Aptamers against the ß-Conglutin Allergen: Insights into the Behavior of the Shortest Multimeric (Intra)Molecular DNA G-Quadruplex.

In previous work, a 93-mer aptamer was selected against the anaphylactic allergen, ß-conglutin and truncated to an 11-mer, improving the affinity by two orders of magnitude, whilst maintaining the specificity. This 11-mer was observed to fold in a G-quadruplex, and preliminary results indicated the existence of a combination of monomeric and higher-order structures. Building on this previous work, in the current study, we aimed to elucidate a deeper understanding of the structural forms of this 11-mer and the effect of the structure on its binding ability. A battery of techniques including polyacrylamide gel electrophoresis, high-performance liquid chromatography in combination with electrospray ionization time-of-flight mass spectrometry, matrix-assisted laser desorption/ionization time-of-flight, thermal binding analysis, circular dichroism and nuclear magnetic resonance were used to probe the structure of both the 11-mer and the 11-mer flanked with TT- at either the 5' or 3' end or at both ends. The TT-tail at the 5' end hinders stacking effects and effectively enforces the 11-mer to maintain a monomeric form. The 11-mer and the TT- derivatives of the 11-mer were also evaluated for their ability to bind its cognate target using microscale thermophoresis and surface plasmon resonance, and biolayer interferometry confirmed the nanomolar affinity of the 11-mer. All the techniques utilized confirmed that the 11-mer was found to exist in a combination of monomeric and higher-order structures, and that independent of the structural form present, nanomolar affinity was observed.

Ultrasensitive and rapid detection of ß-conglutin combining aptamers and isothermal recombinase polymerase amplification.

Lupin is increasingly being used in a variety of food products due to its nutritional, functional and nutraceutical properties. However, several examples of severe and even fatal food-associated anaphylaxis due to lupin inhalation or ingestion have been reported, resulting in the lupin subunit ß-conglutin, being defined as the Lup an 1 allergen by the International Union of Immunological Societies (IUIS) in 2008. Here, we report an innovative method termed aptamer-recombinase polymerase amplification (Apta-RPA) exploiting the affinity and specificity of a DNA aptamer selected against the anaphylactic ß-conglutin allergen termed ß-conglutin binding aptamer II (ß-CBA II), facilitating ultrasensitive detection via isothermal amplification. Combining magnetic beads as the solid phase with Apta-RPA detection, the total assay time was reduced from 210 min to just 25 min, with a limit of detection of 3.5 × 10-11 M, demonstrating a rapid and ultrasensitive generic methodology that can be used with any aptamer. Future work will focus on further simplification of the assay to a lateral flow format. Graphical Abstract Schematic representation of the rapid and novel bead-based Apta-RPA assay.

Ultrasensitive, rapid and inexpensive detection of DNA using paper based lateral flow assay.

Sensitive, specific, rapid, inexpensive and easy-to-use nucleic acid tests for use at the point-of-need are critical for the emerging field of personalised medicine for which companion diagnostics are essential, as well as for application in low resource settings. Here we report on the development of a point-of-care nucleic acid lateral flow test for the direct detection of isothermally amplified DNA. The recombinase polymerase amplification method is modified slightly to use tailed primers, resulting in an amplicon with a duplex flanked by two single stranded DNA tails. This tailed amplicon facilitates detection via hybridisation to a surface immobilised oligonucleotide capture probe and a gold nanoparticle labelled reporter probe. A detection limit of 1 × 10-11 M (190 amol), equivalent to 8.67 × 105 copies of DNA was achieved, with the entire assay, both amplification and detection, being completed in less than 15 minutes at a constant temperature of 37 °C. The use of the tailed primers obviates the need for hapten labelling and consequent use of capture and reporter antibodies, whilst also avoiding the need for any post-amplification processing for the generation of single stranded DNA, thus presenting an assay that can facilely find application at the point of need.

Aptamer Lateral Flow Assays for Ultrasensitive Detection of ß-Conglutin Combining Recombinase Polymerase Amplification and Tailed Primers.

In this work, different methodologies were evaluated in search of robust, simple, rapid, ultrasensitive, and user-friendly lateral flow aptamer assays. In one approach, we developed a competitive based lateral flow aptamer assay, in which ß-conglutin immobilized on the test line of a nitrocellulose membrane and ß-conglutin in the test sample compete for binding to AuNP labeled aptamer. The control line exploits an immobilized DNA probe complementary to the labeled aptamer, forcing displacement of the aptamer from the ß-conglutin-aptamer complex. In a second approach, the competition for aptamer binding takes place off-strip, and following competition, aptamer bound to the immobilized ß-conglutin is eluted and used as a template for isothermal recombinase polymerase amplification, exploiting tailed primers, resulting in an amplicon of a duplex flanked by single stranded DNA tails. The amplicon is rapidly and quantitatively detected using a nucleic acid lateral flow with an immobilized capture probe and a gold nanoparticle labeled reporter probe. The competitive lateral flow is completed in just 5 min, achieving a detection limit of 55 pM (1.1 fmol), and the combined competitive-amplification lateral flow requires just 30 min, with a detection limit of 9 fM (0.17 amol).

ß-Conglutin dual aptamers binding distinct aptatopes.

An aptamer was previously selected against the anaphylactic allergen ß-conglutin (ß-CBA I), which was subsequently truncated to an 11-mer and the affinity improved by two orders of magnitude. The work reported here details the selection and characterisation of a second aptamer (ß-CBA II) selected against a second aptatope on the ß-conglutin target. The affinity of this second aptamer was similar to that of the 11-mer, and its affinity was confirmed by three different techniques at three independent laboratories. This ß-CBA II aptamer in combination with the previously selected ß-CBA I was then exploited to a dual-aptamer approach. The specific and simultaneous binding of the dual aptamer (ß-CBA I and ß-CBA II) to different sites of ß-conglutin was confirmed using both microscale thermophoresis and surface plasmon resonance where ß-CBA II serves as the primary capturing aptamer and ß-CBA I or the truncated ß-CBA I (11-mer) as the secondary signalling aptamer, which can be further exploited in enzyme-linked aptamer assays and aptasensors.

Surface plasmon resonance imaging (SPRi) for analysis of DNA aptamer:ß-conglutin interactions.

Surface plasmon resonance imaging (SPRi) is a label-free detection method that offers a suitable and reliable platform for the real time monitoring of biomolecular interactions. In the work reported here, SPRi was used to evaluate the affinity and specificity of three different aptamers selected against the Lup an 1 anaphylactic allergen ß-conglutin (ß-conglutin binding aptamers I and II (ß-CBA I and ß-CBA II)), as well as an 11-mer truncated version of ß-CBA I. Thiol modified aptamers were immobilised on a gold substrate through a self-assembling process and the use of different blocking strategies to prevent non-specific binding were evaluated. Dissociation constants of 20, 13 and 1 nM were determined for ß-CBA I, ß-CBA II and the 11-mer truncated aptamer, respectively. The three aptamers were then studied in various different sandwich formats and the ß-CBA I/11-mer and ß-CBA II were observed to bind to different aptatopes on the target protein. Each of the aptamers were then used either as surface immobilised aptamer, or as reporter aptamer, and added with the protein target ß-conglutin in either a sequential of simultaneous manner, and the changes in SPR signal monitored. The preferred approach for formation of a sandwich aptacomplex was with immobilised ß-CBA II, followed by addition of pre-incubated ß-conglutin and 11-mer, whilst addition of the 11-mer following addition of the ß-conglutin, resulted in displacement of the bound target. The ability to provide parallel qualitative and quantitative detection establishes SPRi as a powerful tool for the study of immobilised aptamer-target interactions.

Ultrasensitive aptamer based detection of ß-conglutin food allergen.

Lupine has been increasingly used in food applications due to its high nutritional value and excellent functional properties. However, there has been a response to the increasing number of severe cases of lupine allergies reported during the last decade, and as a result lupine was recently added to the list of substances requiring mandatory advisory labelling on foodstuffs sold in the European Union. In this paper we report the robust and ultrasensitive detection of the anaphylactic ß-conglutin allergen using Apta-PCR achieving a detection limit of 85 pM (25 ng mL(-1)). No cross-reactivity with other conglutins or plant species potentially used in lupine containing foodstuffs was observed. This robust method provides an effective analytical tool for the detection and quantification of the toxic ß-conglutin subunit present in lupine flour.

Colorimetric quantification of mRNA expression in rare tumour cells amplified by multiple ligation-dependent probe amplification.

An enzyme-linked oligonucleotide assay (ELONA) for quantification of mRNA expression of five genes involved in breast cancer, extracted from isolated rare tumour cells and amplified by multiplex ligation-dependent probe amplification (MLPA) is presented. In MLPA, a multiplex oligonucleotide ligation assay is combined with a PCR reaction in which all ligation products are amplified by use of a single primer pair. Biotinylated probes complementary to each of the target sequences were immobilised on the surface of a streptavidin-coated microtitre plate and exposed to single-stranded MLPA products. A universal reporting probe sequence modified with horseradish peroxidase (URP-HRP) and complementary to a universal primer used during the MLPA step was further added to the surface-bound duplex as a reporter probe. Simultaneous addition of anchoring probe and target, followed by addition of reporter probe, rather than sequential addition, was achieved with no significant effect on sensitivity and limits of detection, but considerably reduced the required assay time. Detection limits as low as 20 pmol L(-1), with an overall assay time of 95 min could be achieved with negligible cross-reactivity between probes and non-specific targets present in the MLPA-PCR product. The same MLPA-PCR product was analysed using capillary electrophoresis, the technique typically used for analysis of MLPA products, and good correlation was observed. The assay presented is easy to carry out, relatively inexpensive, rapid, does not require sophisticated instrumentation, and enables quantitative analysis, making it very promising for the analysis of MLPA products.

Solid-contact potentiometric aptasensor based on aptamer functionalized carbon nanotubes for the direct determination of proteins.

A facile, solid-contact selective potentiometric aptasensor exploiting a network of single-walled carbon nanotubes (SWCNT) acting as a transducing element is described in this work. The molecular properties of the SWCNT surface have been modified by covalently linking aptamers as biorecognition elements to the carboxylic groups of the SWCNT walls. As a model system to demonstrate the generic application of the approach, a 15-mer thrombin aptamer interacts with thrombin and the affinity interaction gives rise to a direct potentiometric signal that can be easily recorded within 15 s. The dynamic linear range, with a sensitivity of 8.0 mV/log a(Thr) corresponds to the 10(-7)-10(-6) M range of thrombin concentrations, with a limit of detection of 80 nM. The aptasensor displays selectivity against elastase and bovine serum albumin and is easily regenerated by immersion in 2 M NaCl. The aptasensor demonstrates the capacity of direct detection of the recognition event avoiding the use of labels, mediators, or the addition of further reagents or analyte accumulation.

Microfluorimeter with disposable polymer chip for detection of coeliac disease toxic gliadin.

Coeliac disease is an inflammatory disease of the upper small intestine and results from gluten ingestion in genetically susceptible individuals, and is the only life-long nutrient-induced enteropathy. The only treatment is a strict gluten-free diet and the longer the individual fails to adhere to this diet, the greater the chance of developing malnutrition and other complications. The existence of reliable gluten free food is crucial to the well-being of the population. Here we report on a microfluorimeter device for the in situ detection of gliadin in foodstuffs, which could be used for a rapid control of raw materials in food processing, as well as for process control of gliadin contamination. The microfluorimeter is based on a reflector that is used inside a microfluidic chip, exploiting various strategically placed reflective or totally metallised mirrors for efficient collection of the fluorescent light emitted in a large solid angle. The chip is capable of executing five assays in parallel and has been demonstrated to possess detection sensitivity applicable to fluoroimmunoassays. Various immunoassay formats exploiting fluorescence detection, using enzyme/fluorophore labels were developed and compared in terms of sensitivity, ease of assay, assay time and compatibility with buffer used to extract gliadin from raw and cooked foodstuffs, with the best performance observed with an indirect competition assay using a fluorophore-labelled anti-mouse antibody. This assay was exploited within the microfluorimeter device, and a very low detection limit of 4.1 ng/mL was obtained. The system was observed to be highly reproducible, with an RSD of 5.9%, for a concentration of 50 ng/mL of gliadin applied to each of the five channels of the microfluorimeter. Biofunctionalised disposable strips incorporated into the microfluorimeter were subjected to accelerated Arrhenius thermal stability studies and it was demonstrated that strips pre-coated with gliadin could be stored for approximately 2 years at 4 degrees C, with no discernable loss in sensitivity or detectability of the assay. Finally, the microfluorimeter was applied to the analysis of commercial gluten-free food samples, and an excellent correlation with routine ELISA measurements was obtained. The developed microfluorimeter should find widespread application for on-site execution of fluoroimmunoassays.

Iodine atoms: a new molecular feature for the design of potent transthyretin fibrillogenesis inhibitors.

The thyroid hormone and retinol transporter protein known as transthyretin (TTR) is in the origin of one of the 20 or so known amyloid diseases. TTR self assembles as a homotetramer leaving a central hydrophobic channel with two symmetrical binding sites. The aggregation pathway of TTR into amiloid fibrils is not yet well characterized but in vitro binding of thyroid hormones and other small organic molecules to TTR binding channel results in tetramer stabilization which prevents amyloid formation in an extent which is proportional to the binding constant. Up to now, TTR aggregation inhibitors have been designed looking at various structural features of this binding channel others than its ability to host iodine atoms. In the present work, greatly improved inhibitors have been designed and tested by taking into account that thyroid hormones are unique in human biochemistry owing to the presence of multiple iodine atoms in their molecules which are probed to interact with specific halogen binding domains sitting at the TTR binding channel. The new TTR fibrillogenesis inhibitors are based on the diflunisal core structure because diflunisal is a registered salicylate drug with NSAID activity now undergoing clinical trials for TTR amyloid diseases. Biochemical and biophysical evidence confirms that iodine atoms can be an important design feature in the search for candidate drugs for TTR related amyloidosis.

Aptamers: molecular tools for analytical applications.

Aptamers are artificial nucleic acid ligands, specifically generated against certain targets, such as amino acids, drugs, proteins or other molecules. In nature they exist as a nucleic acid based genetic regulatory element called a riboswitch. For generation of artificial ligands, they are isolated from combinatorial libraries of synthetic nucleic acid by exponential enrichment, via an in vitro iterative process of adsorption, recovery and reamplification known as systematic evolution of ligands by exponential enrichment (SELEX). Thanks to their unique characteristics and chemical structure, aptamers offer themselves as ideal candidates for use in analytical devices and techniques. Recent progress in the aptamer selection and incorporation of aptamers into molecular beacon structures will ensure the application of aptamers for functional and quantitative proteomics and high-throughput screening for drug discovery, as well as in various analytical applications. The properties of aptamers as well as recent developments in improved, time-efficient methods for their selection and stabilization are outlined. The use of these powerful molecular tools for analysis and the advantages they offer over existing affinity biocomponents are discussed. Finally the evolving use of aptamers in specific analytical applications such as chromatography, ELISA-type assays, biosensors and affinity PCR as well as current avenues of research and future perspectives conclude this review.