Microfluidic bead-based enzymatic primer extension for single-nucleotide discrimination using quantum dots as labels

The sensitive detection of IVSII-1(G˃A) mutation in beta globin gene using a Nano-based ligation genotyping system

Beta-thalassemia (β-thalassemia) is a globally genetic diseases, and is most prevalent in the Middle East, particularly in Iran. Carrier detection and prenatal diagnosis are the best ways to managing it, and to prevent new community cases from emerging. We report on a simple method for rapid detection of the worst β-thalassemia point mutation in Iran (IVS-II-1 G>A), using a nano-based ligation assay, this was performed using probes with labeled magnetic nanoparticles and quantum dots. After optimizing the technique, 50 DNA samples were genotyped with this method. We found a frequency of 72% for IVSII-1 (G˃A) mutation (42% heterozygote, and 30% mutant homozygote) with a highly sensitive nano-based ligation genotyping system, offering excellent sensitivity and specificity for point mutation detection; it has been demonstrated to be inaccurate, sensitive, cost-effective, and rapid technique for single nucleotide polymorphism (SNP) genotyping.

A dual discrimination mode for improved specificity towards let-7a detection via a single-base mutated padlock probe-based exponential rolling circle amplification

MicroRNA (miRNA) family members are usually highly homologous sequences, and it is a challenging task to selectively detect one miRNA member from other family members in medical diagnosis. Here, we describe the design of a dual discrimination mode for improved specificity towards let-7a detection over the other members of the let-7 family, in which an intentional base mutation was introduced into the padlock probe of an exponential rolling circle amplification. The inherent discrimination power of the padlock probe and the introduced base mutation constituted a dual discrimination mode, which provided enhanced specificity for let-7a, even over single-base mismatched family sequences. Furthermore, the assay enabled the quantitative detection of let-7a in a dynamic range from 200 amol to 100 fmol. This technique has also been successfully applied to real small RNA samples extracted from human lung cancers. For the first time, through intentionally mutating one base on the padlock probe of the exponential rolling circle amplification (RCA), we improved the discrimination capability for let-7 family members, while maintaining adequate sensitivity. Overall, this dual discrimination mode and the high amplification strategy have the potential to be extended to other short, but highly homologous, miRNA sequences.

Fluorescent detection of point mutation via ligase reaction assisted by quantum dots and magnetic nanoparticle-based probes

A nanodiagnostic genotyping method was presented for point mutation detection directly in human genomic DNA based on ligase reaction coupled with quantum dots and magnetic nanoparticle-based probes.

Numerical Study of the Electrothermal Effect on the Kinetic Reaction of Immunoassays for a Microfluidic Biosensor

In this work, we simulate the binding reaction of C-reactive protein in a microchannel of a biosensor. A problem that arises in this device concerns the transport of the analyte toward the reaction surface of the biosensor, which is of a very small dimension. The limitation of mass transport causes the formation of a diffusion boundary layer and restrains the whole kinetic reaction. To enhance the performance of the biosensor by improving the transport, an applied AC electric field and flow confinement are used to stir the flow field. The numerical simulation of these mechanisms on the binding reaction is performed using the finite element method. Swirling patterns are generated in the fluid. They enhance the transport of the analyte and confine it near the reaction surface. The location of the electrode pair on the walls of the microchannel for the design of the biosensor has been studied to find out the effects of varying geometric configurations on the binding efficiency. The best performances of the biosensor are obtained when the electrodes are placed on the same wall of the microchannel as the reaction surface. For the best case, under the effect of the applied electric field alone, the enhancement factors raise up to 2.46 and 2.10 for the association and dissociation phases, respectively. By contrast, under the effect of the electric field with flow confinement, the enhancement factors for the association and the dissociation phases jump to 3.43 and 2.97, respectively, for 30:1 flow confinement (ratio of confining to sample flow).

Nano-enabled bioanalytical approaches to ultrasensitive detection of low abundance single nucleotide polymorphisms

A survey of the recent, significant developments on nanomaterials enabled ultrasensitive DNA and gene mutation assays is presented.

Single nucleotide polymorphisms (SNPs) constitute the most common types of genetic variations in the human genome. A number of SNPs have been linked to the development of life threatening diseases including cancer, cardiovascular diseases and neurodegenerative diseases. The ability for ultrasensitive and accurate detection of low abundant disease-related SNPs in bodily fluids (e.g. blood, serum, etc.) holds a significant value in the development of non-invasive future biodiagnostic tools. Over the past two decades, nanomaterials have been utilized in a myriad of biosensing applications due to their ability of detecting extremely low quantities of biologically important biomarkers with high sensitivity and accuracy. Of particular interest is the application of such technologies in the detection of SNPs. The use of various nanomaterials, coupled with different powerful signal amplification strategies, has paved the way for a new generation of ultrasensitive SNP biodiagnostic assays. Over the past few years, several ultrasensitive SNP biosensors capable of detecting specific targets down to the ultra-low regimes (ca. aM and below) and therefore holding great promises for early clinical diagnosis of diseases have been developed. This mini review will highlight some of the most recent, significant advances in nanomaterial-based ultrasensitive SNP sensing technologies capable of detecting specific targets on the attomolar (10^–18 M) regime or below. In particular, the design of novel, powerful signal amplification strategies that hold the key to the ultrasensitivity is highlighted.

Sensitive, quantitative, and high-throughput detection of angiogenic markers using shape-coded hydrogel microparticles

Demonstration of the application of shape coded hydrogel microparticles for multiplexed detection of angiogenic molecules. Utilization of single fluorophore eliminates the spectral overlap associated with microparticle based multiplexed analysis.

Aptamer-based microfluidic beads array sensor for simultaneous detection of multiple analytes employing multienzyme-linked nanoparticle amplification and quantum dots labels

This study reports the development of an aptamer-mediated microfluidic beads-based sensor for multiple analytes detection and quantification using multienzyme-linked nanoparticle amplification and quantum dots labels. Adenosine and cocaine were selected as the model analytes to validate the assay design based on strand displacement induced by target-aptamer complex. Microbeads functionalized with the aptamers and modified electron rich proteins were arrayed within a microfluidic channel and were connected with the horseradish peroxidases (HRP) and capture DNA probe derivative gold nanoparticles (AuNPs) via hybridization. The conformational transition of aptamer induced by target-aptamer complex contributes to the displacement of functionalized AuNPs and decreases the fluorescence signal of microbeads. In this approach, increased binding events of HRP on each nanosphere and enhanced mass transport capability inherent from microfluidics are integrated for enhancing the detection sensitivity of analytes. Based on the dual signal amplification strategy, the developed aptamer-based microfluidic bead array sensor could discriminate as low as 0.1 pM of adenosine and 0.5 pM cocaine, and showed a 500-fold increase in detection limit of adenosine compared to the off-chip test. The results proved the microfluidic-based method was a rapid and efficient system for aptamer-based targets assays (adenosine (0.1 pM) and cocaine (0.5 pM)), requiring only minimal (microliter) reagent use. This work demonstrated the successful application of aptamer-based microfluidic beads array sensor for detection of important molecules in biomedical fields.

Microfluidic beads-based immunosensor for sensitive detection of cancer biomarker proteins using multienzyme-nanoparticle amplification and quantum dots labels

This study reports the development of a microfluidic beads-based immunosensor for sensitive detection of cancer biomarker α-fetoprotein (AFP) that uses multienzyme-nanoparticle amplification and quantum dots labels. This method utilizes microbeads functionalized with the capture antibodies (Ab₁) and modified electron rich proteins as sensing platform that was fabricated within a microfluidic channel, and uses gold nanoparticles (AuNPs) functionalized with the horseradish peroxidase (HRP) and the detection antibodies (Ab₂) as label. Greatly enhanced sensitivity for the cancer biomarker is based on a dual signal amplification strategy: first, the large surface area of Au nanoparticle carrier allows several binding events of HRP on each nanosphere. Enhanced sensitivity was achieved by introducing the multi-HRP-antibody functionalized AuNPs onto the surface of microbeads through "sandwich" immunoreactions and subsequently multiple biotin moieties could be deposited onto the surface of beads resulted from the oxidation of biotin-tyramine by hydrogen peroxide. Streptavidin-labeled quantum dots were then allowed to bind to the deposited biotin moieties and displayed the signal. Secondly, enhanced mass transport capability inherent from microfluidics leads to higher capture efficiency of targets because continuous flow within micro-channel delivers fresh analyte solution to the reaction site which maintains a high concentration gradient differential to enhance mass transport. Based on the dual signal amplification strategy, the developed microfluidic bead-based immunosensor could discriminate as low as 0.2 pg mL⁻¹ AFP in 10 μL of undiluted calf serum (0.2 fg/chip), and showed a 500-fold increase in detection limit compared to the off-chip test and 50-fold increase in detection limit compared to microfluidic beads-based immunoassay using single label HRP-Ab₂. The immunosensor showed acceptable repeatability and reproducibility. This microfluidic beads-based immunosensor is a promising platform for disease-related biomolecules at the lowest level at their earliest incidence.