An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets

Arroyo‐Currás, Netzahualcóyotl; Sadeia, Muaz; Ng, Alexander K.; Fyodorova, Yekaterina; Williams, Natalie; Afif, Tammy; Huang, Chao Min; Ogden, Nathan E.; Eguiluz, Roberto C. Andresen; Su, Hai‐Jun; Castro, Carlos E.; Lukeman, Philip S.

doi:10.1039/d0nr00952k

Cited by 16 publications

(10 citation statements)

References 37 publications

(33 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similarly, the approach can be used to interrogate E-DNA sensors containing an antibody-binding epitope, 38 aptamer-based sensors binding to protein targets, 13 or DNA-origami-based sensors binding to single-entity, mesoscale targets. 39…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…For example, previous works have shown changes in Δ E P upon hybridization of the surface-bound, MB-modified DNA with complementary strands. , In these cases, DNA hybridization moves MB further away from the electrode surface, leading to an increase in Δ E P (i.e., signal-ON sensors). Similarly, the approach can be used to interrogate E-DNA sensors containing an antibody-binding epitope, aptamer-based sensors binding to protein targets, or DNA-origami-based sensors binding to single-entity, mesoscale targets …”

Section: Results and Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids

2021

Self Cite

View full text Add to dashboard Cite

Electrochemical, aptamer-based (E-AB) sensors support continuous, real-time measurements of specific molecular targets in complex fluids such as undiluted serum. They achieve these measurements by using redox-reporter-modified, electrode-attached aptamers that undergo target binding-induced conformational changes which, in turn, change electron transfer between the reporter and the sensor surface. Traditionally, E-AB sensors are interrogated via pulse voltammetry to monitor binding-induced changes in transfer kinetics. While these pulse techniques are sensitive to changes in electron transfer, they also respond to progressive changes in the sensor surface driven by biofouling or monolayer desorption and, consequently, present a significant drift. Moreover, we have empirically observed that differential voltage pulsing can accelerate monolayer desorption from the sensor surface, presumably via field-induced actuation of aptamers. Here, in contrast, we demonstrate the potential advantages of employing cyclic voltammetry to measure electron-transfer changes directly. In our approach, the target concentration is reported via changes in the peak-to-peak separation, ΔE P, of cyclic voltammograms. Because the magnitude of ΔE P is insensitive to variations in the number of aptamer probes on the electrode, ΔE P-interrogated E-AB sensors are resistant to drift and show decreased batch-to-batch and day-to-day variability in sensor performance. Moreover, ΔE P-based measurements can also be performed in a few hundred milliseconds and are, thus, competitive with other subsecond interrogation strategies such as chronoamperometry but with the added benefit of retaining sensor capacitance information that can report on monolayer stability over time.

show abstract

Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Results and Discussionmentioning

confidence: 99%

Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids

2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, DNA origami nanostructures avoid the use of thiolated probes and, because of their larger surface area, allow the immobilization of a larger number of probes compared to TDNs. [13,14] Nevertheless, to date the use of DNA origami nanostructures in electrochemical biosensors is much smaller than that of TDNs.…”

Section: Dna Nanostructuresmentioning

confidence: 99%

Empowering Electrochemical Biosensing through Nanostructured or Multifunctional Nucleic Acid or Peptide Biomaterials

Campuzano

Pedrero

Barderas

et al. 2022

Adv Materials Technologies

View full text Add to dashboard Cite

Electrochemical biosensors continue to evolve at an astonishing pace, consolidating as competitive tools for determining a wide range of targets and relentlessly strengthening their attributes in terms of sensitivity, selectivity, simplicity, response time, and antifouling ability, making them suitable for getting a foothold in real‐world applications. The design and exploitation of nanostructured or multifunctional nucleic acid or peptide biomaterials are playing a determinant role in these achievements. With the aim of highlighting the potential and opportunities of these biomaterials, this perspective article critically discusses and overviews the electrochemical biosensors reported since 2019 involving nanostructured and multifunctional DNA biomaterials, multifunctional aptamers, modern peptides, and CRISPR/Cas systems. The use of these biomaterials as recognition elements, electrode modifiers (acting as linkers or creating scaffolds with antifouling properties), enzyme substrates, and labeling/carrier agents for signal amplification is discussed through rationally and strategically selected examples, concluding with a personal perspective about the challenges to be faced and future lines of action.

show abstract

“…In particular, the invention of the DNA origami approach, which exploits Watson-Crick base-pairing between a single-stranded DNA scaffold and multiple short staple-strands to fold the scaffold into a specific predefined geometry (2), allowed the folding of nanostructures with large surface area while simultaneously enabling spatially controlled assemblies and site-specific chemical functionalisation (3). These unique characteristics have enabled the assembly of nanostructures and patterns with controlled geometry and function, either by directly folding the scaffold (4,5), or via higher-order assembly of pre-formed DNA tiles (6)(7)(8), which found applications in biosensing (9)(10)(11)(12)(13), drug delivery (14,15), and as tools for studying biological processes (16,17), inter alia. Fuelled by these rapid developments in engineering and fabricating complex DNA nanostructures, there is an increasing demand for their characterisation, including the assessment of assembly yields.…”

Section: Introductionmentioning

confidence: 99%

Nanopore Fingerprinting of Supramolecular DNA Nanostructures

Confederat

Sandei

Mohanan

et al. 2022

Preprint

View full text Add to dashboard Cite

DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilising the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale complex multi-tile arrays. These DNA nanostructures have enabled new applications in biosensing, drug delivery and other multifunctional materials. In this study, we demonstrate real-time, non-destructive and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures using solid-state nanopores. Using this approach, we quantify the assembly yields for each DNA origami nanostructure with single-entity resolution using the nanostructure-induced charge introduced in the nanopore as a discriminant. We compare the assembly yield of the supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and AFM imaging and demonstrate that the nanopore system can provide enhanced information about the nanostructures. We envision that this nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real-time with single-molecule resolution.STATEMENT OF SIGNIFICANCEWe demonstrate a single molecule high-throughput approach for the analysis of higher-order DNA origami assemblies with a crowded nanopore. The technique enables the characterisation of DNA origami nanostructures at statistically relevant numbers in real-time and at single-molecule resolution while being non-destructive and label-free, and without the requirement of lengthy sample preparations or use of expensive reagents. We exemplify the technique by demonstrating the quantification of the assembly yield of DNA origami nanostructures based on their equivalent charge surplus computed from the ion current signals recorded. Compared to the standard analysis methods of AFM and agarose gel electrophoresis, the nanopore measurements provides enhanced information about the nanostructures.

show abstract

An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets

Abstract:
Using DNA origami as the recognition element in an electrochemical biosensor enables the selective and direct detection of “mesoscale” virus-sized analytes.

Cited by 16 publications

References 37 publications

Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids

Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids

Empowering Electrochemical Biosensing through Nanostructured or Multifunctional Nucleic Acid or Peptide Biomaterials

Nanopore Fingerprinting of Supramolecular DNA Nanostructures

Contact Info

Product

Resources

About

An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets

Abstract: Using DNA origami as the recognition element in an electrochemical biosensor enables the selective and direct detection of “mesoscale” virus-sized analytes.

Cited by 16 publications

References 37 publications

Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids

Interrogation of Electrochemical Aptamer-Based Sensors via Peak-to-Peak Separation in Cyclic Voltammetry Improves the Temporal Stability and Batch-to-Batch Variability in Biological Fluids

Empowering Electrochemical Biosensing through Nanostructured or Multifunctional Nucleic Acid or Peptide Biomaterials

Nanopore Fingerprinting of Supramolecular DNA Nanostructures

Contact Info

Product

Resources

About

Abstract:
Using DNA origami as the recognition element in an electrochemical biosensor enables the selective and direct detection of “mesoscale” virus-sized analytes.