Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design

Abstract

We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.

Ultrasensitive Controlled Release Aptasensor Using Thymine–Hg2+–Thymine Mismatch as a Molecular Switch for Hg2+ Detection

“…Gold nanoparticles (Au NPs) are a kind of widely used noble metal nanoparticles with stable properties and controllable size. In addition, gold nanoparticles can also have strong bond cooperation with sulfhydryl and other groups. , Therefore, gold nanoparticles can be applied in various fields. , As a kind of single-stranded DNA (ssDNA) synthesized by exponential enrichment, aptamers possess several characteristics including easy labeling, high affinity, and specificity toward a variety. − The two ends of the aptamer can modify different groups for a bonding reaction. − In this system, Au NPs react with sulfhydryl at the one end of a ssDNA to act as a gatekeeper. The other end of the ssDNA reacts with the aminated mesoporous silica nanocontainers to block the cargos.…”

Surface plasmon resonance aptasensor based on niobium carbide MXene quantum dots for nucleocapsid of SARS-CoV-2 detection

“…1a). Given the self-assembling effect between the Nb 2 C-SH QDs and the Au chip of SPR, Nb 2 C-SH QDs were homogeneously coated over the chip surface, and the N58 aptamer was stably immobilized through π-π * stacking, electrostatic adsorption, and hydrogen bond [54]. In the presence of SARS-CoV-2, the G-quadruplex between the N58 aptamer and N-gene of SARS-CoV-2 was formed [55].…”

Direct Screening for Cytometric Bead Assays for Adenosine Triphosphate

“…ATP is a small molecule that widely exists in cells as a coenzyme and plays key roles in chemical energy transportation within cells for metabolism. , Moreover, ATP is also regarded as an indicator for cell functions such as viability and injury . Thus, ATP detection has proven to be of great biological importance. ,, In detail, we transformed the ss DNA library to a monoclonal library of (∼10 8 ) aptamer particles through emulsion PCR as described in ref , with each aptamer particle displaying ∼10 5 identical aptamers. The aptamer particles were then quantitatively screened via flow cytometry and only those with the highest fluorescent-signal change were isolated for subsequent PCR amplification.…”

“…28 Thus, ATP detection has proven to be of great biological importance. 13,29,30 In detail, we transformed the ss DNA library to a monoclonal library of (∼10 8 ) aptamer particles through emulsion PCR as described in ref 31, with each aptamer particle displaying ∼10 5 identical aptamers. The aptamer particles were then quantitatively screened via flow cytometry and only those with the highest fluorescent-signal change were isolated for subsequent PCR amplification.…”