Highly sensitive and selective detection of single-nucleotide polymorphisms using gold nanoparticle MutS enzymes and a micro cantilever resonator

Multiplex genotyping of SNPs in genomic DNA via hydrogel-based assay mediated with MutS and polyethylene glycol

The simultaneous genotyping of multiple single nucleotide polymorphisms (SNPs) in genomic DNA derived from organisms holds significant potential for applications such as precision medicine and food product authentication. However, conventional assay technologies including qPCR-based techniques, microarrays, and hydrogel-based assays face limitations in efficient multiplexing of SNPs, particularly for large-size DNA beyond kilobase scales, due to constraints in multiplex capability, specificity, or sensitivity. In this study, a hydrogel-based multiplex SNP genotyping platform specifically designed for genomic DNA is presented. This platform integrates the ligation detection reaction (LDR) and rolling circle amplification (RCA) techniques within a hydrogel-based multiplex sensing system, enabling adaptable and sensitive SNP genotyping for genomic DNA. To enhance the specificity of the assay, MutS protein and polyethylene glycol are introduced into the protocol, reducing the non-specific ligation and RCA reactions synergistically. With significant specificity improvement of over 10-fold, three types of SNPs within an artificially constructed ∼1000 bp double-stranded DNA (dsDNA) are successfully genotyped with double-digit picomolar sensitivity. Furthermore, the practical applicability of the developed process for the origin identification of raw materials is demonstrated by genotyping three types of SNPs within genomic DNA obtained from two closely related plant species, Korean ginseng (Panax ginseng) and American ginseng (Panax quinquefolius), containing ca. 3.5 gigabase genome size. Of notable significance, this study marks the premiere achievement in PCR-free multiplex genotyping of SNPs in genomic DNA using a single fluorophore.

A Genosensor Based on the Modification of a Microcantilever: A Review

When the free end of a microcantilever is modified by a genetic probe, this sensor can be used for a wider range of applications, such as for chemical analysis, biological testing, pharmaceutical screening, and environmental monitoring. In this paper, to clarify the preparation and detection process of a microcantilever sensor with genetic probe modification, the core procedures, such as probe immobilization, complementary hybridization, and signal extraction and processing, are combined and compared. Then, to reveal the microcantilever's detection mechanism and analysis, the influencing factors of testing results, the theoretical research, including the deflection principle, the establishment and verification of a detection model, as well as environmental influencing factors are summarized. Next, to demonstrate the application results of the genetic-probe-modified sensors, based on the classification of detection targets, the application status of other substances except nucleic acid, virus, bacteria and cells is not introduced. Finally, by enumerating the application results of a genetic-probe-modified microcantilever combined with a microfluidic chip, the future development direction of this technology is surveyed. It is hoped that this review will contribute to the future design of a genetic-probe-modified microcantilever, with further exploration of the sensitive mechanism, optimization of the design and processing methods, expansion of the application fields, and promotion of practical application.

Gold Nanoparticles as a Biosensor for Cancer Biomarker Determination

Molecular biology applications based on gold nanotechnology have revolutionary impacts, especially in diagnosing and treating molecular and cellular levels. The combination of plasmonic resonance, biochemistry, and optoelectronic engineering has increased the detection of molecules and the possibility of atoms. These advantages have brought medical research to the cellular level for application potential. Many research groups are working towards this. The superior analytical properties of gold nanoparticles can not only be used as an effective drug screening instrument for gene sequencing in new drug development but also as an essential tool for detecting physiological functions, such as blood glucose, antigen-antibody analysis, etc. The review introduces the principles of biomedical sensing systems, the principles of nanomaterial analysis applied to biomedicine at home and abroad, and the chemical surface modification of various gold nanoparticles.

Recent Advances in Nanomechanical Membrane-Type Surface Stress Sensors towards Artificial Olfaction

Nanomechanical sensors have gained significant attention as powerful tools for detecting, distinguishing, and identifying target analytes, especially odors that are composed of a complex mixture of gaseous molecules. Nanomechanical sensors and their arrays are a promising platform for artificial olfaction in combination with data processing technologies, including machine learning techniques. This paper reviews the background of nanomechanical sensors, especially conventional cantilever-type sensors. Then, we focus on one of the optimized structures for static mode operation, a nanomechanical Membrane-type Surface stress Sensor (MSS), and discuss recent advances in MSS and their applications towards artificial olfaction.

Synergistic enhanced rolling circle amplification based on mutS and radical polymerization for single-point mutation DNA detection

The detection of nucleic acids in biofluids is essential for changing the paradigm of disease diagnosis. As there are very few nucleic acids present in human biofluids, a high sensitivity method is required to detect nucleic acids for disease diagnosis. The Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is associated with non-small cell lung cancer. It is a point mutation and requires a highly selective detection technique. In this study, high sensitivity and selectivity were achieved for the detection of KRAS mutation using rolling circle amplification (RCA), atomic transfer radical polymerization (ATRP), mutS enzyme, and electrochemical sensors. Although RCA can isothermally amplify DNA, it has low selectivity for detecting single-base mismatch DNA, and its sensitivity is not suitable for circulating tumor DNA detection. The selectivity of RCA was improved by using mutS, which can bind specifically to point mutations. In addition, as a method of isothermal radical polymerization, ATRP was used to amplify the weak signal of RCA. Since RCA and ATRP reactions occur simultaneously, detection time was reduced, and the calculated detection limit was 3.09 aM. Computational and experimental analyses were conducted to verify each detection step and the combination of mutS, ATRP, and RCA. The experiment was performed using normal human serum samples for biological application, and the proposed detection method was confirmed to have excellent potential for diagnosing cancer patients.

A V-Shaped Microcantilever Sensor Based on a Gap Method for Real-Time Detection of E. coli Bacteria

This paper presents a dynamic-mode microcantilever sensor based on a gap method. The sensor has a V-shaped microcantilever and a fixed structure at a distance of 2 µm from its free end. The microcantilever is excited by applying an ac electric potential (3 Vp) to its piezoelectric pads and vibrates at its fundamental resonant frequency. An independent ac electric potential (200 kHz, 15 Vpp) is applied to the fixed structure. This creates a non-uniform electric field with its maxima at the gap and exerts a dielectrophoresis (DEP) force. The DEP force attracts and adsorbs the E. coli bacteria to the cantilever edge at the gap. The binding of the bacteria to the cantilever creates a shift in the resonant frequency of the microcantilever sensor, which is detected by a laser vibrometer. The real-time detection of E. coli bacteria samples, diluted in distilled water, was performed for concentrations of 105–103 cells/mL and the real-time frequency shifts were −2264.3 to −755 Hz in 4 min, respectively. The tests were expanded to study the effect of the electric potential amplitude (10, 12, 15 Vpp) and higher frequency shifts were observed for higher amplitudes.

A Ti3C2-MXene-functionalized LRSPR biosensor based on sandwich amplification for human IgG detection

Long-range surface plasmon resonance (LRSPR) has demonstrated excellent performance in sensing and detection, due to its higher accuracy and sensitivity compared with conventional surface plasmon resonance (cSPR). In this work, we establish an LRSPR biosensor which employs PDA/Ti₃C₂-MXene/PDA-gold film as a sensing substrate and gold nanoparticles (AuNPs) as enhancers. Ti₃C₂-MXene is an emerging two-dimensional (2D) layered material which is used extensively in immunoassay and biosensing. The sensing substrate comprises two polydopamine (PDA) films between which is sandwiched a Ti₃C₂-MXene film based on a gold film, which provides a large surface area and abundant binding sites to rabbit anti-human IgG (Ab₁). Sandwich amplification is adopted to enhance the sensitivity of the LRSPR biosensor, and AuNPs/staphylococcal protein A (SPA)/mouse anti-human IgG (Ab₂) composites are introduced into the flow cell as enhancers after the immune binding of human IgG to Ab₁. The antigen (human IgG) detection range is 0.075 μg mL^-1 to 40 μg mL^-1, and the limit of detection is almost 20 times lower than that for cSPR biosensors. This novel LRSPR biosensor demonstrates excellent performance in immune sensing over a broad detection range and a low limit of detection. Subsequent modification of the LRSPR sensing platform could be made for extensive application in various biological detection fields.

Nanoplasmonic Structure of a Polycarbonate Substrate Integrated with Parallel Microchannels for Label-Free Multiplex Detection

In this study, a multiplex detection system was proposed by integrating a localized surface plasmon resonance (LSPR) sensing array and parallel microfluidic channels. The LSPR sensing array was fabricated by nanoimprinting and gold sputter on a polycarbonate (PC) substrate. The polydimethylsiloxane (PDMS) microfluidic channels and PC LSPR sensing array were bound together through (3-aminopropyl)triethoxysilane (APTES) surface treatment and oxygen plasma treatment. The resonant spectrum of the LSPR sensing device was obtained by broadband white-light illumination and polarized wavelength measurements with a spectrometer. The sensitivity of the LSPR sensing device was measured using various ratios of glycerol to water solutions with different refractive indices. Multiplex detection was demonstrated using human immunoglobulin G (IgG), IgA, and IgM. The anti-IgG, anti-IgA, and anti-IgM were separately modified in each sensing region. Various concentrations of human IgG, IgA, and IgM were prepared to prove the concept that the parallel sensing device can be used to detect different targets.

Enhancement of electrode performance through surface modification using carbon nanotubes and porous gold nanostructures

Recently, the demand for the sensitive detection of nanomaterials and biomolecules has been increasing for evaluating the toxicity of nanomaterials and early diagnosis of diseases. Although many studies have developed new detection assays, these are heavily influenced by the capabilities of the detection equipment. Therefore, the aim of the present study was to improve electrode performance by modifying the surface of the detection electrode using a simple method. Electrode surface modification was performed using carbon nanotubes (CNT) and porous gold nanostructures (NS) with excellent electrical and chemical properties. Through the simple physical deposition of CNT and electrochemical reduction of NS, the increasement of the electrode surface area was achieved. Because of the CNTs attached to the electrodes at the first step, the metal ions constituting the NS can adhere well to the electrodes. Nanoparticles with a porous structure can be generated through electrochemical reduction (cyclic voltammetry) of metal ions attached to electrodes. Consequently, the surface area of the electrode increased and electrochemical performance was improved (confirmed by atomic force microscopy, Nyquist plot and Bode plot). To quantitatively confirm the improvement of electrode performance according to the surface change through the proposed treatment technique, DNA was detected. Unlike previous surface modification studies, the developed surface treatment technique can be applied to a variety of detection equipment. To confirm this, the detection was performed using two detection devices with different operating principles. DNA detection using the two types of equipment confirmed that the detection limit was increased by approximately 1000-fold through applying a simple surface treatment. In addition, this method is applicable to detect various sizes of nanomaterials. The method proposed in this study is simple and has the advantage that it can be applied to various devices and various materials.

Application of Nanotechnology for Sensitive Detection of Low-Abundance Single-Nucleotide Variations in Genomic DNA: A Review

Single-nucleotide polymorphisms (SNPs) are the simplest and most common type of DNA variations in the human genome. This class of attractive genetic markers, along with point mutations, have been associated with the risk of developing a wide range of diseases, including cancer, cardiovascular diseases, autoimmune diseases, and neurodegenerative diseases. Several existing methods to detect SNPs and mutations in body fluids have faced limitations. Therefore, there is a need to focus on developing noninvasive future polymerase chain reaction (PCR)-free tools to detect low-abundant SNPs in such specimens. The detection of small concentrations of SNPs in the presence of a large background of wild-type genes is the biggest hurdle. Hence, the screening and detection of SNPs need efficient and straightforward strategies. Suitable amplification methods are being explored to avoid high-throughput settings and laborious efforts. Therefore, currently, DNA sensing methods are being explored for the ultrasensitive detection of SNPs based on the concept of nanotechnology. Owing to their small size and improved surface area, nanomaterials hold the extensive capacity to be used as biosensors in the genotyping and highly sensitive recognition of single-base mismatch in the presence of incomparable wild-type DNA fragments. Different nanomaterials have been combined with imaging and sensing techniques and amplification methods to facilitate the less time-consuming and easy detection of SNPs in different diseases. This review aims to highlight some of the most recent findings on the aspects of nanotechnology-based SNP sensing methods used for the specific and ultrasensitive detection of low-concentration SNPs and rare mutations.

Fluorescence and colorimetric dual-mode sensor for visual detection of malathion in cabbage based on carbon quantum dots and gold nanoparticles

A dual-mode fluorescence/colorimetric sensor based on carbon quantum dots (CQDs) and gold nanoparticles (GNPs) was developed for visual detection of malathion in cabbage. The CQDs-GNPs nanocomposite exhibited emission wavelength at 527 nm and absorption wavelength at 524 nm. The fluorescence intensity increased and absorption decreased with addition of malathion. Fluorescence and colorimetric calibration curves were established based on fluorescence intensity (R² = 0.9914) and absorbance (R² = 0.9608) in the range of 1 × 10^-9-1 × 10^-2 M, respectively. Furthermore, fluorescence and colorimetric standard arrays were prepared for visual detection of malathion according to the change of fluorescence brightness and color. Finally, the approximate concentrations of malathion in cabbage samples were estimated by the standard arrays and naked eyes. The calibration curves were used for accurate detection in cabbage samples with recoveries of 89.9%-103.4% (fluorescence) and 88.7%-107.6% (colorimetric). The established sensor for visual malathion detection in cabbage was accurate with strong application potential, especially for rapid screening.

All-in-one approaches for rapid and highly specific quantifcation of single nucleotide polymorphisms based on ligase detection reaction using molecular beacons as turn-on probes

Rapid, simple, specific and sensitive approaches for single nucleotide polymorphisms (SNPs) detection are essential for clinical diagnosis. In this study, all-in-one approaches, consisting of the whole detection process including ligase detection reaction (LDR) and real time quantitative polymerase chain reaction performed in one PCR tube by a one-step operation on a real-time PCR system using molecular beacon (MB) as turn-on probe, were developed for rapid, simple, specific and sensitive quantifcation of SNPs. High specificity of the all-in-one approach was achieved by using the LDR, which employs a thermostable and single-base discerning Hifi Taq DNA ligase to ligate adjacently hybridized LDR-specific probes. In addition, a highly specific probe, MB, was used to detect the products of all-in-one approach, which doubly enhances the specificity of the all-in-one approach. The linear dynamic range and high sensitivity of mutant DNA (MutDNA) and wild-type DNA (WtDNA) all-in-one approaches for the detection of MutDNA and WtDNA were studied in vitro, with a broad linear dynamic range of 0.1 fM to 1 pM and detection limits of 65.3 aM and 31.2 aM, respectively. In addition, the MutDNA and WtDNA all-in-one approaches were able to accurately detect allele frequency changes as low as 0.1%. In particular, the epidermal growth factor receptor T790M MutDNA frequency in the tissue of five patients with non-small cell lung cancer detected by all-in-one approaches were in agreement with clinical detection results, indicating the excellent practicability of the developed approaches for the quantification of SNPs in real samples. In summary, the developed all-in-one approaches exhibited promising potential for further applications in clinical diagnosis.