A Universal Nucleic Acid Sequence Biosensor with Nanomolar Detection Limits

Loop-mediated isothermal amplification for rapid detection of Bacillus anthracis spores

A loop-mediated isothermal amplification (LAMP) assay system was employed for detecting Bacillus anthracis spores in pure cultures as well as in various simulated powder samples. The specificity of the designed LAMP primer sets was validated by assaying 13 B. anthracis strains and 33 non-B. anthracis species. The detection limits of the LAMP assay were 10 spores/tube for pure cultures and 100 spores/2 mg powder for simulated powder samples. The results show that the LAMP protocol is a promising method for detecting B. anthracis.

Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography

Widely used nucleic acid assays are poorly suited for field deployment where access to laboratory instrumentation is limited or unavailable. The need for field deployable nucleic acid detection demands inexpensive, facile systems without sacrificing information capacity or sensitivity. Here we describe a novel microarray platform capable of rapid, sensitive nucleic acid detection without specialized instrumentation. The approach is based on a miniaturized lateral flow device that makes use of hybridization-mediated target capture. The miniaturization of lateral flow nucleic acid detection provides multiple advantages over traditional lateral flow devices. Ten-microliter sample volumes reduce reagent consumption and yield analyte detection times, excluding sample preparation and amplification, of <120 s while providing sub-femtomole sensitivity. Moreover, the use of microarray technology increases the potential information capacity of lateral flow. Coupled with a hybridization-based detection scheme, the lateral flow microarray (LFM) enables sequence-specific detection, opening the door to highly multiplexed implementations for broad-range assays well suited for point-of-care and other field applications. The LFM system is demonstrated using an isothermal amplification strategy for detection of Bacillus anthracis, the etiologic agent of anthrax. RNA from as few as two B. anthracis cells was detected without thermocycling hardware or fluorescence detection systems.

Antioxidant redox sensors based on DNA modified carbon screen-printed electrodes

Antioxidant redox sensors based on DNA modified carbon screen-printed electrodes were developed. The carbon ink was doped with TiO2 nanoparticles, onto which double-strand DNA was adsorbed. A redox mediator, namely, tris-2,2'-bipyridine ruthenium(II) [Ru(bpy)3(2+)] was electrooxidized on the electrode surface to subsequently oxidize both the adsorbed ds-DNA and the antioxidants in solution. The resulting oxidation damage of the adsorbed ds-DNA was then detected by square wave voltammetry in a second solution containing only Ru(bpy)3Cl2 at a low concentration (microM). A kinetic model was developed to study the protecting role of antioxidants in aqueous solutions. The electrochemical sensor has been applied to evaluate the redox antioxidant capacity of different molecules.

Antioxidant sensors based on DNA-modified electrodes

TiO2/ITO modified electrodes were developed to quantitatively photooxidize adsorbed ds-DNA and to study the effect of antioxidants as ds-DNA protecting agents. TiO2 films are used for efficient ds-DNA immobilization, for ds-DNA oxidation through photogenerated hydroxyl radicals, and as electrodes for amperometric sensing. The films, prepared by a sol-gel process, are deposited on ITO glass electrodes. Damages occurring after ds-DNA oxidation by ROS are detected by adding MB as an intercalant probe and by monitoring the electrochemical reduction current of the intercalated redox probe. The MB electrochemical signal is found to be sensitive enough to monitor ds-DNA structure changes, and the electrochemical sensor has been applied to the evaluation of the antioxidant properties of glutathione and gallic acid.

Fiber-optic microsphere-based arrays for multiplexed biological warfare agent detection

We report a multiplexed high-density DNA array capable of rapid, sensitive, and reliable identification of potential biological warfare agents. An optical fiber bundle containing 6000 individual 3.1-mum-diameter fibers was chemically etched to yield microwells and used as the substrate for the array. Eighteen different 50-mer single-stranded DNA probes were covalently attached to 3.1-mum microspheres. Probe sequences were designed for Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella melitensis, Clostridium botulinum, Vaccinia virus, and one biological warfare agent (BWA) simulant, Bacillus thuringiensis kurstaki. The microspheres were distributed into the microwells to form a randomized multiplexed high-density DNA array. A detection limit of 10 fM in a 50-microL sample volume was achieved within 30 min of hybridization for B. anthracis, Y. pestis, Vaccinia virus, and B. thuringiensis kurstaki. We used both specific responses of probes upon hybridization to complementary targets as well as response patterns of the multiplexed array to identify BWAs with high accuracy. We demonstrated the application of this multiplexed high-density DNA array for parallel identification of target BWAs in spiked sewage samples after PCR amplification. The array's miniaturized feature size, fabrication flexibility, reusability, and high reproducibility may enable this array platform to be integrated into a highly sensitive, specific, and reliable portable instrument for in situ BWA detection.

RNA Internal Standard Synthesis by Nucleic Acid Sequence-Based Amplification for Competitive Quantitative Amplification Reactions

Nucleic acid sequence-based amplification (NASBA) reactions have been demonstrated to successfully synthesize new sequences based on deletion and insertion reactions. Two RNA internal standards were synthesized for use in competitive amplification reactions in which quantitative analysis can be achieved by coamplifying the internal standard with the wild type sample. The sequences were created in two consecutive NASBA reactions using the E. coli clpB mRNA sequence as model analyte. The primer sequences of the wild type sequence were maintained, and a 20-nt-long segment inside the amplicon region was exchanged for a new segment of similar GC content and melting temperature. The new RNA sequence was thus amplifiable using the wild type primers and detectable via a new inserted sequence. In the first reaction, the forwarding primer and an additional 20-nt-long sequence was deleted and replaced by a new 20-nt-long sequence. In the second reaction, a forwarding primer containing as 5' overhang sequence the wild type primer sequence was used. The presence of pure internal standard was verified using electrochemiluminescence and RNA lateral-flow biosensor analysis. Additional sequence deletion in order to shorten the internal standard amplicons and thus generate higher detection signals was found not to be required. Finally, a competitive NASBA reaction between one internal standard and the wild type sequence was carried out proving its functionality. This new rapid construction method via NASBA provides advantages over the traditional techniques since it requires no traditional cloning procedures, no thermocyclers, and can be completed in less than 4 h.

Optimization of DNA-tagged dye-encapsulating liposomes for lateral-flow assays based on sandwich hybridization

A novel protocol for the synthesis of dye-encapsulating liposomes tagged with DNA oligonucleotides at their outer surface was developed. These liposomes were optimized for use as signal enhancement agents in lateral-flow sandwich-hybridization assays for the detection of single-stranded RNA and DNA sequences. Liposomes were synthesized using the reverse-phase evaporation method and tagged with oligonucleotides by adding cholesteryl-modified DNA probes to the initial lipid mixture. This resulted in a greatly simplified protocol that provided excellent control of the probe coverage on the liposomes and cut the preparation time from 16 hours to just 6 hours. Liposomes were prepared using probe concentrations ranging from 0.00077 to 0.152 mol% of the total lipid, several hydrophobic and polyethylene glycol-based spacers between the cholesteryl anchor and the probe, and liposome diameters ranging from 208 nm to 365 nm. The liposomes were characterized by dynamic light scattering, visible spectroscopy, and fluorescence spectroscopy. Their signal enhancement functionality was compared by using them in lateral-flow optical biosensors for the detection of single-stranded DNA sequences. In these assays, an optimal reporter probe concentration of 0.013 mol%, liposome diameter of 315 nm, and liposome optical density of 0.4-0.6 at 532 nm were found. The spacer length between the cholesteryl anchor and the probe showed no significant effect on the signals in the lateral-flow assays. The results presented here provide important data for the general use of liposomes as labels in analytical assays, with specific emphasis on nucleic acid detection via lateral flow assays.

A microsystem compatible strategy for viable Escherichia coli detection

This study delineates a microsystem compatible strategy that enables the rapid determination of Escherichia coli viability for the application in food and water monitoring. This approach differentiates the living cells from the dead ones by detecting the presence of a "viability indicator", i.e. mRNAs of a common E. coli GroEL heat shock protein (hsp). Our method starts with a stimulated and controlled transcription of hsp mRNA under an elevated temperature (47 degrees C) for 20min. Following that, the short-life mRNA is rapidly extracted using streptavidin-modified magnetic particles containing biotin-labeled DNA probes complementary to a specific region of the mRNA. The quantification of mRNA by gel electrophoresis and Ag/Au-based electrochemical detection is done after the amplification of mRNAs by reverse transcription-polymerase chain reaction (RT-PCR). Heat shock temperatures and durations that have profound effect to the mRNA transcription were studied and it was found that the mRNA undergoes a rapid minute-by-minute self-degradation after the environment resumes room temperature. Issues such as the DNA contamination that interfere the magnetic particle-based mRNA extraction technique were tackled. A sensitive Ag/Au-based electrochemical analysis method was used to detect the RT-PCR products and a cell concentration as low as 10(2)cfu/ml can be achieved by the electrochemical method, but not by the conventional gel electrophoresis. The strategy demonstrated in this study can be readily implemented in a microsystem and is a step forward for the realization of an integrated bioanalytical microsystem (lab on a chip) for the viable cell detection.

Microfluidic Biosensor for the Serotype-Specific Detection of Dengue Virus RNA

The development of a microfluidic biosensor with fluorescence detection for the rapid, sensitive, and serotype-specific detection of Dengue virus is presented. The biosensor chip consists of poly(dimethylsiloxane) (PDMS) substrate with fabricated microchannels and a glass substrate used to seal the microchannels. These two substrates are packaged within a pressure-closed Plexiglas housing to provide a watertight reversible sealing at the PDMS-glass interface. The ability to reversibly seal the device permits easy disassembly and quick interchange of the device parts, which is ideal for developmental purposes. The biosensor employs a magnetic bead-based sandwich hybridization system in conjugation with liposome amplification for the specific detection of nucleic acids. The concentrations of the various biosensor components were optimized using a synthesized fragment of Dengue virus RNA. To evaluate the sensitivity of the assay, two detection systems, based on fluorescence measurements of intact and lysed liposomes, were analyzed. The entire analysis was complete within 20 min (including incubation time) with RNA detection limits of 0.125 nM and 50 pM for intact and lysed liposome detection systems, respectively. Subsequently, the biosensor was applied to the analysis of actual RNA obtained from Dengue virus serotypes 1-4. The resulting signals were compared to those obtained using standard electrochemiluminescence detection and shown to correspond perfectly with respect to serotype identification.

Nucleic acid amplification-based techniques for pathogen detection and identification

Nucleic acid amplification techniques have revolutionised diagnostic and research industries. Current technologies that allow the detection of amplification in real-time are fast becoming industry standards, particularly in a diagnostic context. In this review, we describe and explore the application of numerous real-time detection chemistries and amplification techniques for pathogen detection and identification, including the polymerase chain reaction, nucleic acid sequence-based amplification, strand displacement amplification and the ligase chain reaction. The emergence of newer technologies, such as lab-on-a-chip devices and photo-cleavable linkers, is also discussed.

Development of a microfluidic biosensor module for pathogen detection

The development of a microfluidic biosensor module with fluorescence detection for the identification of pathogenic organisms and viruses is presented in this article. The microfluidic biosensor consists of a network of microchannels fabricated in polydimethylsiloxane (PDMS) substrate. The microchannels are sealed with a glass substrate and packed in a Plexiglas housing to provide connection to the macro-world and ensure leakage-free flow operation. Reversible sealing permits easy disassembly for cleaning and replacing the microfluidic channels. The fluidic flow is generated by an applied positive pressure gradient, and the module can be operated under continuous solution flow of up to 80 microL min(-1). The biosensor recognition principle is based on DNA/RNA hybridization and liposome signal amplification. Superparamagnetic beads are incorporated into the system as a mobile solid support and are an essential part of the analysis scheme. In this study, the design, fabrication and the optimization of concentrations and amounts of the different biosensor components are carried out. The total time required for an assay is only 15 min including sample incubation time. The biosensor module is designed so that it can be easily integrated with a micro total analysis system, which will combine sample preparation and detection steps onto a single chip.

Trends in dengue diagnosis

The conventional diagnosis of dengue virus infections includes the detection of the virus in serum or tissue samples, both by isolation in culture or through detection of specific viral molecules (genome RNA or dengue antigens) and detection of specific anti-dengue antibodies (serology). Isolation of dengue virus provides the most direct and conclusive approach to diagnosis, despite the demand for high-level equipment, technical skills and manpower. However, it is useless in early diagnosis because several days are required to isolate and classify the virus. Serology, despite being simpler, is not able to afford an accurate early diagnosis in primary infections because 4-5 days are required for the immune system to produce a sufficient amount of antibodies. Moreover, it leads to misleading results in secondary infections owing to cross-reactivity among serotype-specific antibodies and with other flavivirus antibodies. The RT-PCR and other PCR-based techniques are fast, serotype-discriminating, more sensitive and easier to carry out than conventional nucleic-acid hybridisation, but are handicapped by easy sample contamination and high technological demands. Recently, advances in bioelectronics have generated commercial kits and new techniques for detection of dengue antibodies and RNA, based on biosensor technology. Most of them are rapid, easy to operate, reusable, cheap, sensitive and serotype-specific. Nevertheless, their accuracy is still questionable because most still lack validation and standardisation. This review summarises and describes the techniques currently employed and anticipated in the near future for diagnosis of dengue disease.

Cryptosporidiosis: an update in molecular epidemiology

PURPOSE OF REVIEW

Molecular tools have been developed to detect and differentiate Cryptosporidium at the species/genotype and subtype levels. These tools have been increasingly used in the characterization of the transmission of Cryptosporidium spp. This review addresses the most recent developments in molecular epidemiology of cryptosporidiosis.

RECENT FINDINGS

The recent development of subtyping tools has led to better understanding of the population genetics and transmission of Cryptosporidium in humans. The population structure of C. parvum and C. hominis is apparently more complicated than previously suggested, with the likely existence of both clonal and panmictic populations. Thus, the transmission of C. parvum (genotype II) in humans is shown to be different in different areas, with zoonotic transmission important in certain places and anthroponotic transmission in others. The use of molecular tools has also led to the identification of geographic and temporal differences in the transmission of C. parvum and C. hominis, and better appreciation of the public health importance of other Cryptosporidium species/genotypes and the frequency of infections with mixed genotypes or subtypes.

SUMMARY

Factors involved in the transmission of human cryptosporidiosis are difficult to examine using conventional methods. The use of molecular tools has been helpful in the assessment of the zoonotic potential of various Cryptosporidium spp. and sources of human infections, and has started to play a significant role in the characterization of transmission dynamic in endemic and epidemic areas.