The challenge of long-term stability for nucleic acid-based electrochemical sensors

Nucleic acid-based electrochemical sensors are a versatile technology enabling affinity-based detection of a great variety of molecular targets, regardless of inherent electrochemical activity or enzymatic reactivity. Additionally, their modular interface and ease of fabrication enable rapid prototyping and sensor development. However, the technology has inhibiting limitations in terms of long-term stability that have precluded translation into clinically valuable platforms like continuous molecular monitors. In this opinion, we discuss published methods to address various aspects of sensor stability, including thiol-based monolayers and anti-biofouling capabilities. We hope the highlighted works will motivate the field to develop innovative strategies for extending the long-term operational life of nucleic acid-based electrochemical sensors.     

Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review

Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.     

Establishing a quality assurance plan for nucleic acid-based diagnostic laboratories: from planning to implementation

Nucleic acid-based technologies have opened new perspectives in diagnosis, prognosis, and treatment in clinical medicine. To maintain patient confidence in this rapidly expanding field and to provide the highest standard of analysis, strict laboratory quality assurance procedures must be followed. While impressive break-through are taking place in this field, the need for an appropriate and suitable quality assurance (QA) plan for nucleic acid-based diagnostic laboratories must be a top priority. In this study, we developed a systematic QA plan for this kind of diagnostic laboratories that would enable us to assure the highest quality standards of their services. We focus on those labs that would like to start introducing a quality system for the first time and discuss the most appropriate ways to pave the way to implement a QA plan from the beginning. This QA plan is suitable for any nucleic acid-based techniques laboratory regardless of the field or services provided.     

Duplex probes: a new approach for the detection of specific nucleic acids in homogenous assays

A novel method for the detection of specific nucleic acids in homogenous solution was developed. The method is based on the use of duplex probes in which fluorescent donor and quencher labeled on either oligonucleotide are held in close proximity, so that fluorescence is quenched. Amplification of the target sequence results in the cleavage of the probe and the resulting fluorescence can be detected. The fluorescent data analysis demonstrated that the duplex probes can specifically recognize the presence of target, and a significantly higher lever of relative fluorescent signal than TaqMan probes is obtainable. Combined with real-time PCR instruments, the assay can be used to quantify the input target molecules. As few as five copies of initial target molecules can be detected, and a large dynamic linear ranger (five orders of magnitude) is obtained.     

Two simple protocols for the preparation of diallylaminoethyl-substituted nucleic bases: a comparison

The syntheses of pyrimidine and purine nucleic bases substituted with diallylaminoethyl groups are reported following two different protocols. A comparison is made between the yield, expense, and difficulty of each route.     

Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: A review

Point-of-care (POC) genetic diagnostics critically depends on miniaturization and integration of sample processing, nucleic acid amplification, and detection systems. Polymerase chain reaction (PCR) assays have extensively applied for the diagnosis of genetic markers of disease. Microfluidic chips for microPCR with different materials and designs have been reported. Temperature cycling systems with varying thermal masses and conductivities, thermal cycling times, flow-rates, and cross-sectional areas, have also been developed to reduce the nucleic acid amplification time. Similarly, isothermal amplification techniques (e.g., loop-mediated isothermal amplification or LAMP), which are still are emerging, have a better potential as an alternative to PCR for POC diagnostics. Isothermal amplification techniques have: (i) moderate incubation temperature leading to simplified heating and low power consumption, (ii) yield high amount of amplification products, which can be detected either visually or by simple detectors, (iii) allow direct genetic amplification from bacterial cells due to the superior tolerance to substances that typically inhibit PCR, (iv) have high specificity, and sensitivity, and (v) result in rapid detection often within 10–20 min. The aim of this review is to provide a better understanding of the advantages and limitations of microPCR and microLAMP systems for rapid and POC diagnostics.     

Synthesis of functionalised nucleosides for incorporation into nucleic acid-based serine protease mimics

The synthesis of nucleosides modified with an extra imidazole, carboxyl and hydroxyl group is described. These nucleosides can be incorporated into an oligonucleotide duplex, thus generating a novel type of serine protease mimic.     

Framework nucleic acid-based confined enzyme cascade for efficient synergistic cancer therapy in vivo

Artificial enzyme cascade systems with confinement effect are highly important in synthetic biology and biomedicine.Herein,a framework nucleic acid-based confined enzyme cascade(FNA-CEC)for synergistic cancer therapy in vivo was developed.The FNA-CEC consisted of glucose oxidase and horseradish peroxidase precisely assembled on an addressable DNA tetrahedron scaffold within few nanometers.Glucose oxidase(GOx)can trigger efficient glucose depletion for tumor starvation therapy,and increase the local concentration of H₂O₂ in situ for enhanced downstream horseradish peroxidase(HRP)-activated prodrug therapy.Due to the spatial-confinement on DNA tetrahedron scaffold,the efficiency of intermediate metabolites transportation between the enzyme cascades was improved.Moreover,FNA-CEC was applied for efficient synergistic cancer therapy in vitro and in vivo.As a simple and efficient approach,the FNA-CEC is expected to expand the toolbox of technologies in synthetic biology and biomedicine.     

Sample preparation for chromatography: an African perspective

Africa as a continent has its unique challenges for analytical chemists in sample preparation for chromatographic analyses. The areas of agriculture, environment, food and health provide formidable challenges when it comes to method development, for example, drought can result in inadequate supplies of good quality water. The testing of water quality necessitates the development of assay methods that can be employed to not only determine the quantities of pesticides associated with malaria and tsetse fly eradication programmes, but also to monitor mycotoxins or neurotoxins. Urbanisation has also meant that endocrine disruptors such as phthalate esters need to be monitored. This review will profile some of the activities by analytical chemists practising in the African continent, who seek to address some of the challenges in sample preparation for chromatographic analyses.     

Sample preparation for chromatographic separations: an overview

Chromatographic methods dominate the field of organic analysis. However, many samples are too dilute, too complex or incompatible with the chromatographic system to render separation or detection possible without preliminary matrix simplification and/or preconcentration. A broad selection of the most common, recent and emerging isolation, clean-up and concentration techniques used to prepare samples for chromatographic separations are reviewed.     

High-throughput ribozyme-based assays for detection of viral nucleic acids

Many reports have suggested that target-activated ribozymes hold potential value as detection reagents. We show that a "half"-ribozyme ligase is activated similarly by three unstructured oligoribonucleotides representing the major sequence variants of a hepatitis C virus 5'-untranslated region (5'-UTR) target and by a structured RNA corresponding to the entire 5'-UTR. Half-ribozyme ligation product was detected both in an ELISA-like assay and in an optical immunoassay through the use of hapten-carrying substrate RNAs. Both assay formats afford a limit of detection of approximately 1 x 10(6) HCV molecules (1.6 attomol, 330 fM), a sensitivity which compares favorably to that provided by standard immunoassays. These data suggest that target-activated ribozyme systems are a viable approach for the sensitive detection of viral nucleic acids using high-throughput platforms.     

Sample preparation for the analysis of heavy metals in foods

The analysis of foodstuffs for heavy metals continues to be an area of intense activity for analytical chemists. Methods of sample preparation are changing to allow a growing number of samples to be handled and to facilitate 'speciation' studies.     

Progress toward the development of a point-of-care photonic crystal ammonia sensor

We have developed an ammonia-sensitive material by coupling the Berthelot reaction to our polymerized crystalline colloidal array (PCCA) technology. The material consists of a periodic array of highly charged colloidal particles (110 nm diameter) embedded in a poly(hydroxyethyl acrylate) hydrogel. The particles have a lattice spacing such that they Bragg-diffract visible light. In the Berthelot reaction, ammonia, hypochlorite, and phenol react to produce the dye molecule indophenol blue in an aqueous solution. We use this reaction in our sensor by covalently attaching 3-aminophenol to the hydrogel backbone, which forms cross-links through the Berthelot mechanism. Ammonia reacts with hypochlorite, forming monochloramine, which then reacts with a pendant aminophenol to form a benzoquinone chlorimine. The benzoquinone chlorimine reacts with another pendant aminophenol to form a cross-link. The creation of new cross-links causes the hydrogel to shrink, which reduces the lattice spacing of the embedded colloidal array. This volume change results in a blue-shift in the diffracted light proportional to the concentration of NH₃ in the sample. We demonstrate that the NH₃ photonic crystal sensing material is capable of quantitative determination of concentrations in the physiological range (50–350 μmol NH₃ L⁻¹) in human blood serum.     

Sample preparation for organic acids in biological fluids

A review of sample preparation methods for organic acids in biological fluids, in particular serum and urine, is presented. It covers techniques on organic acid determination without sample preparation, release of organic acids from binding locations, removal of proteins by protein precipitation and ultrafiltration, isolation of the organic acids by liquid-liquid and liquid-solid extraction, purification of the extract, derivatization and pre-fractionation. The various alternative sample preparation steps are compared and critically discussed. Examples of applications including profile analysis of organic acids by gas chromatography (GC), determination of particular organic acids by GC or liquid chromatography and determination of fatty acids as a distinct chemical class of acids demonstrate that the kind of sample preparation chosen depends strongly on the analytical aims.     

Sample preparation for high-performance liquid chromatography in the clinical laboratory

Techniques for the preparation of clinical specimens for high-performance liquid chromatography are described. Liquid samples containing high enough concentrations of analytes may be injected directly or after centrifugation. Proteins may be removed by precipitation with organic, anionic or cationic precipitants or by ultrafiltration. Compounds having large partition coefficients may be extracted with an organic solvent. Extraction may also be performed following derivatization, ion-suppression, ion-pairing, salt addition or complex formation. Solid phase extraction may be off-line using disposable cartridges or on-line with an Advanced Automated Sample Processor. The advantages and disadvantages of each method and the trends in sample preparation techniques are discussed.     

Sample preparation for the analysis of flavors and off-flavors in foods

Off-flavors in foods may originate from environmental pollutants, the growth of microorganisms, oxidation of lipids, or endogenous enzymatic decomposition in the foods. The chromatographic analysis of flavors and off-flavors in foods usually requires that the samples first be processed to remove as many interfering compounds as possible. For analysis of foods by gas chromatography (GC), sample preparation may include mincing, homogenation, centrifugation, distillation, simple solvent extraction, supercritical fluid extraction, pressurized-fluid extraction, microwave-assisted extraction, Soxhlet extraction, or methylation. For high-performance liquid chromatography of amines in fish, cheese, sausage and olive oil or aldehydes in fruit juice, sample preparation may include solvent extraction and derivatization. Headspace GC analysis of orange juice, fish, dehydrated potatoes, and milk requires almost no sample preparation. Purge-and-trap GC analysis of dairy products, seafoods, and garlic may require heating, microwave-mediated distillation, purging the sample with inert gases and trapping the analytes with Tenax or C18, thermal desorption, cryofocusing, or elution with ethyl acetate. Solid-phase microextraction GC analysis of spices, milk and fish can involve microwave-mediated distillation, and usually requires adsorption on poly(dimethyl)siloxane or electrodeposition on fibers followed by thermal desorption. For short-path thermal desorption GC analysis of spices, herbs, coffee, peanuts, candy, mushrooms, beverages, olive oil, honey, and milk, samples are placed in a glass-lined stainless steel thermal desorption tube, which is purged with helium and then heated gradually to desorb the volatiles for analysis. Few of the methods that are available for analysis of food flavors and off-flavors can be described simultaneously as cheap, easy and good.     

Sample preparation in analysis of pharmaceuticals

Sample preparation is a very important and essential step in environmental analysis. This article presents an overview of extraction methods for environmental samples, focusing especially on pharmaceuticals as there is great concern about them as pollutants.     

Thermal neutron activation: Sample preparation utilizing graphite as a diluent

A sample preparation method has been developed which produces both standard and unknown samples of the same size, shape, composition and density (a necessary condition for minimum error). A solution of standard or unknown material was pipetted onto graphite wetted with acetone, the material was dried and mixed with additional graphite to give a homogeneous mixture containing≥99% graphite. Portions of the mixture were pressed into uniform cylindrical pellets. Application of the method to the activation analysis of several copper compounds gave results which generally agreed with analysis by thiosulfate titration of liberated iodine to within less than 1%. This work was supported by the United States Atomic Energy Commission.