Utility of intercalator displacement assays for screening of ligands for i-motif DNA structures

Cytosine rich sequences can form intercalated, i-motif DNA structures stabilized by hemi-protonated cytosine:cytosine base pairing. These sequences are often located in regulatory regions of genes such as promoters. Ligands targeting i-motif structures may provide potential leads for treatments for genetic disease. The focus on ligands interacting with i-motif DNA has been increasing in recent years. Here, we describe the fluorescent intercalator displacement (FID) assay using thiazole orange binding i-motif DNA and assess the binding affinity of a ligand to the i-motif DNA by displacing thiazole orange. This provides a time and cost-effective high throughput screening of ligands against secondary DNA structures for hit identification.

Small Molecule Interactions with Biomacromolecules: DNA Binding Interactions of a Manganese(III) Schiff Base Complex with Potential Anticancer Activities

A manganese(III) complex, [MnIII(L)(SCN)(enH)](NO3)·H2O (1•H2O) (H2L = 2-((E)-(2-((E)-2-hydroxy-3-methoxybenzylidene-amino)-ethyl-imino)methyl)-6-methoxyphenol), has been synthesized and characterized by single-crystal X-ray diffraction analysis. The interaction of 1•H2O with DNA was studied by monitoring the decrease in absorbance of the complex at λ = 324 nm with the increase in DNA concentration, providing an opportunity to determine the binding constant of the 1•H2O-ct-DNA complex as 5.63 × 103 M-1. Similarly, fluorescence titration was carried out by adding ct-DNA gradually and monitoring the increase in emission intensity at 453 nm on excitation at λex = 324 nm. A linear form of the Benesi-Hildebrand equation yields a binding constant of 4.40 × 103 M-1 at 25 °C, establishing the self-consistency of our results obtained from absorption and fluorescence titrations. The competitive displacement reactions of dyes like ethidium bromide, Hoechst, and DAPI (4',6-diamidine-2'-phenylindole dihydrochloride) from dye-ct-DNA conjugates by 1•H2O were analyzed, and the corresponding KSV values are 1.05 × 104, 1.25 × 104, and 1.35 × 104 M-1 and the Kapp values are 2.16 × 103, 8.34 × 103, and 9.0 × 103 M-1, from which it is difficult to infer the preference of groove binding over intercalation by these DNA trackers. However, the molecular docking experiments and viscosity measurement clearly indicate the preference for minor groove binding over intercalation, involving a change in Gibbs free energy of -8.56 kcal/mol. The 1•H2O complex was then evaluated for its anticancer potential in breast cancer MCF-7 cells, which severely abrogates the growth of the cells in both 2D and 3D mammospheres, indicating its promising application as an anticancer drug through a minor groove binding interaction with ct-DNA.

Colorimetric Sensing of Amoxicillin Facilitated by Molecularly Imprinted Polymers

The scope of the presented research orientates itself towards the development of a Molecularly Imprinted Polymer (MIP)-based dye displacement assay for the colorimetric detection of the antibiotic amoxicillin in aqueous medium. With this in mind, the initial development of an MIP capable of such a task sets focus on monolithic bulk polymerization to assess monomer/crosslinker combinations that have potential towards the binding of amoxicillin. The best performing composition (based on specificity and binding capacity) is utilized in the synthesis of MIP particles by emulsion polymerization, yielding particles that prove to be more homogenous in size and morphology compared to that of the crushed monolithic MIP, which is an essential trait when it comes to the accuracy of the resulting assay. The specificity and selectivity of the emulsion MIP proceeds to be highlighted, demonstrating a higher affinity towards amoxicillin compared to other compounds of the aminopenicillin class (ampicillin and cloxacillin). Conversion of the polymeric receptor is then undertaken, identifying a suitable dye for the displacement assay by means of binding experiments with malachite green, crystal violet, and mordant orange. Once identified, the optimal dye is then loaded onto the synthetic receptor, and the displaceability of the dye deduced by means of a dose response experiment. Alongside the sensitivity, the selectivity of the assay is scrutinized against cloxacillin and ampicillin. Yielding a dye displacement assay that can be used (semi-)quantitatively in a rapid manner.

A Molecularly Imprinted Polymer-based Dye Displacement Assay for the Rapid Visual Detection of Amphetamine in Urine

The rapid sensing of drug compounds has traditionally relied on antibodies, enzymes and electrochemical reactions. These technologies can frequently produce false positives/negatives and require specific conditions to operate. Akin to antibodies, molecularly imprinted polymers (MIPs) are a more robust synthetic alternative with the ability to bind a target molecule with an affinity comparable to that of its natural counterparts. With this in mind, the research presented in this article introduces a facile MIP-based dye displacement assay for the detection of (±) amphetamine in urine. The selective nature of MIPs coupled with a displaceable dye enables the resulting low-cost assay to rapidly produce a clear visual confirmation of a target's presence, offering huge commercial potential. The following manuscript characterizes the proposed assay, drawing attention to various facets of the sensor design and optimization. To this end, synthesis of a MIP tailored towards amphetamine is described, scrutinizing the composition and selectivity (ibuprofen, naproxen, 2-methoxphenidine, quetiapine) of the reported synthetic receptor. Dye selection for the development of the displacement assay follows, proceeded by optimization of the displacement process by investigating the time taken and the amount of MIP powder required for optimum displacement. An optimized dose-response curve is then presented, introducing (±) amphetamine hydrochloride (0.01-1 mg mL^-1) to the engineered sensor and determining the limit of detection (LoD). The research culminates in the assay being used for the analysis of spiked urine samples (amphetamine, ibuprofen, naproxen, 2-methoxphenidine, quetiapine, bupropion, pheniramine, bromopheniramine) and evaluating its potential as a low-cost, rapid and selective method of analysis.

Polymer - Nanoparticle Assemblies for Array Based Sensing

Sensing clinically relevant biomolecules is crucial for the detection and prevention of disease. Currently used detection methods tend to be expensive, time intensive, and specific for only one particular biomolecule of interest. Nanoparticle-based arrays using conjugated polymers have emerged as an analytical and potential clinical tool, allowing detection of a wide range of biomolecules using selective, not specific, sensor components. In this report, we highlight recent progress in nanoparticle - polymer sensor arrays in both the fundamental understanding of how the sensor arrays function as well as the detection of clinically relevant bacteria and cells.

Fabrication of surface plasmon resonance sensor surface with control of the non-specific adsorption and affinity for the detection of 2,4,6-trinitrotoluene using an antifouling copolymer

We fabricated a surface plasmon resonance (SPR) sensor using a hydrophilic polymer for the highly sensitive detection of 2,4,6-trinitrotoluene (TNT). The hydrophilic polymer was made from mono-2-(methacryloyloxy)ethylsuccinate (MES) and 2-hydroxyethylmethacrylate (HEMA) by surface-initiated atom transfer radical polymerization. The detection of TNT was carried out by displacement assay with the SPR measurement. In displacement assay, the affinity between anti-TNT antibody and the sensor surface, affects to the sensitivity. In the SPR measurement, non-specific adsorption should be controlled because SPR sensor cannot discriminate between specific and non-specific adsorption. Therefore, the affinity and non-specific adsorption were controlled by changing the ratio of HEMA to MES. A detection limit of 0.4 ng/ml (ppb) for TNT was achieved using a sensor surface with the lowest affinity without non-specific adsorption.