA or human plasma total circulating RNA extracts. Self-assembled targets can be then sensitively distinguished from non-assembled or mismatched targets after gel electrophoresis. The disulfide reaction method and integrating self-assembled DNAs/RNAs targets with bare AuNPs as a sensitive indicator provide us a powerful and simple visual detection tool for a wide range of applications.

'Squeezed' interparticle properties for plasmonic coupling and SERS characteristics of duplex DNA conjugated/linked gold nanoparticles of homo/hetero-sizes

The formation of interparticle duplex DNA conjugates with gold nanoparticles constitutes the basis for interparticle plasmonic coupling responsible for surface-enhanced Raman scattering signal amplification, but understanding of its correlation with interparticle spatial properties and particle sizes, especially in aqueous solutions, remains elusive. This report describes findings of an investigation of interparticle plasmonic coupling based on experimental measurements of localized surface plasmon resonance and surface enhanced Raman scattering characteristics for gold nanoparticles in aqueous solutions upon introduction of interparticle duplex DNA conjugates to define the interparticle spatial properties. Theoretical simulations of the interparticle optical properties and electric field enhancement based on a dimer model have also been performed to aid the understanding of the experimental results. The results have revealed a 'squeezed' interparticle spatial characteristic in which the duplex DNA-defined distance is close or shorter than A-form DNA conformation, which are discussed in terms of the interparticle interactions, providing fresh insight into the interparticle double-stranded DNA-defined interparticle spatial properties for the design of highly-sensitive nanoprobes in solutions for biomolecular detection.

Galvanic replacement-free deposition of Au on Ag for core-shell nanocubes with enhanced chemical stability and SERS activity

We report a robust synthesis of Ag@Au core-shell nanocubes by directly depositing Au atoms on the surfaces of Ag nanocubes as conformal, ultrathin shells. Our success relies on the introduction of a strong reducing agent to compete with and thereby block the galvanic replacement between Ag and HAuCl4. An ultrathin Au shell of 0.6 nm thick was able to protect the Ag in the core in an oxidative environment. Significantly, the core-shell nanocubes exhibited surface plasmonic properties essentially identical to those of the original Ag nanocubes, while the SERS activity showed a 5.4-fold further enhancement owing to an improvement in chemical enhancement. The combination of excellent SERS activity and chemical stability may enable a variety of new applications.

Chromium(VI) but not chromium(III) species decrease mitoxantrone affinity to DNA

Binding of mitoxantrone (MXT) to double-stranded DNA has been investigated as a model drug-DNA binding system to evaluate the effects of various forms of chromium on the binding properties. We have found that Cr(III), which binds strongly to DNA, does not affect the MXT affinity to DNA. In contrast, Cr(VI), in the form of chromate ions CrO(4)(2-), decreases the MXT affinity to DNA despite electrostatic repulsions with phosphate-deoxyribose chains of DNA. The MXT-DNA binding constant was found to decrease from (1.96 ± 0.005) × 10(5) to (0.77 ± 0.018) × 10(5) M(-1) for Cr(VI) concentration changing from 0 to 30 μM. The influence of Cr(VI) on MXT-DNA binding has been attributed to the oxidation of guanine residue, thus interrupting the intercalation of MXT into the DNA double helix at the preferential CpG intercalation site. This supposition is corroborated by the observed increase in the MXT binding site size from 2 bp (base pairs) to 4-6 bp in the presence of Cr(VI). The measurements of the MXT-DNA binding constant and the MXT binding site size on a DNA molecule have been carried out using spectroscopic, voltammetric, and nanogravimetric techniques, providing useful information on the mechanism of the interactions.

Double-shell gold nanoparticle-based DNA-carriers with poly-L-lysine binding surface

In view of the prospective applications of polyamine coatings in functional gold nanoparticles for use as carriers in gene delivery systems, in tissue repair and as bactericidal and virucidal non-toxic vehicle, we have investigated the interactions of poly-l-lysine (PLL) with gold nanoparticles (AuNP). Since direct binding of PLL to AuNP is not strong at neutral pH, we have focused on PLL interactions with carboxylated self-assembled monolayers (SAM) on AuNP, such as the citrate-capped AuNP. The double-shell nanoparticles AuNP@Cit/PLL thus produced do not contain any toxic thiols. We have observed strong electrostatic interactions between polycationic chains of PLL and AuNP@Cit in weakly acidic to weakly alkaline solutions (pH 5-9), as evidenced by the bathochromic shift of the local surface plasmon (SP) band and strong increase in resonance elastic light scattering (RELS) intensity. The stoichiometry of interactions evaluated on the basis of RELS data indicates on a hyper-Langmuirian type of interactions with stoichiometric coefficient n = 1.35 (PLL : AuNP@Cit). From the RELS titration data, a shift of the deprotonation constant for the bound PLL has been determined (pK(a) = 11.6 for the bound PLL vs. 10.48 for the free PLL). The deprotonation of PLL leads to AuNP aggregate disassembly, evidenced by sharp RELS decline and hypsochromic shift of SP band. We have found that under these conditions, a residual aggregation due to the interparticle interactions between β-sheets of PLL overcoat become predominant. The molecular dynamics simulations indicate that multiple hydrogen bonds can also be formed between the PLL linker and the shell molecules of AuNP@Cit. The double-shell nanoparticles, AuNP@Cit/PLL, have been shown to attract DNA molecules using highly sensitive RELS measurements presenting the proof-of-concept for the suitability of this non-toxic nanostructured material for gene delivery applications. The advantage of the proposed material is no toxicity related to the ligand release in gene delivery processes in contrast to the thiol-functionalized AuNP.

The use of enzymes for construction of DNA-based objects and assemblies

DNA has found wide applications in DNA-based nanotechnology due to its simplicity and predictability of its secondary structure. Selecting DNA for the nanoconstruction of objects and assemblies bears the inherent potential for manipulations and control by DNA modifying enzymes. In this tutorial review, we present an overview of the enzyme-catalysed construction of DNA-based objects and assemblies. It is illustrated how a diversity of enzyme-based biochemical reactions are transferred in nanotechnological applications.

Sensing of transcription factor through controlled-assembly of metal nanoparticles modified with segmented DNA elements

We have developed a unique metal nanoparticle (mNPs)-based assay to detect sequence-specific interactions between transcription factor and its corresponding DNA-binding elements. This assay exploits the interparticle-distance dependent optical properties of noble mNPs as sensing element and utilizes specific protein-DNA interactions to control the dispersion status of the mNPs. The assay involves two sets of double-stranded (ds)DNA modified-mNPs, each carrying a half site segment of a functional DNA sequence for the protein of interest. Each of these half sites is designed to contain a short complementary sticky end that introduces base-pairing forces to facilitate particle aggregation and to form a transient full dsDNA sequence. The detection of specific protein-DNA binding is founded on the premise that the mixture of these two sets of dsDNA-mNPs experiences a remarkable particle aggregation under certain salt conditions; whereas the aggregation can be retarded in the presence of a specific protein that binds and stabilizes the transient full dsDNA structure and therefore introduces steric protection forces between particles. We have demonstrated the concept using estrogen receptor α and its response elements, with gold and silver NPs as the sensing platform. UV-vis spectroscopy, transmission electron spectroscopy, and dynamic light scattering measurements were conducted to provide full characterization of the particle aggregation/dispersion mechanism. Differing from most of the mNP-based colorimetric sensors that are designed based on the analyte-induced aggregation mechanism, current protein binding-stabilization sensing strategy reduces the false signals caused by unrelated particle destabilizing effects. It is expected that this assay principle can be directed toward other transcription factors by simply changing the recognition sequence to form different segmented dsDNA-mNP constructs.

Colorimetric assay of glutathione based on the spontaneous disassembly of aggregated gold nanocomposites conjugated with water-soluble polymer

This article describes the glutathione-triggered disassembly of gold nanocomposites composed of gold cores and water-soluble copolymers [poly(N-n-isopropylacrylamide-co-acryloyldiethyletriamine)] attached to the surfaces of gold cores. The gold nanocomposites exhibit a bluish purple color because of the assembled gold cores that are conjugated with the diethylenetriamine groups incorporated into the copolymers. Glutathione added to the gold nanocomposite solution adsorbs onto the surface of the gold cores to liberate diethylenetriamine groups, resulting in spontaneous disassembly that changes the color of the solution to a reddish shade. Increasing the glutathione concentration facilitates the spontaneous disassembly of the gold nanocomposites. For the determination of glutathione, the colorimetric change of the gold nanoparticles is quantified with the a* value of the L*a*b* color coordinates defined by the CIE (Commission Internationale de l'Eclairage) chromaticity diagram. A linear relationship between the a* value and the glutathione concentration of up to 6 x 10(-6) mol/L is obtained 15 min after the addition of glutathione that has a detection limit (defined as 3sigma) of 2.9 x 10(-8) mol/L. The colorimetric assay is successfully applied to the determination of glutathione in eye drops and health supplements.

Molecularly mediated processing and assembly of nanoparticles: exploring the interparticle interactions and structures

The harnessing of the nanoscale properties of nanoparticles in most technological applications requires the abilities of controlled processing and assembly, which has been an important challenge because of the difficulty in manipulating interparticle properties. Molecularly mediated processing and assembly of nanoparticles have emerged as an important strategy for addressing this challenge. The capability of this strategy in manipulating size, shape, composition, and interparticle properties has significant implications for designing sensing, biosensing, nanoprobing, and many other functional nanostructures. This Account highlights some of the important findings in investigating both interparticle and collective properties as a forum for discussing new opportunities in exploiting nanoparticle-based designs and applications. The concept of mediator-template assembly of nanoparticles explores the combination of the forces from a mediator and a templating molecule for designing and controlling the interparticle interactions. The manipulation of the interparticle interaction properties and the detection of the molecular signatures are two of the key elements in this concept. A series of well-defined molecular mediators ranging from inorganic, organic, supramolecular, to biological molecules have been explored to ascertain how these two elements can be achieved in nanoparticle assemblies. The emphasis is the fundamental understanding of interparticle molecular interactions, such as covalent, electrostatic, hydrogen bonding, multidentate coordination, pi-pi interactions, etc. Each of these molecular interactions has been examined using specific molecules, such as multifunctional ligands, tunable sizes, shapes, or charges, well-defined molecular rigidity and chirality, or spectroscopic signatures, such as fluorescence and Raman scattering. Examples included thiols, thioethers, carboxylic acids, fullerenes, dyes, homocysteines, cysteines, glutathiones, proteins, and DNAs as molecular mediators for the assembly of gold, alloy, and magnetic nanoparticles. The understanding of these systems provided insights into how the unique electrical, optical, magnetic, and spectroscopic properties of the nanoparticle assemblies can be exploited for potential applications. This Account also highlights a few examples in chemical sensing and bioprobing to illustrate the importance of interparticle interactions and structures in exploiting these properties. One example involves thin-film assemblies of metal nanoparticles as biomimetic ion channels or chemiresistor sensing arrays by exploiting the nanostructured ligand framework interactions. Other examples explore the surface-enhanced Raman scattering signature as nanoprobes for the detection of protein binding or the enzyme-based cutting of interparticle DNAs. The detailed understanding of the design and control parameters in these and other systems should have a profound impact on the exploration of nanoparticles in a wide range of technological applications.