An ultrasensitive method for the detection of gene fragment from transgenics using label-free gold nanoparticle probe and dynamic light scattering

A sensitive electrochemiluminescence DNA biosensor based on the signal amplification of ExoIII enzyme-assisted hybridization chain reaction combined with nanoparticle-loaded multiple probes

An electrochemiluminescence (ECL) DNA biosensor based on ExoIII exonuclease assistance and hybridization chain reaction (HCR) amplification technology has been constructed. ExoIII exonuclease and triple-helix DNA molecular switch are used in detecting a target in circulation. By combining HCR with AuNPs@DNA, a novel signal probe is built, which enables multiple signal amplification and the high-sensitive detection of transgenic rice BT63 DNA. The Fe₃O₄@Au solution is added to a magneto-controlled glassy carbon electrode, and sulfhydryl-modified capture DNA (CP) is immobilized on Fe₃O₄@Au through the Au-S bond. Mercaptoethanol is added to close sites and prevent the nonspecific adsorption of CP on the magnetron glassy carbon electrode. A target DNA is added to a constructed triple-helix DNA molecular centrifuge tube for reaction. Owing to base complementation and the reversible switching of the triple-helix DNA molecular state, the target DNA turns on the triple-helix DNA molecular switch and hybridizes with a long-strand recognition probe (RP) to form a double-stranded DNA (dsDNA). Exonuclease ExoIII is added to specifically recognize and cut the dsDNA and to release the target DNA. The target DNA strand then circulates back completely to open the multiple triple-helix DNA molecular switch, releasing a large number of signal transduction probes (STP). To hybridize with CP, a large amount of STP is added to the electrode. Finally, a AuNPs@DNA signal probe is added to hybridize with STP. H1 and H2 probes are added for the hybridization chain reaction and the indefinite extension of the primer strand on the probe. Then, tris-(bipyridyl)ruthenium(II) is added for ECL signal detection with PBS-tri-n-propylamine as the base solution. In the concentration range 1.0 × 10^-16 to 1.0 × 10^-8 mol/L of the target DNA, good linear relationship was achieved with the corresponding ECL signal. The detection limit is 3.6 × 10^-17 mol/L. The spiked recovery of the rice samples range from 97.2 to 101.5%. The sensor is highly sensitive and has good selectivity, stability, and reproducibility. A novel electrochemiluminescence biosensor with extremely higher sensitivity was prepared for the determination of ultra-trace amount transgenic rice BT63 DNA. The sensitivity was significantly improved by multiple signal enhancements. Firstly, a large number of signal transduction probes are released when the triple-helix DNA molecular switch unlock after recycles assisted by ExoIII exonuclease under target BT63 DNA; and then the signal transduction probes hybridize with the signal probes of AuNPs@(DNA-HCR) produced through hybridization chain reaction. Finally, the signal probes which were embedded with a large amount of electrochemiluminescence reagent produce high luminescence intensity. The detection limit was 3.6 × 10^-17 mol/L, which is almost the most sensitive methods reported.

Single-Step DNA Detection Assay Monitoring Dual-Color Light Scattering from Individual Metal Nanoparticle Aggregates

Efficiently detecting DNA sequences within a limited time is vital for disease screening and public health monitoring. This calls for a new method that combines high sensitivity, fast read-out time, and easy manipulation of the sample, avoiding the extensive steps of DNA amplification, purification, or grafting to a surface. Here, we introduce photon cross-correlation spectroscopy as a new method for specific DNA sensing with high sensitivity in a single-step homogeneous solution phase. Our approach is based on confocal dual-color illumination and detection of the scattering intensities from individual silver nanoparticles and gold nanorods. In the absence of the target DNA, the nanoparticles move independently and their respective scattering signals are uncorrelated. In the presence of the target DNA, the probe-functionalized gold and silver nanoparticles assemble via DNA hybridization with the target, giving rise to temporal coincidence between the signals scattered by each nanoparticle. The degree of coincidence accurately quantifies the amount of target DNA. To demonstrate the efficiency of our technique, we detect a specific DNA sequence of sesame, an allergenic food ingredient, for a range of concentration from 5 pM to 1.5 nM with a limit of detection of 1 pM. Our method is sensitive and specific enough to detect single nucleotide deletion and mismatch. With the dual-color scattering signals being much brighter than fluorescence-based analogs, the analysis is fast, quantitative, and simple to operate, making it valuable for biosensing applications.

Application of nanomaterials in the bioanalytical detection of disease-related genes

In the diagnosis of genetic diseases and disorders, nanomaterials-based gene detection systems have significant advantages over conventional diagnostic systems in terms of simplicity, sensitivity, specificity, and portability. In this review, we describe the application of nanomaterials for disease-related genes detection in different methods excluding PCR-related method, such as colorimetry, fluorescence-based methods, electrochemistry, microarray methods, surface-enhanced Raman spectroscopy (SERS), quartz crystal microbalance (QCM) methods, and dynamic light scattering (DLS). The most commonly used nanomaterials are gold, silver, carbon and semiconducting nanoparticles. Various nanomaterials-based gene detection methods are introduced, their respective advantages are discussed, and selected examples are provided to illustrate the properties of these nanomaterials and their emerging applications for the detection of specific nucleic acid sequences.

Kinetic adsorption profile and conformation evolution at the DNA-gold nanoparticle interface probed by dynamic light scattering

The kinetic adsorption profile at the DNA–gold nanoparticle (AuNP) interface is probed by following the binding and organization of thiolated linear DNA and aptamers of varying chain lengths (15, 30, 44, and 51 mer) to the surface of AuNPs (13.0 ± 1.0 nm diameter). A systematic investigation utilizing dynamic light scattering has been performed to directly measure the changes in particle size during the course of a typical aging-salting thiolated DNA/AuNP preparation procedure. We discuss the effect of DNA chain length, composition, salt concentration, and secondary structure on the kinetics and conformation at the DNA–AuNP interface. The adsorption kinetics are chain-length dependent, composition independent, and not diffusion rate limited for the conditions we report here. The kinetic data support a mechanism of stepwise adsorption of thiols to the surface of AuNPs and reorganization of the thiols at the interface. Very interestingly, the kinetic increases of the particle sizes are modeled accurately by the pseudo-second-order rate model, suggesting that DNA could possess the statistically well-defined conformational evolution. Together with other experimental evidence, we propose a dynamic inner-layer and outer-tail (DILOT) model to describe the evolution of the DNA conformation after the initial adsorption of a single oligonucleotide layer. According to this model, the length of the tails that extend from the surface of AuNPs, capable for hybridization or molecular recognition, can be conveniently calculated. Considering the wide applications of DNA/AuNPs, the results should have important implications in sensing and DNA-directed nanoparticle assembly.

Label free fluorometric characterization of DNA interaction with cholate capped gold nanoparticles using ethidium bromide as a fluorescent probe

We demonstrated label free ethidium bromide assisted characterization of DNA interaction with cholate capped AuNPs. Interactions between ss/ds DNA and AuNPs with two different lengths (0.5 and 0.85 kb) were analyzed through fluorescence spectrophotometer and agrose gel electrophoresis analysis. Further results were confirmed by UV-globally visible spectrophotometer, DLS and TEM. As 0.5 and 0.85 kb of ssDNA effectively interacted with AuNPs through the van der Waals interaction which consequently led to the prevention of salt induced aggregation, EtBr intercalations as well as fluorescence shift with less binding constant 0.098 and 0.108 μM, respectively. On the contrary, the same length of dsDNA (0.5 and 0.85 kb) not interacted with AuNPs which led to the NPs aggregation, EtBr intercalation as well as fluorescence shift with increased binding constant 0.166 and 0.599 μM, respectively. This approach helped to understand the mode of interactions of DNA with cholate capped AuNPs without any modifications in a simple method and the results could be readout through the naked eye under the UV transilluminator.

Direct colorimetric biosensing of mercury(II) ion based on aggregation of poly-(γ-glutamic acid)-functionalized gold nanoparticles

A simple and sensitive method for colorimetric detection of mercury ion (Hg(2+)) has been developed by using a poly (γ-glutamic acid) functionalized gold nanoparticles (PGA-AuNPs) system. Electrostatic self-assembly technique was used to assemble negatively charged PGA on the surface of positively charged CTAB-capped AuNPs. With the increase of Hg(2+) concentration, the color of the solution would progress from light red to purple blue. The results showed that the absorbance ratio (A750/A580) was linear with the Hg(2+) concentration in the range of 0.01-10 μM and from 50 to 300 μM, with the correlation coefficients of 0.998 and 0.991, respectively. The reported probe is suitable for real-time detection of Hg(2+) in water with the limit of detection (LOD) of 1.9 nM obtained by UV-vis spectrum, and exhibits selectivity toward one order of magnitude over other metal ions. This approach was applied successfully to the determination of Hg(2+) in tap water and mineral water, and the recoveries were from 90% to 103% and from 103.53% to 113%, respectively. The proposed method is rapid, low-cost and free of complex equipment, making it possible to analyze Hg(2+) in various water samples.

Biomarker discovery and applications for foods and beverages: proteomics to nanoproteomics

Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics.

Label-free, sensitive detection of Hg(II) with gold nanoparticles by using dynamic light scattering technique

A label-free method for sensitive detection of Hg(2+) was developed with gold nanoparticles (AuNPs) by using dynamic light scattering (DLS) technique. Oligonucleotide 5'-TTT CTT CTT CGT TGT TGT TT-3' could transform from uncoil to rigid duplex or hairpin structure upon addition of Hg(2+) ions, which was confirmed by experiments of fluorescence resonance energy transfer and change of melting temperature. The change of DNA structure reduced its adsorption ability on the surface of AuNPs, and resulted in the aggregation of AuNPs in the salt solution, which could be estimated with average hydrodynamic diameter by using DLS technique. Under the optimum conditions, the average diameter increased linearly with the concentration of Hg(2+) over the range from 0.75 nM to 25 nM, the linear regression equation was D=46.7+2.0C (nM, R=0.9958), with a detection limit of 0.43 nM.