Selective Hemin Binding by a Non-G-quadruplex Aptamer with Higher Affinity and Better Peroxidase-like Activity

Increasing Aptamer Affinity from Millimolar to Nanomolar by Forming a Covalent Adduct for Detecting Acrylamide

Being a neurotoxin and carcinogen, acrylamide has been an important target for developing biosensors. DNA aptamers are attractive for making biosensors due to their programmable structure, low cost, and ease of modification. However, DNA aptamers have poor affinities to low-binding epitope target molecules such as acrylamide. In this work, an aptamer for acrylamide was isolated with an apparent Kd of 10.5 mM using a thioflavin T fluorescence assay and 4.7 mM using the fluorescence strand-displacement assay. To improve binding affinity, acrylamide was reacted with xanthydrol to form a covalent adduct, and a new aptamer selected for this adduct achieved a Kd of 20 nM using the strand-displacement assay, representing an improvement of 235,000-fold. Using the strand-displacement biosensor, a limit of detection of 4.2 nM was achieved for the adduct. This work demonstrates a practical route to convert low epitope targets to high-affinity targets for aptamer binding and bioanalytical applications.

CRISPR/Cas12a Protein Switch Powered Label-Free Electrochemical Biosensor for Sensitive Viral Protease Detection

Viral proteases are critical molecular targets in viral pathogenesis, representing pivotal biomarkers for understanding viral infection mechanisms and developing antiviral therapeutics. This study introduces a label-free electrochemical biosensor that enables sensitive viral protease detection by integrating protease-responsive CRISPR/Cas protein switches (CasPSs) with a hemin aptamer-functionalized electrochemical interface. The biosensor's mechanism relies on viral protease-mediated proteolysis, which leads to the release of active Cas12a proteins from CasPSs and generates amplified electrochemical responses through continuous cleavage of immobilized redox-active hemin/aptamer complexes. This biosensor achieved specific hepatitis C virus NS3/4A protease sensing with femtomolar sensitivity and could be readily expanded to other viral proteases by replacing the CasPS module. The feasibility of this biosensor was demonstrated by monitoring enterovirus 71 3C protease activities in virus-infected cell samples with different viral loads and postinfection times. This study provides a promising strategy for integrating CRISPR biosensing with electrochemical platforms, offering a helpful analytical tool for viral infection monitoring and antiviral drug screening.

Visualizing Reactive Oxygen Species-Induced DNA Damage Process in Higher-Ordered Origami Nanostructures

The genetic information on organisms is stored in the cell nucleus in the form of higher-ordered DNA structures. Here, we use DNA framework nanostructures (DFNs) to simulate the compaction and stacking density of nucleosome DNA for precise conformational and structure determination, particularly the dynamic structural changes, preferential reaction regions, and sites of DFNs during the reactive oxygen species (ROS) reaction process. By developing an atomic force microscopy-based single-particle analysis (SPA) data reconstruction method to collect and reanalyze imaging information, we demonstrate that the geometric morphology of DFNs constrains their reaction kinetics with ROS, where local mechanical stress and regional base distribution are two key factors affecting their kinetics. Furthermore, we plot the reaction process diagram for ROS and DFNs, showing the reaction process and intermediate products with individual activation energies. This SPA method offers new research tools and insights for studying the dynamic changes of highly folded and organized DNA structural domains within the nucleus and helps to reveal the key mechanisms behind their functional differences in topologically associating domains.

Exploration and Application of the Catalytic Superiority of Non-G-Quadruplex Hemin Aptamers

A newly identified hemin aptamer with a non-G-quadruplex structure exhibits stronger peroxidase activity and selectivity than traditional G-quadruplex/hemin DNAzymes, addressing challenges such as weak hemin binding, low catalytic activity, and poor selectivity. In this study, we optimized ion activation conditions, refined reaction parameters, and developed a spontaneous recombination method via aptamer splitting to enhance DNAzyme activity and enable activity regulation. The aptamer demonstrated superior performance in enzyme-free sensing, polymerase-assisted amplification, and CRISPR/Cas12a systems, achieving higher sensitivity and improved colorimetric thresholds compared to G-quadruplexes. We have also developed a comprehensive operational guide for aptamer/hemin DNAzymes, which is poised to revolutionize colorimetric sensor signal generation elements.

Kinetic and Affinity Profiling Rare Earth Metals Using a DNA Aptamer

Rare earth elements (REEs) are widely used in various high-tech industries. Developing affinity ligands that can detect and distinguish REEs is at the forefront of analytical chemistry. It is also interesting to understand the limits of natural biomolecules for the recognition of REEs. In this study, Sc3+ was used as a target for the isolation of DNA aptamers, and an aptamer named Sc-1 was obtained. Using a thioflavin T (ThT) fluorescence assay, Sc-1 bound only to REEs, but not other metal ions. Additionally, the binding of Sc-1 to Sc3+ exhibited slow kinetics, and the binding complex resisted dissociation by EDTA. Furthermore, Sc-1 displayed varying binding kinetics with trivalent lanthanide ions, allowing for the discrimination of 17 REEs into three major groups: (1) La3+, Ce3+, Pr3+, Nd3+, Sm3+, Eu3+, and Gd3+; (2) Tb3+, Dy3+, Ho3+, Er3+, Tm3+, Yb3+, Lu3+, and Y3+; and (3) Sc3+. NMR spectroscopy confirmed binding-induced conformational changes in the aptamer. Using the fluorescence strand-displacement method, the true Kd of the aptamer was measured to range from 0.6 to 258.5 nM for the REE ions, and it showed effective detection of Sc3+ in real samples.

Dissociation Constant (Kd) Measurement for Small-Molecule Binding Aptamers: Homogeneous Assay Methods and Critical Evaluations

Since 1990, numerous aptamers have been isolated and discovered for use in various analytical, biomedical, and environmental applications. This trend continues to date. A critical step in the characterization of aptamer binding is to measure its binding affinity toward both target and non-target molecules. Dissociation constant (Kd) is the most commonly used value in characterizing aptamer binding. In this article, homogenous assays are reviewed for aptamers that can bind small-molecule targets. The reviewed methods include label-free methods, such as isothermal titration calorimetry, intrinsic fluorescence of target molecules, DNA staining dyes, and nuclease digestion assays, and labeled methods, such as the strand displacement reaction. Some methods are not recommended, such as those based on the aggregation of gold nanoparticles and the desorption of fluorophore-labeled DNA from nanomaterials. The difference between the measured apparent Kd and the true Kd of aptamer binding is stressed. In addition, avoiding the titration regime and paying attention to the time required to reach equilibrium are discussed. Finally, it is important to include mutated non-binding sequences as controls.

DNA aptamers for common buffer molecules: possibility of buffer interference in SELEX

During a typical aptamer selection experiment, buffer molecules are used at the 10 to 50 mM range, whereas target molecules could be used at much lower concentrations even in low μM levels. Therefore, doubts existed regarding the potential enrichment of buffer binding aptamers, particularly for failed selections that cannot validate binding of enriched sequences. In this study, we used two common buffer molecules, Tris and HEPES, as target molecules. While we successfully isolated aptamers for Tris buffer, our attempts to generate aptamers for HEPES buffer failed. Thioflavin T (ThT) fluorescence spectroscopy showed the dissociation constant (Kd) of the Tris buffer aptamer to be 2.9 mM, while isothermal titration calorimetry showed a Kd of 43 μM. NMR spectroscopy also confirmed aptamer binding. Finally, we discussed the implications of this buffer selection work and recommended the use of certain buffers.

DNA Catalysis: Design, Function, and Optimization

Catalytic DNA has gained significant attention in recent decades as a highly efficient and tunable catalyst, thanks to its flexible structures, exceptional specificity, and ease of optimization. Despite being composed of just four monomers, DNA's complex conformational intricacies enable a wide range of nuanced functions, including scaffolding, electrocatalysis, enantioselectivity, and mechano-electro spin coupling. DNA catalysts, ranging from traditional DNAzymes to innovative DNAzyme hybrids, highlight the remarkable potential of DNA in catalysis. Recent advancements in spectroscopic techniques have deepened our mechanistic understanding of catalytic DNA, paving the way for rational structural optimization. This review will summarize the latest studies on the performance and optimization of traditional DNAzymes and provide an in-depth analysis of DNAzyme hybrid catalysts and their unique and promising properties.

Bioinspired Dual Hemin-Bonded G-Quadruplex and Histidine-Functionalized Metal-Organic Framework for Sensitive Biosensing

Biomimetic enzymes have emerged as ideal alternatives to natural enzymes, and there is considerable interest in designing biomimetic enzymes with enhanced catalytic performance to address the low activity of the current biomimetic enzymes. In this study, we proposed a meaningful strategy for constructing an efficient peroxidase-mimicking catalyst, called HhG-MOF, by anchoring histidine (H) and dual hemin-G-quadruplex DNAzyme (double hemin covalently linked to 3' and 5' terminals of G-quadruplex DNA, short as hG) to a mesoporous metal-organic framework (MOF). This design aims to mimic the microenvironment of natural peroxidase. Remarkably, taking a terbium MOF as a typical model, the initial rate of the resulting catalyst was found to be 21.1 and 4.3 times higher than that of Hh-MOF and hG-MOF, respectively. The exceptional catalytic properties of HhG-MOF can be attributed to its strong affinity for substrates. Based on the inhibitory effect of thiocholine (TCh) produced by the reaction between acetylcholinesterase (AChE) and acetylthiocholine, a facile, cost-effective, and sensitive colorimetric method was designed based on HhG-MOF for the measurement of AChE, a marker of several neurological diseases, and its inhibitor. This allowed a linear response in the 0.002 to 1 U L-1 range, with a detection limit of 0.001 U L-1. Furthermore, the prepared sensor demonstrated great selectivity and performed well in real blood samples, suggesting that it holds promise for applications in the clinical field.

Unexpected enrichment of DNA aptamers for Zn2+ ions from an insulin selection

We serendipitously discovered Zn2+-binding DNA aptamers when selecting insulin aptamers. The Zn-1 aptamer binds to Zn2+ with a dissociation constant (Kd) of ∼1 μM, and has 450-fold higher selectivity for Zn2+ over Cd2+. A strand-displacement based fluorescent sensor achieved a limit of detection of 0.2 μM Zn2+.

Adsorption of DNA and Aptamers to Sodium Urate Crystals and Inhibition of Crystal Growth

An elevated level of blood uric acid (UA) can cause the formation of kidney stones, gout, and other diseases. We recently isolated a few DNA aptamers that can selectively bind to UA. In this work, we investigated the adsorption of a UA aptamer and random sequence DNA onto sodium urate crystals. Both DNA strands adsorbed similarly to urate crystals. In addition, both the UA aptamer and random DNA can inhibit the growth of urate crystals, suggesting a nonspecific adsorption mechanism rather than specific aptamer binding. In the presence of 500 nM DNA, the growth of needle-like sodium urate crystals was inhibited, and the crystals appeared granular after 6 h. To understand the mechanism of DNA adsorption, a few chemicals were added to desorb DNA. DNA bases contributed more to the adsorption than the phosphate backbone. Surfactants induced significant DNA desorption. Finally, DNA could also be adsorbed onto real UA kidney stones. This study provides essential insights into the interactions between DNA oligonucleotides and urate crystals, including the inhibition of growth and interface effects of DNA on sodium urate crystals.