arXiv subjects

Netzahualcóyotl Arroyo-Currás

Publications and source records attributed to Netzahualcóyotl Arroyo-Currás.

4 recordsLinked to original sources

arXiv2026

Electrochemical DNA Hairpin Sensors for Differentiating Small Molecule Intercalation from Minor Groove Binding

Small molecule double-stranded DNA intercalators have significant potential for therapeutic applications. However, screening for and confirming a drug candidate's intercalative behavior remains labor-intensive and costly. To address this, we investigated the sequence and biophysical parameters that affect the performance of electrochemical DNA hairpin sensors for streamlined identification of structural intercalators. These sensors utilize oligonucleotide (oligo) sequences that form hairpins upon intercalator binding. The 3prime end of the oligo is modified with alkylthiol linkers for gold electrode surface monolayer self-assembly, while the 5prime end carries a methylene blue redox reporter. Hairpin formation enhances electron transfer between methylene blue and the gold electrode, which can be detected via voltammetry. We tested seven hairpin structures varying in stem length and sequence. Our optimal oligo, HP4, features a four-base-pair stem and responds to five DNA intercalators over a broad detection range, with EC50 in close agreement with published affinity (KD) values for these interactions. We further demonstrate HP4s ability to discriminate intercalator binding from a series of minor groove binders through significant differences in signal gain upon incubation. Altogether, our strategy establishes a platform for identifying intercalative compounds that should support the development of DNA-targeting therapeutics.

physics.bio-ph↗

arXiv2024

Extended electrochemical monitoring of biomolecular binding using commercially available, reusable electrodes in microliter volumes

Electrochemical biosensors ("E-AB" or "E-DNA" type sensors) that utilize square-wave voltammetry originated in academic labs with a few standard experimental configurations for the electrochemical cell and data analysis. We report here on adaptations of these approaches that are friendly to novice scientists such as those in undergraduate laboratories. These approaches utilize commercially available components, low volumes, work over extended periods and enable facile analysis using a custom excel sheet.

physics.bio-ph↗

arXiv2024

Modular DNA origami-based electrochemical detection of DNA and proteins

The diversity and heterogeneity of biomarkers has made the development of general methods for single-step quantification of analytes difficult. For individual biomarkers, electrochemical methods that detect a conformational change in an affinity binder upon analyte binding have shown promise. However, because the conformational change must operate within a nanometer-scale working distance, an entirely new sensor, with a unique conformational change, must be developed for each analyte. Here, we demonstrate a modular electrochemical biosensor, built from DNA origami, which is easily adapted to diverse molecules by merely replacing its analyte binding domains. Instead of relying on a unique nanometer-scale movement of a single redox reporter, all sensor variants rely on the same 100-nanometer scale conformational change, which brings dozens of reporters close enough to a gold electrode surface that a signal can be measured via square wave voltammetry, a standard electrochemical technique. To validate our sensor's mechanism, we used single-stranded DNA as an analyte, and optimized the number of redox reporters and various linker lengths. Adaptation of the sensor to streptavidin and PDGF-BB analytes was achieved by simply adding biotin or anti-PDGF aptamers to appropriate DNA linkers. Geometrically-optimized streptavidin sensors exhibited signal gain and limit of detection markedly better than comparable reagentless electrochemical sensors. After use, the same sensors could be regenerated under mild conditions: performance was largely maintained over four cycles of DNA strand displacement and rehybridization. By leveraging the modularity of DNA nanostructures, our work provides a straightforward route to the single-step quantification of arbitrary nucleic acids and proteins.

physics.bio-ph↗

arXiv2024

Extending the Operational Lifetime of Nucleic Acid-Based Electrochemical Sensors via Protection Against Competitive Displacement of Oligonucleotides

Nucleic acid-based electrochemical sensors (NBEs) have emerged as a promising approach to continuous molecular monitoring in vivo. NBEs consist of electrically conducting gold surfaces coated with self-assembled monolayers of a mixture of electrode-passivating alkylthiols and functional alkylthiol-modified oligos. These oligos also display binding sites for the target analyte and redox reporters able to transfer electrons to the underlying gold electrode. Although sufficiently robust for continuous, multi-hour sensing of small molecules and proteins in biological fluids both in vitro and in vivo, NBEs decay over periods longer than 12 hours of continuous operation in these fluids. To address this issue, here we report a biofluid mimetic that can be leveraged to specifically study competitive displacement of oligonucleotides from NBEs, a critical sensor degradation pathway. Using this mimetic, we demonstrate three strategies that drastically mitigate competitive displacement and improve sensor stability in vitro. A combination of these strategies also improves sensor stability in vivo, demonstrated here via sensors emplaced in the brain cortex of live rats.

physics.bio-ph↗