Electrochemical detection of DNA hybridization based on bio-bar code method

Colorimetric determination of carbendazim based on the specific recognition of aptamer and the poly-diallyldimethylammonium chloride aggregation of gold nanoparticles

This paper proposes the idea of establishing carbendazim (CBZ) colorimetric determination in spiked water samples by specific aptamers of unlabeled carbendazim (CBZ), gold nanoparticles (AuNPs) and cationic polymer poly-diallyldimethylammonium chloride (PDDA). In the absence of CBZ, the CBZ aptamer will react with the cationic polymer PDDA by electrostatic interaction to form a complex structure. Therefore, the gold nanoparticles will remain dispersed due to the lack of PDDA. However, when CBZ is added into the sensory system, the CBZ-specific aptamer can selectively capture CBZ to form a stable complex structure. Due to the consumption of the aptamer, PDDA is unable to interact with the aptamer and begins to induce aggregation of AuNPs, thereby causing the color of the solution to change from red to blue. Colorimetric determination of CBZ based on the specific recognition of aptamer and the PDDA-induced aggregation of AuNPs has a detection limit of 2.2 nM, a linear range (R = 0.9960) from 2.2 to 500 nM. The method has good sensitivity and specificity, and the average recovery of CBZ is 94.9-104.8% in the application of actual water samples. This colorimetric method is simple, time-saving and low requirements for equipment, therefore, it holds great potential for CBZ detection in the environmental water samples.

Investigating the potential of multiwalled carbon nanotubes based zinc nanocomposite as a recognition interface towards plant pathogen detection

The emergence of nanotechnology has opened new horizons for constructing efficient recognition interfaces. This is the first report where the potential of a multiwalled carbon nanotube based zinc nanocomposite (MWCNTs-Zn NPs) investigated for the detection of an agricultural pathogen i.e. Chili leaf curl betasatellite (ChLCB). Atomic force microscope analyses revealed the presence of multiwalled carbon nanotubes (MWCNTs) having a diameter of 50-100nm with zinc nanoparticles (Zn-NPs) of 25-500nm. In this system, these bunches of Zn-NPs anchored along the whole lengths of MWCNTs were used for the immobilization of probe DNA strands. The electrochemical performance of DNA biosensor was assessed in the absence and presence of the complementary DNA during cyclic and differential pulse voltammetry scans. Target binding events occurring on the interface surface patterned with single-stranded DNA was quantitatively translated into electrochemical signals due to hybridization process. In the presence of complementary target DNA, as the result of duplex formation, there was a decrease in the peak current from 1.89×10^-04 to 5.84×10^-05A. The specificity of this electrochemical DNA biosensor was found to be three times as compared to non-complementary DNA. This material structuring technique can be extended to design interfaces for the recognition of the other plant viruses and biomolecules.

Sub-attomolar electrochemical measurement of DNA hybridization based on the detection of high coverage biobarcode latex labels at PNA-modified screen printed electrodes

We have constructed biobarcode labels based on 468nm diameter latex spheres. Modification with polyallylamine and then glutaraldehyde was used to attach a high DNA loading, consisting of aminated probe DNA (approx. 1.01×10² molecules per sphere) and biobarcode DNA (approx. 1.66×10⁴ molecules per sphere). Detection of the biobarcodes was performed by application of a Ag enhancer solution, causing association of the Ag⁺ ions with the phosphate groups of the DNA. The deposited Ag was detected by differential pulse voltammetry. A 30 mer sequence from the BL21 strain of E. coli was detected with an LOD of 2.6fM (calibration range 10 aM to 0.1pM, r²=0.91, n=45). The LOD was lowered to 0.56aM (calibration range 100zM to 0.1nM, r²=0.991, n=50) by utilizing a sandwich assay with PNA-modified screen printed electrodes, which lowered the Ag background current. The sandwich assay platform was used to calibrate E. coli strain BL2(DE3) with an LOD of 17.0 CFU mL^-1 (calibration range 10 to 10⁶ CFU mL^-1, r²=0.99, n=33) with good discrimination against Salmonella.

Fractal circuit sensors enable rapid quantification of biomarkers for donor lung assessment for transplantation

Biomarker profiling is being rapidly incorporated in many areas of modern medical practice to improve the precision of clinical decision-making. This potential improvement, however, has not been transferred to the practice of organ assessment and transplantation because previously developed gene-profiling techniques require an extended period of time to perform, making them unsuitable in the time-sensitive organ assessment process. We sought to develop a novel class of chip-based sensors that would enable rapid analysis of tissue levels of preimplantation mRNA markers that correlate with the development of primary graft dysfunction (PGD) in recipients after transplant. Using fractal circuit sensors (FraCS), three-dimensional metal structures with large surface areas, we were able to rapidly (<20 min) and reproducibly quantify small differences in the expression of interleukin-6 (IL-6), IL-10, and ATP11B mRNA in donor lung biopsies. A proof-of-concept study using 52 human donor lungs was performed to develop a model that was used to predict, with excellent sensitivity (74%) and specificity (91%), the incidence of PGD for a donor lung. Thus, the FraCS-based approach delivers a key predictive value test that could be applied to enhance transplant patient outcomes. This work provides an important step toward bringing rapid diagnostic mRNA profiling to clinical application in lung transplantation.

Ultrasensitive electrochemical biomolecular detection using nanostructured microelectrodes

Electrochemical sensors have the potential to achieve sensitive, specific, and low-cost detection of biomolecules--a capability that is ever more relevant to the diagnosis and monitored treatment of disease. The development of devices for clinical diagnostics based on electrochemical detection could provide a powerful solution for the routine use of biomarkers in patient treatment and monitoring and may overcome the many issues created by current methods, including the long sample-to-answer times, high cost, and limited prospects for lab-free use of traditional polymerase chain reaction, microarrays, and gene-sequencing technologies. In this Account, we summarize the advances in electrochemical biomolecular detection, focusing on a new and integrated platform that exploits the bottom-up fabrication of multiplexed electrochemical sensors composed of electrodeposited noble metals. We trace the evolution of these sensors from gold nanoelectrode ensembles to nanostructured microelectrodes (NMEs) and discuss the effects of surface morphology and size on assay performance. The development of a novel electrocatalytic assay based on Ru(3+) adsorption and Fe(3+) amplification at the electrode surface as a means to enable ultrasensitive analyte detection is discussed. Electrochemical measurements of changes in hybridization events at the electrode surface are performed using a simple potentiostat, which enables integration into a portable, cost-effective device. We summarize the strategies for proximal sample processing and detection in addition to those that enable high degrees of sensor multiplexing capable of measuring 100 different analytes on a single chip. By evaluating the cost and performance of various sensor substrates, we explore the development of practical lab-on-a-chip prototype devices. By functionalizing the NMEs with capture probes specific to nucleic acid, small molecule, and protein targets, we can successfully detect a wide variety of analytes at clinically relevant concentrations and speeds. Using this platform, we have achieved attomolar detection levels of nucleic acids with overall assay times as short as 2 min. We also describe the adaptation of the sensing platform to allow for the measurement of uncharged analytes--a challenge for reporter systems that rely on the charge of an analyte. Furthermore, the capabilities of this system have been applied to address the many current and important clinical challenges involving the detection of pathogenic species, including both bacterial and viral infections and cancer biomarkers. This novel electrochemical platform, which achieves large molecular-to-electrical amplification by means of its unique redox-cycling readout strategy combined with rapid and efficient analyte capture that is aided by nanostructured microelectrodes, achieves excellent specificity and sensitivity in clinical samples in which analytes are present at low concentrations in complex matrices.

An electrochemiluminescence strategy based on aptamers and nanoparticles for the detection of cancer cells

A PCR (polymerase chain reaction)-free electrochemiluminescence (ECL) strategy based on aptamers and ECL nanoprobes was developed for rapid collection and detection of Ramos cells. The ECL nanoprobes consisted of gold nanoparticles (AuNPs), linker DNA and tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled signal DNA. The linker DNA and signal DNA were modified on the surface of the AuNPs through AuS bonds. The linker DNA can hybridize partly with the aptamers loaded on the magnetic beads to construct the magnetic biocomplex. In the presence of the cancer cells, the aptamers conjugated with the cancer cells with higher affinity. The ECL nanoprobe released from the biocomplex and subsequently hybridized with the capture DNA modified on the Au electrode. The ECL intensity of the TBR loaded on the nanoprobes directly reflected the amount of the cancer cells. With the use of the developed ECL probe, a limit of detection as low as 50 Ramos cells per mL could be achieved. The proposed methods based on ECL should have wide applications in the diagnosis of cancers due to their high sensitivity, simplicity and low cost.

Detection of non-PCR amplified S. enteritidis genomic DNA from food matrices using a gold-nanoparticle DNA biosensor: a proof-of-concept study

Bacterial pathogens pose an increasing food safety and bioterrorism concern. Current DNA detection methods utilizing sensitive nanotechnology and biosensors have shown excellent detection, but require expensive and time-consuming polymerase chain reaction (PCR) to amplify DNA targets; thus, a faster, more economical method is still essential. In this proof-of-concept study, we investigated the ability of a gold nanoparticle-DNA (AuNP-DNA) biosensor to detect non-PCR amplified genomic Salmonella enterica serovar Enteritidis (S. enteritidis) DNA, from pure or mixed bacterial culture and spiked liquid matrices. Non-PCR amplified DNA was hybridized into sandwich-like structures (magnetic nanoparticles/DNA/AuNPs) and analyzed through detection of gold voltammetric peaks using differential pulse voltammetry. Our preliminary data indicate that non-PCR amplified genomic DNA can be detected at a concentration as low as 100 ng/mL from bacterial cultures and spiked liquid matrices, similar to reported PCR amplified detection levels. These findings also suggest that AuNP-DNA biosensors are a first step towards a viable detection method of bacterial pathogens, in particular, for resource-limited settings, such as field-based or economically limited conditions. Future efforts will focus on further optimization of the DNA extraction method and AuNP-biosensors, to increase sensitivity at lower DNA target concentrations from food matrices comparable to PCR amplified DNA detection strategies.

Enabling fiber optic serotyping of pathogenic bacteria through improved anti-fouling functional surfaces

Significant research efforts are continually being directed towards the development of sensitive and accurate surface plasmon resonance biosensors for sequence specific DNA detection. These sensors hold great potential for applications in healthcare and diagnostics. However, the performance of these sensors in practical usage scenarios is often limited due to interference from the sample matrix. This work shows how the co-immobilization of glycol(PEG) diluents or 'back filling' of the DNA sensing layer can successfully address these problems. A novel SPR based melting assay is used for the analysis of a synthetic oligomer target as well as PCR amplified genomic DNA extracted from Legionella pneumophila. The benefits of sensing layer back filling on the assay performance are first demonstrated through melting analysis of the oligomer target and it is shown how back filling enables accurate discrimination of Legionella pneumophila serogroups directly from the PCR reaction product with complete suppression of sensor fouling.

Label free DNA detection based on gold nanoparticles quenching fluorescence of Rhodamine B

A novel and sensitive label free DNA detection method using gold nanoparticles (GNPs) and Rhodamine B (RB) has been developed. The assay is based on the following two properties. One is the different adsorption properties of single-stranded and double-stranded DNA on GNPs in colloidal solution. The other is the different quenching ability of aggregated GNPs and dispersed GNPs on RB. Un-aggregated GNPs could effectively quench the fluorescence of RB. However, the quenching ability greatly decreases after GNPs aggregated. The hybridization of probe DNA and target DNA is monitored by the fluorescence detection after the RB is added to the solution. Under the optimal experimental conditions, the detection limit of this assay is 2.9×10(-13) mol L(-1).

Evanescent wave fluorescence biosensor combined with DNA bio-barcode assay for platelet genotyping

An evanescent wave fluorescence biosensor was combined with a DNA bio-barcode assay to resolve problems met in detection of poor biologic samples. Human platelet antigen (HPA) genotyping was used as a demonstrator. Our bio-barcode assay was based on magnetic carboxylatex particles and non-magnetic carboxylatex particles, both functionalized with oligonucleotides. It was assessed for detecting 84mer synthetic oligonucleotides as targets. The assay allows to specifically detect single nucleotide polymorphism with a detection limit of 2 pM of target nucleic acids. The fluorescence detection is achieved in 150 s.

Nanomaterials as analytical tools for genosensors

Nanomaterials are being increasingly used for the development of electrochemical DNA biosensors, due to the unique electrocatalytic properties found in nanoscale materials. They offer excellent prospects for interfacing biological recognition events with electronic signal transduction and for designing a new generation of bioelectronic devices exhibiting novel functions. In particular, nanomaterials such as noble metal nanoparticles (Au, Pt), carbon nanotubes (CNTs), magnetic nanoparticles, quantum dots and metal oxide nanoparticles have been actively investigated for their applications in DNA biosensors, which have become a new interdisciplinary frontier between biological detection and material science. In this article, we address some of the main advances in this field over the past few years, discussing the issues and challenges with the aim of stimulating a broader interest in developing nanomaterial-based biosensors and improving their applications in disease diagnosis and food safety examination.

Aptamer based electrochemical assay for the determination of thrombin by using the amplification of the nanoparticles

A novel electrochemical assay based on the aptamer and the signal of amplification of nanoparticles (NPs) was constructed for the determination of thrombin. Aptamers immobilized on the electrode and Au NPs could be assembled with the target protein to form a sandwich structure in the presence of the latter. Differential pulse voltammetry (DPV) was employed to detect the CdS NPs loaded on the surface of the Au NPs through the linker DNA, which was related to the concentration of the target protein. The assay took advantage of the amplification ability of Au nanoparticles carrying multiplex CdS NPs and the specific affinity of aptamers. Thrombin was detected in this assay in the linear range of 1.0x10(-15) to 1.0x10(-11) M with the detection limit of 5.5x10(-16) M of target protein. In addition, the assay could be used to detection thrombin in real samples with high sensitivity and good selectivity.