Microfluidics-based lab-on-chip systems in DNA-based biosensing: An overview.

Microfluidics-based lab-on-chip (LOC) systems are an active research area that is revolutionising high-throughput sequencing for the fast, sensitive and accurate detection of a variety of pathogens. LOCs also serve as portable diagnostic tools. The devices provide optimum control of nanolitre volumes of fluids and integrate various bioassay operations that allow the devices to rapidly sense pathogenic threat agents for environmental monitoring. LOC systems, such as microfluidic biochips, offer advantages compared to conventional identification procedures that are tedious, expensive and time consuming. This paper aims to provide a broad overview of the need for devices that are easy to operate, sensitive, fast, portable and sufficiently reliable to be used as complementary tools for the control of pathogenic agents that damage the environment

Detection and control of Ganoderma boninense : strategies and perspectives

The oil palm, an economically important tree, has been one of the world’s major sources of edible oil and a significant precursor of biodiesel fuel. Unfortunately, it now faces the threat of a devastating disease. Many researchers have identified Ganoderma boninense as the major pathogen that affects the oil palm tree and eventually kills it. But identification of the pathogen is just the first step. No single method has yet been able to halt the continuing spread of the disease. This paper discusses the modes of infection and transmission of Ganoderma boninense and suggests techniques for its early detection. Additionally, the paper proposes some possible ways of controlling the disease. Such measures, if implemented, could contribute significantly to the sustainability of the palm oil industry in South East Asia

A novel DNA nanosensor based on CdSe/ZnS quantum dots and synthesized Fe3O4 magnetic nanoparticles

Although nanoparticle-enhanced biosensors have been extensively researched, few studies have systematically characterized the roles of nanoparticles in enhancing biosensor functionality. This paper describes a successful new method in which DNA binds directly to iron oxide nanoparticles for use in an optical biosensor. A wide variety of nanoparticles with different properties have found broad application in biosensors because their small physical size presents unique chemical, physical, and electronic properties that are different from those of bulk materials. Of all nanoparticles, magnetic nanoparticles are proving to be a versatile tool, an excellent case in point being in DNA bioassays, where magnetic nanoparticles are often used for optimization of the hybridization and separation of target DNA. A critical step in the successful construction of a DNA biosensor is the efficient attachment of biomolecules to the surface of magnetic nanoparticles. To date, most methods of synthesizing these nanoparticles have led to the formation of hydrophobic particles that require additional surface modifications. As a result, the surface to volume ratio decreases and nonspecific bindings may occur so that the sensitivity and efficiency of the device deteriorates. A new method of large-scale synthesis of iron oxide (Fe3O4) nanoparticles which results in the magnetite particles being in aqueous phase, was employed in this study. Small modifications were applied to design an optical DNA nanosensor based on sandwich hybridization. Characterization of the synthesized particles was carried out using a variety of techniques and CdSe/ZnS core-shell quantum dots were used as the reporter markers in a spectrofluorophotometer. We showed conclusively that DNA binds to the surface of ironoxide nanoparticles without further surface modifications and that these magnetic nanoparticles can be efficiently utilized as biomolecule carriers in biosensing devices

DNA-based biosensor for detection of ganoderma boninense, an oil palm pathogen utilizing newly synthesized ruthenium complex [Ru(phen)2,(qtpy)]2+ based on a PEDOT-PSS/Ag nanoparticles modified electrode

An electrochemical DNA biosensor has been developed for detection of ganoderma boninense, an oil palm pathogen utilizing newly synthesized ruthenium [Ru(phen)2,(qtpy)]2+ complex as hybridization indicator. The sensor incorporated the use of a gold electrode (AuE), modified with a conducting nanocomposite of poly(3,4-ethylene-dioxythiophen) -poly(styrenesulfonate) (PEDOT-PSS) and silver nanoparticles (AgNPs). A specific sequence of a ganoderma boninense DNA probe has been immobilized on the modified electrode and the hybridization event was monitored via intercalation of the ruthenium complex to the hybridized DNA. Effect of hybridization temperature and time was evaluated and found to be optimal at 45 °C in 25 minutes for the hybridization. Detection of target DNA ranged from 1.0 x 10-15 M to 1.0 × 10-9 M was performed, and a correlation relationship of 0.9756 and detection limit of 5 × 10-16 M were obtained. The newly synthesized ruthenium complex was able to be used is a novel redox marker and can be adopted for routine detection of DNA

An electrochemical biosensor for the determination of Ganorderma boninense pathogen based on a novel modified gold nanocomposite film electrode

A sensitive approach for the determination of Ganoderma boninense DNA is reported based on an electrochemical affinity system using a modified gold sensor. Covalent attachment of probe DNA was achieved by attachment of the amine group to a carboxylic acid group of a 3,3’-dithiodipropionic acid monolayer on a nanocomposite film of gold nanoparticles bound to poly(3,4-ethylenedioxythiophen)–poly(styrenesulfonate) on a gold working electrode. The electrochemical detection of sequence-specific DNA of probe and target DNA hybridization was monitored using a new ruthenium complex [Ru(dppz) 2 (qtpy)Cl 2 ; dppz = dipyrido [3,2–a:2’,3’-c] phenazine; qtpy = 2,2’,-4,4”.4’4”’-quarterpyridyl redox marker. The potential was selected through the study of the electrochemical behavior of trisaminomethane-hydrochloride containing a ethylenediaminetetraacetic acid supporting electrolyte on the bare and modified gold electrode. The effect of the hybridization temperature and time were measured. The sensor demonstrated specific detection for the target over a concentration range of 1.0 × 10− 15 M to 1.0 × 10− 9 M with a detection limit of 1.59 × 10− 17 M. Control experiments verified the specificity of the biosensor in the presence of a single mismatched DNA sequence. This detection technology was shown to be effective in terms of sensitivity and selectivity of hybridization events and is a promising device for early detection of Ganoderma boninense and other pathogenic threat agents

Conductivity of Pedot-Pss with Gold and Silver Nanocomposites Modified Gold Electrodes for Ganoderma Boninense DNA Detection

The conductivity of a designed electrochemical DNA biosensor was improved using gold and or silver nanoparticles. A gold electrode modified with a conductive nanocomposite of poly(3,4-ethylene dioxythiophen)–poly (styrenesulfonate) (Pedot-Pss) and gold or silver nano particles enhanced the conductivity of the electrode surface area. Bare and modified gold electrode surfaces were characterized using cyclic voltammetry (CV) technique in ethylenediaminetetraacetic acid (TE) supporting electrolyte. Immobilization of a 20-mer DNA probe was achieved by covalent attachment of the amine group of the capture probe to a carboxylic group of an activated 3,3’-dithiodipropionic acid layer using EDC/NHSS for Hybridization. The effect of hybridization temperature and time was optimized and the sensor demonstrated specific detection for the target concentration ranged between 1.0´10-15 M to 1.0´10-9 M with a detection limit of 9.70´10-19 M. Control experiments verified the specificity of the biosensor in the presence of mismatched DNA sequence. The DNA hybridization was monitored using a new ruthenium complex [Ru(dppz)2(qtpy)Cl2; dppz = dipyrido [3,2–a:2’,3’-c] phenazine; qtpy=2,2’,-4,4”.4’4”’-quarterpyridyl redox indicator

A modified electrode for detection of biological material

The present invention relates to a modified electrode for detection of biological material. The modified electrode is used in electrochemical DNA biosensor for detecting Ganoderma boninense. The modified electrode comprises of a polymer, a nanoparticles and an oligonucleotide probe. Utilization of the modified electrode in detecting Ganoderma boninense enhances sensitivity of the detection

Facilitating the indirect detection of genomic DNA in an electrochemical DNA biosensor using magnetic nanoparticles and DNA ligase

A common problem in applying biosensors for the detection of genomic DNA is detecting short sequences in large amounts of long double stranded DNA. A gold electrode modified with a conductive nanocomposite, poly(3,4-ethylene-dioxythiophene), and gold nanoparticles was functionalized with 2,6-Pyridinedicarboxylic acid. Immobilization of a 20-mer DNA probe as the bioreceptor was successfully carried out via a peptide bond on the surface of the modified electrode. Two segments of 15 and 20 base probes were designed and named as Capture and Reporter probes respectively. The 20-mer Reporter probe was complementary to the bioreceptor and the 15-mer Capture probe was designed to bind on to the surface of the iron oxide magnetic nanoparticles. A 35-base Target DNA complementary to the Capture and the Reporter probes was used as Template in the ligation process, with the ligation between the Reporter and Capture probes mediated by T4 ligase. Iron oxide magnetic nanoparticles functionalized with carboxylic groups on their surface synthesized in a new method were attached to the 15-mer Capture probe. After the denaturation of the final ligation product, the separation of the attached probes was carried out using 5 G permanent magnets in a three step washing procedure in TE buffer. The hybridization of the DNA bioreceptor and the Reporter probe attached to the Capture probe-Fe3O4 was monitored via oxidation and reduction of the new redox marker (ruthenium complex) intercalated into the double helix. This technique was found to be reliably repeatable. The indirect detection of genomic DNA using this method is significantly improved and showed high efficiency in small amounts of samples with the detection limit of 5.37 × 10−14 M