Fluorescence Polarization for Probing DNA Adsorption by Nanomaterials and Fluorophore/DNA Interactions

EEPD1 promotes repair of oxidatively-stressed replication forks

Unrepaired oxidatively-stressed replication forks can lead to chromosomal instability and neoplastic transformation or cell death. To meet these challenges cells have evolved a robust mechanism to repair oxidative genomic DNA damage through the base excision repair (BER) pathway, but less is known about repair of oxidative damage at replication forks. We found that depletion or genetic deletion of EEPD1 decreases clonogenic cell survival after oxidative DNA damage. We demonstrate that EEPD1 is recruited to replication forks stressed by oxidative damage induced by H2O2 and that EEPD1 promotes replication fork repair and restart and decreases chromosomal abnormalities after such damage. EEPD1 binds to abasic DNA structures and promotes resolution of genomic abasic sites after oxidative stress. We further observed that restoration of expression of EEPD1 via expression vector transfection restores cell survival and suppresses chromosomal abnormalities induced by oxidative stress in EEPD1-depleted cells. Consistent with this, we found that EEPD1 preserves replication fork integrity by preventing oxidatively-stressed unrepaired fork fusion, thereby decreasing chromosome instability and mitotic abnormalities. Our results indicate a novel role for EEPD1 in replication fork preservation and maintenance of chromosomal stability during oxidative stress.

Aptamer Switches Regulated by Post-Transition/Transition Metal Ions

We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb²⁺ , Cd²⁺ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.

Nanomaterial and Aptamer-Based Sensing: Target Binding versus Target Adsorption Illustrated by the Detection of Adenosine and ATP on Metal Oxides and Graphene Oxide

Target molecule-induced desorption of aptamer probes from nanomaterials has been a very popular sensing method, taking advantage of the fluorescence quenching or catalytic activity of nanomaterials for signal generation. While it is generally conceived that aptamers desorb due to binding to target molecules, in this work, we examined the effect of competitive target adsorption. From five metal oxide nanoparticles including CeO₂, ZnO, NiO, Fe₃O₄, and TiO₂, only ATP was able to induce desorption of its aptamer. Adenosine could not, even though it had an even higher affinity than ATP to the aptamer. The same conclusion was also observed with a random DNA that cannot bind ATP, indicating that the desorption of DNA was due to competitive adsorption of ATP instead of aptamer binding. On graphene oxide, however, adenosine produced slightly more aptamer desorption than ATP under most of the conditions, and this can be partially attributed to the weaker interaction of negatively charged ATP with negatively charged graphene oxide. For such surface-based biosensors, it is recommended that a nonaptamer control DNA be tested side-by-side to ensure the sensing mechanism to be related to aptamer binding instead of target adsorption.

Functional nucleic acid-based fluorescence polarization/anisotropy biosensors for detection of biomarkers

The sensitive and selective detection of biomarkers plays a crucial role in disease diagnostics, drug discovery, and early screening of cancers. The achievement of this goal highly depends on the continuous development of biosensing technologies. Among them, fluorescence anisotropy/polarization (FA/FP) analysis receives increasing interest due to the advantage of simple operation, fast response, and no background interference. In recent decades, great progress has been achieved in FA/FP sensors thanks to the development of functional nucleic acids (FNAs) including aptamers and nucleic acid enzymes. This review focuses on FNA-based FA/FP sensors for the quantitative detection of biomarkers, such as nucleic acid, small molecules, and proteins. The design strategies, recognition elements, and practical applications are fully highlighted. The article also discusses the challenges of applying FNA-based FA/FP sensors in the next generation and the potential solutions along with future prospects. Graphical abstract.

Translating in vitro diagnostics from centralized laboratories to point-of-care locations using commercially-available handheld meters

There is a growing demand for high-performance point-of-care (POC) diagnostic technologies where in vitro diagnostics (IVD) is fundamental for prevention, identification, and treatment of many diseases. Over the past decade, a shift of IVDs from the centralized laboratories to POC settings is emerging. In this review, we summarize recent progress in translating IVDs from centralized labs to POC settings using commercially available handheld meters. After introducing typical workflows for IVDs and highlight innovative technologies in this area, we discuss advantages of using commercially available handheld meters for translating IVDs from centralized labs to POC settings. We then provide comprehensive coverage of different signal transduction strategies to repurpose the commercially-available handheld meters, including personal glucose meter, pH meter, thermometer and pressure meter, for detecting a wide range of targets by integrating biochemical assays with the meters for POC testing. Finally, we identify remaining challenges and offer future outlook in this area.

Yttrium Oxide as a Strongly Adsorbing but Nonquenching Surface for DNA Oligonucleotides

A large number of nanomaterials can strongly adsorb DNA and quench fluorescence, such as graphene oxide, gold nanoparticles, and most metal oxides. On the other hand, noncationic nanomaterials that adsorb DNA but cannot quench fluorescence are less known. These materials are attractive for studying the mechanism of DNA-based surface reactions. Y₂O₃ was found to have this property. Herein, we used fluorescently labeled oligonucleotides as probes to study the mechanism of DNA adsorption. The fluorescence was quenched at low concentrations of Y₂O₃ and then recovered and even enhanced with higher Y₂O₃ concentrations. The reason was attributed to the intermolecular quenching by the DNA bases of the neighboring strands. The fluorescence enhancement was due to breaking of the intramolecular fluorophore/DNA interactions, and the most enhancement was observed with a Cy3-labeled DNA. DNA adsorption followed the Langmuir isotherm on Y₂O₃. Desorption experiments suggested that DNA was adsorbed through the phosphate backbone, with FAM-G₁₅ and FAM-C₁₅ adsorbed more strongly than the other two DNA homopolymers. With a high salt concentration, no fluorescence change was observed, suggesting that the DNA adsorbed in a folded state reducing intermolecular quenching. Overall, Y₂O₃ might be useful as a model surface for investigating DNA hybridization on a surface.

Adsorption Promoted Aggregation-Induced Emission Showing Strong Dye Lateral Interactions

Aggregation-induced emission (AIE) is a powerful method to produce fluorescence for a diverse range of applications. While most previous work induced aggregation by change of solvent, ionic strength, pH, or self-assembly, we herein explored adsorption-induced aggregation using 4,4'-(hydrazine-1,2-diylidene bis(methanylylidene)) bis(3-hydroxybenzoic acid) (HDBB) as an AIE luminogen. HDBB is known to aggregate with AIE at low pH but not at neutral pH, and its aggregation facilitates excited state intramolecular proton transfer for enhanced emission. Using a nonquenching nanomaterial, Y₂O₃ nanoparticles, HDBB showed sevenfold fluorescence increase at pH 7.0. Fluorescence lifetime showed that HDBB was in the aggregated state in the presence of Y₂O₃. For comparison, a fluorescent porphyrin compound showed that adsorption caused quenching after mixing with Y₂O₃, whereas other dyes such as fluorescein, calcein, and rhodamine B failed to be adsorbed by Y₂O₃. Adsorption did not follow a Langmuir isotherm, but it showed strong lateral HDBB interactions because adsorption was only achieved with a high concentration of HDBB. Adsorption was inhibited by salt and by phosphate, indicating the importance of electrostatic and metal-binding interactions. Comparisons were made with other nanomaterials, where graphene oxide and CeO₂ quenched HDBB and a cationic liposome also enhanced its emission, although with a less red-shifted peak wavelength. This study provides a simple method to induce aggregation of an AIE dye and its aggregation in turn-enhanced adsorption.