Diagnostics of single base-mismatch DNA hybridization on gold nanoparticles by using the hyper-Rayleigh scattering technique

Silver-coated silicon nanowire platform discriminates genomic DNA from normal and malignant human epithelial cells using label-free Raman spectroscopy

Genomic deoxyribonucleic acid (DNA) stores and carries the information required to maintain and replicate cellular life. While much efforts have been devoted in decoding the sequence of DNA basis to detect the genetic mutations related to cancer disease, it is becoming clear that physical properties, like structural conformation, stiffness and shape, can play an important role to recognize DNA modifications. Here, silver-coated silicon nanowires (Ag/SiNWs) are exploited as Raman spectroscopic platform to easily discriminate healthy and cancer genomic DNA, extracted from human normal skin and malignant melanoma cells, respectively. In particular, aqueous DNA droplets are directly deposited onto a forest of Ag/SiNWs and Raman maps are acquired after sample dehydration. By applying principal component analysis (PCA) to the Raman spectra collected within the droplets, healthy and cancer cell DNA can be distinguished without false negative identifications and with few false positive results (< 2%). The discrimination occurs regardless the analysis of specific DNA sequencing, but through Raman bands strictly related to the interfacing of the DNA and the NWs. The observed phenomenon can be ascribed to conformational differences and/or diverse charge properties between healthy and cancer cell DNA determining a different arrangement of the molecules adsorbed onto the NWs upon water evaporation. The unique interaction with DNA and facile fabrication technology make Ag/SiNWs an effective platform for a robust, rapid and label-free cancer diagnosis, as well as a potential tool to investigate physical properties of DNA.

A nanoplasmonic probe as a triple channel colorimetric sensor array for protein discrimination

The salt-induced aggregation, nanoparticle regrowth and self-assembly behaviors of gold nanoparticles (AuNPs) and DNA conjugates could be changed after interaction with different proteins, generating various color changes and a unique fingerprint pattern for each protein.

Optical Second Harmonic Generation in Plasmonic Nanostructures: From Fundamental Principles to Advanced Applications

Plasmonics has emerged as an important research field in nanoscience and nanotechnology. Recently, significant attention has been devoted to the observation and the understanding of nonlinear optical processes in plasmonic nanostructures, giving rise to the new research field called nonlinear plasmonics. This review provides a comprehensive insight into the physical mechanisms of one of these nonlinear optical processes, namely, second harmonic generation (SHG), with an emphasis on the main differences with the linear response of plasmonic nanostructures. The main applications, ranging from the nonlinear optical characterization of nanostructure shapes to the optimization of laser beams at the nanoscale, are summarized and discussed. Future directions and developments, made possible by the unique combination of SHG surface sensitivity and field enhancements associated with surface plasmon resonances, are also addressed.

Selection of a DNA aptamer for cadmium detection based on cationic polymer mediated aggregation of gold nanoparticles

The demand for selection of aptamers against various small chemical molecules has substantially increased in recent years. To incubate and separate target-specific aptamers, the conventional SELEX procedures generally need to immobilize target molecules on a matrix, which may be impotent to screen aptamers toward small molecules without enough sites for immobilization. Herein we chose Cd(II) as a model of a small molecule with less sites, and proposed a novel SELEX strategy of immobilizing ssDNA libraries rather than target molecules on a matrix, for selection of aptamers with high affinity to Cd(II). After eleven rounds of positive and negative selection, twelve T and G-rich of nonrepeating ssDNA sequences were identified, of which the Cd-4 aptamer displayed the highest binding affinity to Cd(II). The secondary structures of these sequences revealed that a stem-loop structure folded by the domain of their 30-random sequence is critical for aptamers to bind targets. Then the interaction between the selected Cd-4 aptamer and Cd(II) was confirmed by CD analysis, and the binding specificity toward other competitive metal ions was also investigated. The dissociation constant (Kd) of Cd-4 aptamer was determined as 34.5 nM for Cd(II). Moreover, the Cd-4 aptamer was considered a recognition element for the colorimetric detection of Cd(II) based on the aggregation of AuNPs by cationic polymer. Through spectroscopic quantitative analysis, Cd(II) in aqueous solution can be detected as low as 4.6 nM. The selected Cd-4 aptamer will offer a new substitute for the detection of Cd(II) or other applications like recovery of cadmium from polluted samples.

Molybdenum disulfide-based amplified fluorescence DNA detection using hybridization chain reactions

A simple, sensitive, and selective amplified fluorescence DNA detection strategyviaenzyme-free molybdenum disulfide-assisted hybridization chain reactions.

Optical reading of contaminants in aqueous media based on gold nanoparticles

With increasing trends of global population growth, urbanization, pollution over-exploitation, and climate change, the safe water supply has become a global issue and is threatening our society in terms of sustainable development. Therefore, there is a growing need for a water-monitoring platform with the capability of rapidness, specificity, low-cost, and robustness. This review summarizes the recent developments in the design and application of gold nanoparticles (AuNPs) based optical assays to detect contaminants in aqueous media with a high performance. First, a brief discussion on the correlation between the optical reading strategy and the optical properties of AuNPs is presented. Then, we summarize the principle behind AuNP-based optical assays to detect different contaminants, such as toxic metal ion, anion, and pesticides, according to different optical reading strategies: colorimetry, scattering, and fluorescence. Finally, the comparison of these assays and the outlook of AuNP-based optical detection are discussed.

A proposed mechanism of the influence of gold nanoparticles on DNA hybridization

A combination of gold nanoparticles (AuNPs) and nucleic acids has been used in biosensing applications. However, there is a poor fundamental understanding of how gold nanoparticle surfaces influence the DNA hybridization process. Here, we measured the rate constants of the hybridization and dehybridization of DNA on gold nanoparticle surfaces to enable the determination of activation parameters using transition state theory. We show that the target bases need to be detached from the gold nanoparticle surfaces before zipping. This causes a shift of the rate-limiting step of hybridization to the mismatch-sensitive zipping step. Furthermore, our results propose that the binding of gold nanoparticles to the single-stranded DNA segments (commonly known as bubbles) in the duplex DNA stabilizes the bubbles and accelerates the dehybridization process. We employ the proposed mechanism of DNA hybridization/dehybridization to explain the ability of 5 nm diameter gold nanoparticles to help discriminate between single base-pair mismatched DNA molecules when performed in a NanoBioArray chip. The mechanistic insight into the DNA-gold nanoparticle hybridization/dehybridization process should lead to the development of new biosensors.

Hyper-Rayleigh scattering from gold nanoparticles: effect of size and shape

We report hyper-Rayleigh scattering (HRS) properties of gold nanoparticles (GNPs) of five different shapes, quasi-spherical (∼10 and ∼20 nm diameter), rod (aspect ratio ∼2), and branched shapes, tetrapod, flower and star with 800 nm, 150 fs laser excitation. Using ∼10 nm spherical GNPs as reference, the first hyperpolarizability (β) values were calculated for all other shapes. Star and flower shaped GNPs have the highest hyperpolarizability (∼130 and ∼52 times higher, respectively), while rod and tetrapod shaped GNPs only have modest enhancement (∼7 times), which is similar to ∼20 nm size quasi-spherical particles. These enhancements are attributed to reduced symmetry as well as the presence of sharp tips on GNP surface. When the β values are normalized with respect to the number of atoms per particle, the flower and star shaped GNPs still have the highest hyperpolarizability values. The polar plots of vertically polarized HRS signal as a function of the angle of polarization of the incoming incident light shows two lobes, indicating that excitation is predominantly dipolar in nature although the size of some GNPs are big enough to show a quadrupolar response. It is believed that the presence of sharp tips at the surface of these large sized GNPs is responsible for the observed dipolar response. This study shows that GNPs having sharp tips might be a better candidate when their nonlinear properties are used for sensing applications.

A surface enhanced Raman scattering probe for highly selective and ultra sensitive detection of iodide in water and salt samples

Iodine is a biophilic and essential trace element for all life and especially for vertebrates, which require it to produce indispensable thyroid hormones in their thyroid glands. As a result, the adequate measurement of iodine in water and food samples is crucial to lead a healthy life. Motivated by its importance, this is the first time in the literature that the highly selective and ultra sensitive (30 ppt limit) surface enhanced Raman scattering (SERS)-based detection of iodide ions (I(-)) from environmental and food samples has been reported. The desired sensitivity and selectivity has been achieved by measuring the change in the SERS intensity originating from Rh6G-adsorbed 30 nm gold nanoparticles (GNPs) upon the addition of I(-). The strong chemical affinity offered by I(-) towards the gold surface results in extra negative charge being deposited on it. As a result, the GNP surface attracts a greater number of positively charged Rh6G molecules and induces a marked increase in the number of hot spots through aggregation, providing a significant enhancement of the Raman signal intensity. The oxidation of I(-) to molecular iodine (I(2)) by hydrogen peroxide (H(2)O(2)) is employed for the successful screening of the bromide ion (Br(-)) which shows substantial interference at higher concentrations.

Localized surface plasmon resonance: a unique property of plasmonic nanoparticles for nucleic acid detection

Localized surface plasmon resonance (LSPR) of noble metal nanoparticles (a.k.a. plasmonic nanoparticles) opens up a new horizon for advanced biomolecule sensing. However, an effective and practical sensing system still requires meticulous design to achieve good sensitivity and distinctive selectivity for routine use and high-throughput detection. In particular, the detection of DNA and RNA is crucial in biomedical research and clinical diagnostics. This review describes the fundamental aspects of LSPR and provides an overall account of how it is exploited to assist in nucleic acid sensing. The detection efficiency of each LSPR-based approach is assessed with respect to the assay design, the selection of plasmonic nanoparticles, and the choice of nucleic acid probes which influence the duplex hybridization. Judicious comparison is made among various LSPR-based approaches in terms of the assaying time, the sensitivity or lowest sensing concentration (i.e. limit of detection or LOD), and the single-base mismatch (SBM) selectivity.

Sensitive and selective detection of trivalent chromium using Hyper Rayleigh Scattering with 5,5'-dithio-bis-(2-nitrobenzoic acid)-modified gold nanoparticles

Hyper Rayleigh Scattering (HRS) and absorption spectral assays using surface-modified gold nanoparticles (AuNP) have been developed for sensitive and selective detection of trivalent chromium (Cr³⁺) from other metal ions including hexavalent chromium (as Cr₂O₇^2-). Gold nanoparticles of 13 nm, covalently attached with 5,5'-dithio-bis-(2-nitrobenzoic acid) (AuNP-DTNBA), is used as a probe for both the absorption and HRS assays. AuNP-DTNBA is able to detect Cr³⁺ at 20 ppb level at pH 6.0 using absorption spectral change of the AuNP-DTNBA. Visible color change can be observed when mixed with 250 ppb of Cr³⁺, while there is no color change when mixed with 2 ppm level of some of the most common metal ions such as Cr₂O₇^2-, Hg²⁺, Ba²⁺, Fe³⁺, Pb²⁺, Na⁺, Zn²⁺, Cd²⁺, Co²⁺, Mn²⁺, Ca²⁺, and Ni²⁺. However, a color change is observed when mixed with Ni²⁺, Zn²⁺, and Cd²⁺ at a concentration higher than 2 ppm. The detection limit for the HRS assay is on a remarkable 25 ppt level, and there is no detectable HRS signal at 2 ppm level for Cr₂O₇^2-, Hg²⁺, Ba²⁺, Fe³⁺, Pb²⁺, Na⁺, Zn²⁺, Cd²⁺, Co²⁺, Mn²⁺, Ca²⁺, and Ni²⁺.

DNAzyme-functionalized gold nanoparticles for biosensing

Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.

Trace mercury ion determination based on the highly selective redox reaction between stannous ion and mercury ion enhanced by gold nanoparticles

A novel resonance light scattering (RLS) spectrometric method for mercury ions (Hg(2+)) determination has been established in this article. Mercury (Hg) nanoparticle formed from the highly selective redox reaction between citrate-stabilized stannous ions (Sn(2+)) and Hg(2+). As a result, the RLS intensities of the system can be enhanced and it can be sensitized in the presence of very little amount of gold nanoparticles (AuNPs). According to this phenomenon, trace Hg(2+) in real water sample has been determined directly by RLS spectrometry. It has been found that the enhanced RLS intensities (ΔI(RLS)) characterized at 395 nm are proportional to the concentration of Hg(2+) in the range of 0.1-30 μmol L(-1) with a detection limit (3σ) of 0.051 μmol L(-1). The method described herein has good sensitivity, selectivity, and without complicated sample pretreatment. Moreover, the feasibility for the analysis of Hg(2+) in a wastewater sample was identified with a good recovery (100.2-106.3%).

Ultrasensitive aptamer biosensor for arsenic(III) detection in aqueous solution based on surfactant-induced aggregation of gold nanoparticles

This paper reports the colorimetric and resonance scattering (RS)-based biosensor for the ultrasensitive detection of As(III) in aqueous solution via aggregating gold nanoparticles (AuNPs) by the special interactions between arsenic-binding aptamer, target and cationic surfactant. Aptamers and the cationic surfactant could assemble to form a supramolecule, which prevented AuNPs from aggregating due to the exhaustion of cationic surfactant. The introduction of As(III) specifically interacted with the arsenic-binding aptamer to form the aptamer-As(III) complex, so that the following cationic surfactant could aggregate AuNPs and cause the remarkable change in color and RS intensity. The results of circular dichroism (CD) and scanning probe microscope (SPM) testified to the formation of the supramolecule and aptamer-As(III) complex, and the observation of transmission electron microscope (TEM) further confirmed that the aggregation of AuNPs could be controlled by the interactions among the aptamer, As(III) and cationic surfactant. The variations of absorbance and RS intensity were exponentially related to the concentration of As(III) in the range from 1 to 1500 ppb, with the detection limit of 40 ppb for the naked eye, 0.6 ppb for colorimetric assay and 0.77 ppb for RS assay. Additionally, the speed of the present biosensor was rapid, and it also exhibited high selectivity over other metal ions with an excellent recovery for detection in real water samples, suggesting that the proposed biosensor will play an important role in environmental detection.

Gold nano-popcorn attached SWCNT hybrid nanomaterial for targeted diagnosis and photothermal therapy of human breast cancer cells

Breast cancer presents greatest challenge in health care in today's world. The key to ultimately successful treatment of breast cancer disease is an early and accurate diagnosis. Current breast cancer treatments are often associated with severe side effects. Driven by the need, we report the design of novel hybrid nanomaterial using gold nano popcorn-attached single wall carbon nanotube for targeted diagnosis and selective photothermal treatment. Targeted SK-BR-3 human breast cancer cell sensing have been performed in 10 cancer cells/mL level, using surface enhanced Raman scattering of single walls carbon nanotube's D and G bands. Our data show that S6 aptamer attached hybrid nanomaterial based SERS assay is highly sensitive to targeted human breast cancer SK-BR-3 cell line and it will be able to distinguish it from other non targeted MDA-MB breast cancer cell line and HaCaT normal skin cell line. Our results also show that 10 min of photothermal therapy treatment by 1.5 W/cm(2) power, 785 nm laser is enough to kill cancer cells very effectively using S6 aptamer attached hybrid nanomaterials. Possible mechanisms for targeted sensing and operating principle for highly efficient photothermal therapy have been discussed. Our experimental results reported here open up a new possibility for using aptamers modified hybrid nanomaterial for reliable diagnosis and targeted therapy of cancer cell lines quickly.

A label-free gold-nanoparticle-based SERS assay for direct cyanide detection at the parts-per-trillion level

Cyanide is an extremely toxic lethal poison known to humankind. Developing rapid, highly sensitive, and selective detection of cyanide from water samples is extremely essential for human life safety. Driven by the need, here we report a gold-nanoparticle-based label-free surface-enhanced Raman spectroscopy (SERS) system for highly toxic cyanide ion recognition in parts-per-trillion level and to examine gold-nanoparticle-cyanide interaction. We have shown that the SERS assay can be used to probe the gold nanoparticle dissociation process in the presence of cyanide ions. Our experimental data indicates that gold-nanoparticle-based SERS can detect cyanide from a water sample at the 110 ppt level with excellent discrimination against other common anions and cations. The results also show that the SERS probe can be used to detect cyanide from environmental samples.

Toxic effects of gold nanoparticles on Salmonella typhimurium bacteria

Nanometer-sized gold, due to its beautiful and bountiful color and unique optical properties, is a versatile material for many industrial and societal applications. We have studied the effect of gold nanoparticles on Salmonella typhimurium strain TA 102. The gold nanoparticles in solution prepared using the citrate reduction method is found not to be toxic or mutagenic but photomutagenic to the bacteria; however, careful control experiments indicate that the photomutagenicity is due to the co-existing citrate and Au³⁺ ions, not due to the gold nanoparticle itself. Au³⁺ is also found to be photomutagenic to the bacteria at concentrations lower than 1 µM, but toxic at higher concentrations. The toxicity of Au³⁺ is enhanced by light irradiation. The photomutagenicity of both citrate and Au³⁺ is likely due to the formation of free radicals, as a result of light-induced citrate decarboxylation or Au³⁺ oxidation of co-existing molecules. Both processes can generate free radicals that may cause DNA damage and mutation. Studies of the interaction of gold nanoparticles with the bacteria indicate that gold nanoparticles can be absorbed onto the bacteria surface but not able to penetrate the bacteria wall to enter the bacteria.

A one-step sensitive dynamic light scattering method for detection using split aptamer fragments

A one-step sensitive method using dynamic light scattering (DLS) was introduced for direct detection of adenosine with high selectivity. For the first time, DLS was used to detect small molecules directly and quantitatively.

Nanogold-based sensing of environmental toxins: excitement and challenges

There have been tremendous advances in the past ten years on the development of various nanomaterials-based sensors for detection of environmental toxins. Nanogold is of special interest because of its unique shape- and size-dependent optical properties, hyper-quenching ability, super surface-enhanced Raman and dynamic light scattering, and surface-modifiability by small organic molecules and biomolecules. These unique optical properties of nanogold have been explored for ultra-sensitive detection, while its surface-modifiability has been explored for selectivity. In general, the nanogold-based sensors are highly selective and sensitive along with simple sample preparation and sensor design. In this review article, we intend to capture some of the recent advances in nanogold-based sensor development and mechanistic studies, especially for bacteria, heavy metals, and nitroaromatic compounds. Undoubtedly, these developments will generate a lot of excitement for environmental scientists and toxicologists as well as the general public.

Highly sensitive and selective dynamic light-scattering assay for TNT detection using p-ATP attached gold nanoparticle

TNT is one of the most commonly used nitro aromatic explosives for landmines of military and terrorist activities. As a result, there is an urgent need for rapid and reliable methods for the detection of trace amount of TNT for screenings in airport, analysis of forensic samples, and environmental analysis. Driven by the need to detect trace amounts of TNT from environmental samples, this article demonstrates a label-free, highly selective, and ultrasensitive para-aminothiophenol (p-ATP) modified gold nanoparticle based dynamic light scattering (DLS) probe for TNT recognition in 100 pico molar (pM) level from ethanol:acetonitile mixture solution. Because of the formation of strong π-donor-acceptor interaction between TNT and p-ATP, para-aminothiophenol attached gold nanoparticles undergo aggregation in the presence of TNT, which changes the DLS intensity tremendously. A detailed mechanism for significant DLS intensity change has been discussed. Our experimental results show that TNT can be detected quickly and accurately without any dye tagging in 100 pM level with excellent discrimination against other nitro compounds.

Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device

Two simple gold nanoparticle (GNP)-based DNA analysis methods using a microfluidic device are presented. In the first method, probe DNA molecules are immobilized on the surface of a self-assembled submonolayer of GNPs. The hybridization efficiency of the target oligonulceotides was improved due to nanoscale spacing between probe molecules. In the second method, target DNA molecules, oligonulceotides or polymerase chain reaction (PCR) amplicons, are first bound to GNPs and then hybridized to the immobilized probe DNA on a glass slide. With the aid of GNPs, we have successfully discriminated, at room temperature, between two PCR amplicons (derived from closely related fungal pathogens, Botrytis cinerea and Botrytis squamosa) with one base-pair difference. DNA analysis on the microfluidic chip avoids the use of large sample volumes, and only a small amount of oligonucelotides (8 fmol) or PCR products (3 ng), was needed in the experiment. The whole procedure was accomplished at room temperature in 1 h, and apparatus for high temperature stringency was not required.

Multifunctional oval-shaped gold-nanoparticle-based selective detection of breast cancer cells using simple colorimetric and highly sensitive two-photon scattering assay

Breast cancer is the most common cancer among women, and it is the second leading cause of cancer deaths in women today. The key to the effective and ultimately successful treatment of diseases such as cancer is early and accurate diagnosis. Driven by the need, in this article, we report for the first time a simple colorimetric and highly sensitive two-photon scattering assay for highly selective and sensitive detection of breast cancer SK-BR-3 cell lines at a 100 cells/mL level using a multifunctional (monoclonal anti-HER2/c-erb-2 antibody and S6 RNA aptamer-conjugated) oval-shaped gold-nanoparticle-based nanoconjugate. When multifunctional oval-shaped gold nanoparticles are mixed with the breast cancer SK-BR-3 cell line, a distinct color change occurs and two-photon scattering intensity increases by about 13 times. Experimental data with the HaCaT noncancerous cell line, as well as with MDA-MB-231 breast cancer cell line, clearly demonstrated that our assay was highly sensitive to SK-BR-3 and it was able to distinguish from other breast cancer cell lines that express low levels of HER2. The mechanism of selectivity and the assay's response change have been discussed. Our experimental results reported here open up a new possibility of rapid, easy, and reliable diagnosis of cancer cell lines by monitoring the colorimetric change and measuring TPS intensity from multifunctional gold nanosystems.

Ultrahighly sensitive homogeneous detection of DNA and microRNA by using single-silver-nanoparticle counting

DNA and RNA analysis is of high importance for clinical diagnoses, forensic analysis, and basic studies in the biological and biomedical fields. In this paper, we report the ultrahighly sensitive homogeneous detection of DNA and microRNA by using a novel single-silver-nanoparticle counting (SSNPC) technique. The principle of SSNPC is based on the photon-burst counting of single silver nanoparticles (Ag NPs) in a highly focused laser beam (about 0.5 fL detection volume) due to Brownian motion and the strong resonance Rayleigh scattering of single Ag NPs. We first investigated the performance of the SSNPC system and then developed an ultrasensitive homogeneous detection method for DNA and microRNA based on this single-nanoparticle technique. Sandwich nucleic acid hybridization models were utilized in the assays. In the hybridization process, when two Ag-NP-oligonucleotide conjugates were mixed in a sample containing DNA (or microRNA) targets, the binding of the targets caused the Ag NPs to form dimers (or oligomers), which led to a reduction in the photon-burst counts. The SSNPC method was used to measure the change in the photon-burst counts. The relationship between the change of the photon-burst counts and the target concentration showed a good linearity. This method was used for the assay of sequence-specific DNA fragments and microRNAs. The detection limits were at about the 1 fM level, which is 2-5 orders of magnitude more sensitive than current homogeneous methods.

Dynamic light scattering as a powerful tool for gold nanoparticle bioconjugation and biomolecular binding studies

Dynamic light scattering (DLS) is an analytical tool used routinely for measuring the hydrodynamic size of nanoparticles and colloids in a liquid environment. Gold nanoparticles (GNPs) are extraordinary light scatterers at or near their surface plasmon resonance wavelength. In this study, we demonstrate that DLS can be used as a very convenient and powerful tool for gold nanoparticle bioconjugation and biomolecular binding studies. The conjugation process between protein A and gold nanoparticles under different experimental conditions and the quality as well as the stability of the prepared conjugates were monitored and characterized systematically by DLS. Furthermore, the specific interactions between protein A-conjugated gold nanoparticles and a target protein, human IgG, can be detected and monitored in situ by measuring the average particle size change of the assay solution. For the first time, we demonstrate that DLS is able to directly and quantitatively measure the binding stoichiometry between a protein-conjugated GNP probe and a target analyte protein in solution.