MutS protein-based fiber optic particle plasmon resonance biosensor for detecting single nucleotide polymorphisms

Colorimetric detection of single-nucleotide mutations based on rolling circle amplification and G-quadruplex-based DNAzyme

In this work, we proposed a sensitive and selective colorimetric assay for single nucleotide mutation (SNM) detection combining rolling circle amplification (RCA) and G-quadruplex/hemin DNAzyme complex formation. In the detection principle, the first step involves ssDNA hybridization with a padlock probe (PLP) DNA, which can discriminate a single base mismatch. The successful ligation is followed by an RCA event to generate an abundance of G-quadruplexes (GQ-RCA) which are then transformed into a DNAzyme (G-quadruplex/hemin complex) by the addition of hemin. The color change from colorless 3,3',5,5'-tetramethylbenzidine (TMB) into colored oxTMB when hydrogen peroxide (H2O2) is added indicated the presence of a mutation. The assay had a limit of detection (LOD) of 2.14 pM. Mutations in samples from breast cancer patients were successfully detected with an accuracy of 100% when compared to Sanger sequencing results. The method is easily applicable even in resource poor setting regions given that it doesn't require any sophisticated or expensive instruments, and the signal readout is detectable simply by the naked eye. Our assay might be a useful tool for genetic analysis and clinical molecular diagnosis for breast cancer risk assessment and early detection.

Noninvasive Prenatal Genetic Screening of Cell-Free Fetal DNA for Early Prediction of β-Thalassemia Using Fiber Optic Nanogold-Linked Sorbent Assay

β-Thalassemia is a prevalent type of severe inherited chronic anemia, primarily identified in developing countries. The identification of single nucleotide polymorphisms (SNPs) plays a vital role in the early diagnosis of genetic diseases. Here, we reported the development of an amplification-free fiber optic nanogold-linked sorbent assay method using a fiber optic particle plasmon resonance (FOPPR) biosensor for rapid and ultrasensitive detection of SNPs. Herein, MutS protein was selected as the biorecognition capture probe and immobilized on the sensing region to capture the target mutant DNA, which was hybridized with a single-base mismatched single-stranded DNA labeled by a gold nanoparticle (AuNP). The AuNP acts as a signaling agent to be detected by the FOPPR biosensor when it is bound on the fiber core surface. The method effectively differentiates mismatched double-stranded DNA by MutS protein from perfectly matched/complementary dsDNA. It exhibits an impressively low detection limit for the detection of SNPs at approximately 10-16 M using low-cost sensor chips and devices. By determination of the ratio of mutant DNA to normal DNA in cell-free genomic DNA from blood samples, this method is promising for diagnosing β-thalassemia in fetuses without invasive testing techniques.

Recent Progress on Microfluidics Integrated with Fiber-Optic Sensors for On-Site Detection

This review introduces a micro-integrated device of microfluidics and fiber-optic sensors for on-site detection, which can detect certain or several specific components or their amounts in different samples within a relatively short time. Fiber-optics with micron core diameters can be easily coated and functionalized, thus allowing sensors to be integrated with microfluidics to separate, enrich, and measure samples in a micro-device. Compared to traditional laboratory equipment, this integrated device exhibits natural advantages in size, speed, cost, portability, and operability, making it more suitable for on-site detection. In this review, the various optical detection methods used in this integrated device are introduced, including Raman, ultraviolet-visible, fluorescence, and surface plasmon resonance detections. It also provides a detailed overview of the on-site detection applications of this integrated device for biological analysis, food safety, and environmental monitoring. Lastly, this review addresses the prospects for the future development of microfluidics integrated with fiber-optic sensors.

Ultrasensitive and Quantitative DNA Methylation Detection Method Based on the MutS Protein

DNA methylation is closely related to cancer. It is generally accepted that DNA methylation detection is crucial in cancer diagnosis, prognosis, and treatment monitoring. Therefore, there is an urgent demand for developing a simple, rapid, highly sensitive, and highly specific methylation detection method to detect DNA methylation at specific sites quantitatively. In this work, we introduce a DNA methylation detection method based on MutS and methylation-specific PCR, named MutS-based methylation-specific PCR (MB-MSP), which has the advantages of simplicity, speed, high specificity, sensitivity, and broad applicability. Utilizing the MutS's ability to bind mismatched base pairs, we inhibit not only the amplification of unmethylated DNA but also nonspecific primer amplification. We achieved a detection sensitivity of 0.5% for the methylated genes of ACP1, CLEC11A, and SEPT9 by MB-MSP. It has a good linear relationship and a detection time of only 1.5 h. To validate the feasibility of the MB-MSP method in clinical application, we conducted methylation detection on plasma-circulating tumor DNA samples from 10 liver cancer patients and 5 healthy people, achieving a 100% accuracy rate. In conclusion, MB-MSP, as a novel and reliable DNA methylation detection tool, holds significant application value and potential for advancing early cancer diagnosis.

A flash signal amplification approach for ultrasensitive and rapid detection of single nucleotide polymorphisms in tuberculosis

In recent years, the demand for rapid, sensitive, and simple methods for diagnosing deoxyribonucleic acid (DNA) has grown due to the increase in the variation of infectious diseases. This work aimed to develop a flash signal amplification method coupled with electrochemical detection for polymerase chain reaction (PCR)-free tuberculosis (TB) molecular diagnosis. We exploited the slightly miscible properties of butanol and water to instantly concentrate a capture probe DNA, a single-stranded mismatch DNA, and gold nanoparticles (AuNPs) to a small volume to reduce the diffusion and reaction time in the solution. In addition, the electrochemical signal was enhanced once two strands of DNA were hybridized and bound to the surface of the gold nanoparticle at an ultra-high density. To eliminate non-specific adsorption and identify mismatched DNA, the self-assembled monolayers (SAMs) and Muts proteins were sequentially modified on the working electrode. This sensitive and specific approach can detect as low as attomolar levels of DNA targets (18 aM) and is successfully applied to detecting tuberculosis-associated single nucleotide polymorphisms (SNPs) in synovial fluid. More importantly, as this biosensing strategy can amplify the signal in only a few seconds, it possesses a great potential for point-of-care and molecular diagnosis applications.

Multi working mode SPR chip laboratory for high refractive index detection

The Fiber SPR chip laboratory has become a popular choice in biochemical detection. To meet the needs of different kinds of analytes for the detection range and number of channels of the chip, we proposed a multi-mode SPR chip laboratory based on microstructure fiber in this paper. The chip laboratory was integrated with microfluidic devices made from PDMS and detection units made of bias three-core fiber and dumbbell fiber. By injecting light into different cores of a bias three-core fiber, different detection areas of dumbbell fiber can be selected, enabling the chip laboratory to enter high refractive index detection, multi-channel detection and other working modes. In the high refractive index detection mode, the chip can detect liquid samples with a refractive index range of 1.571-1.595. In multi-channel detection mode, the chip can achieve dual parameter detection of glucose and GHK-Cu, with sensitivities of 4.16 nm/(mg/mL) and 9.729 nm/(mg/mL), respectively. Additionally, the chip can switch to temperature compensation mode. The proposed multi working mode SPR chip laboratory, based on micro structured fiber, offers a new approach for the development of portable testing equipment that can detect multiple analytes and meet multiple requirements.

Poly cytosine (C)/poly adenine (A) modified probe for signal "on-off-on" assay of single-base mismatched dsDNA by a competitive mechanism

Direct discrimination of single-base mismatched dsDNA by a simple method or strategy would provide enormous opportunities for applications in the fields of life sciences and disease diagnosis. Herein, the peroxidase-mimicking activity of a metal-organic framework nanoprobe (MOF) was well exploited for the direct discrimination of single-base mismatched dsDNA based on a competition-induced signal on-off-on mechanism. The single-base mismatched dsDNA related with FecB gene (usually guanine (G)/thymine (T) mismatch) and MIL-88B-NH₂ were used as target and MOF model, respectively. Firstly, polyA/polyC were loosely adsorbed onto the MOFs via the weak interaction to block the peroxidase activity of MOF, inducing the signal transition from on to off. Unexpectedly, the single-base mismatched (GT) dsDNA could reverse the signal response of MOF probe from off to on. But it could not occur for other nonspecific mismatches, such as CT and TT-mismatched dsDNA. A synergistic interaction mechanism between multiple GT mismatches and polyA/polyC was attempted to explain the competitive dissociation of polyA/polyC from MOF for the recovery of peroxidase activity. With it, a wide linear detection ranges from 10^-9 M-10^-5 M of GT mismatched dsDNA and a low detection limit of 0.247 nM could be achieved, even in the real samples. The effect of mismatched base number or position was also studied. Such a simple, rapid, cost-effective, and one-step mixing and checking method for single-base mismatched dsDNA discrimination eliminates the complex sample pretreatment, special DNA probe design, exclusive amplification or signal readout means. It thus offers a simple and effective route for direct discrimination of mismatched dsDNA and might hold a huge potential for the applications in gene analysis, disease diagnosis, and elementary research in life sciences.

Trace Determination of Grouper Nervous Necrosis Virus in Contaminated Larvae and Pond Water Samples Using Label-Free Fiber Optic Nanoplasmonic Biosensor

We developed a fast (<20 min), label-free fiber optic particle plasmon resonance (FOPPR) immunosensing method to detect nervous necrosis virus (NNV), which often infects high-value economic aquatic species, such as grouper. Using spiked NNV particles in a phosphate buffer as samples, the standard calibration curve obtained was linear (R2 = 0.99) and the limit of detection (LOD) achieved was 2.75 × 104 TCID50/mL, which is superior to that obtained using enzyme-linked immunosorbent assay (ELISA). By using an enhancement method called fiber optic nanogold-linked immunosorbent assay (FONLISA), the LOD can be further improved to <1 TCID50/mL, which is comparable to that found by the conventional qPCR method. Employing the larvae homogenate samples of NNV-infected grouper, the results obtained by the FOPPR biosensor agree with those obtained by the quantitative polymerase chain reaction (qPCR) method. We also examined pond water samples from an infected container in an indoor aquaculture facility. The lowest detectable level of NNV coat protein was found to be 0.17 μg/mL, which is one order lower than the LOD reported by ELISA. Therefore, we demonstrated the potential of the FOPPR biosensor as an outbreak surveillance tool, which is able to give warning indication even when the trend of larvae death toll increment is still not clear.

Quantitative and amplification-free detection of SOCS-1 CpG methylation percentage analyses in gastric cancer by fiber optic nanoplasmonic biosensor

A new innovative approach is essential for early and effective diagnosis of gastric cancer, using promoter hypermethylation of the tumor suppressor, SOCS-1, that is frequently inactivated in human cancers. We have developed an amplification-free fiber optic nanoplasmonic biosensor for detecting DNA methylation of the SOCS-1 human genome. The method is based on the fiber optic nanogold-linked sorbent assay of PCR-free DNA from human gastric tumor tissue and cell lines. We designed a specific DNA probe fabricated on the fiber core surface while the other probe is bioconjugated with gold nanoparticles in free form to allow percentage determination and differentiating the methylated and unmethylated cell lines, further demonstrating the SOCS-1 methylation occurs in cancer patients but not in normal cell lines. The observed detection limit is 0.81 fM for methylated DNA, and the detection time is within 15 min. In addition, our data were significantly correlated to the data obtained from PCR-based pyrosequencing, and yet with superior accuracy. Hence our results provide new insight to the quantitative evaluation of methylation status of the human genome and can act as an alternative to PCR with a great potential.

Integration of Power-Free and Self-Contained Microfluidic Chip with Fiber Optic Particle Plasmon Resonance Aptasensor for Rapid Detection of SARS-CoV-2 Nucleocapsid Protein

The global pandemic of COVID-19 has created an unrivalled need for sensitive and rapid point-of-care testing (POCT) methods for the detection of infectious viruses. For the novel coronavirus SARS-CoV-2, the nucleocapsid protein (N-protein) is one of the most abundant structural proteins of the virus and it serves as a useful diagnostic marker for detection. Herein, we report a fiber optic particle plasmon resonance (FOPPR) biosensor which employed a single-stranded DNA (ssDNA) aptamer as the recognition element to detect the SARS-CoV-2 N-protein in 15 min with a limit of detection (LOD) of 2.8 nM, meeting the acceptable LOD of 10⁶ copies/mL set by the WHO target product profile. The sensor chip is a microfluidic chip based on the balance between the gravitational potential and the capillary force to control fluid loading, thus enabling the power-free auto-flowing function. It also has a risk-free self-contained design to avoid the risk of the virus leaking into the environment. These findings demonstrate the potential for designing a low-cost and robust POCT device towards rapid antigen detection for early screening of SARS-CoV-2 and its related mutants.

Label-free optical biosensors in the pandemic era

The research in the field of optical biosensors is continuously expanding, thanks both to the introduction of brand new technologies and the ingenious use of established methods. A new awareness on the potential societal impact of this research has arisen as a consequence of the Covid-19 pandemic. The availability of a new generation of analytical tools enabling a more accurate understanding of bio-molecular processes or the development of distributed diagnostic devices with improved performance is now in greater demand and more clearly envisioned, but not yet achieved. In this review, we focus on emerging innovation opportunities conveyed by label-free optical biosensors. We review the most recent innovations in label-free optical biosensor technology in consideration of their competitive potential in selected application areas. The operational simplicity implicit to label-free detection can be exploited in novel rapid and compact devices for distributed diagnostic applications. The adaptability to any molecular recognition or conformational process facilitates the integration of DNA nanostructures carrying novel functions. The high sensitivity to nanoscale objects stimulates the development of ultrasensitive systems down to digital detection of single molecular binding events enhanced by nanoparticles and direct enumeration of bio-nanoparticles like viruses.

Advantages of optical fibers for facile and enhanced detection in droplet microfluidics

Droplet microfluidics offers a unique opportunity for ultrahigh-throughput experimentation with minimal sample consumption and thus has obtained increasing attention, particularly for biological applications. Detection and measurements of analytes or biomarkers in tiny droplets are essential for proper analysis of biological and chemical assays like single-cell studies, cytometry, nucleic acid detection, protein quantification, environmental monitoring, drug discovery, and point-of-care diagnostics. Current detection setups widely use microscopes as a central device and other free-space optical components. However, microscopic setups are bulky, complicated, not flexible, and expensive. Furthermore, they require precise optical alignments, specialized optical and technical knowledge, and cumbersome maintenance. The establishment of efficient, simple, and cheap detection methods is one of the bottlenecks for adopting microfluidic strategies for diverse bioanalytical applications and widespread laboratory use. Together with great advances in optofluidic components, the integration of optical fibers as a light guiding medium into microfluidic chips has recently revolutionized analytical possibilities. Optical fibers embedded in a microfluidic platform provide a simpler, more flexible, lower-cost, and sensitive setup for the detection of several parameters from biological and chemical samples and enable widespread, hands-on application much beyond thriving point-of-care developments. In this review, we examine recent developments in droplet microfluidic systems using optical fiber as a light guiding medium, primarily focusing on different optical detection methods such as fluorescence, absorbance, light scattering, and Raman scattering and the potential applications in biochemistry and biotechnology that are and will be arising from this.

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.