Single-molecule DNA origami aptasensors for real-time biomarker detection

Cervantes-Salguero, Keitel; Freeley, Mark; Chávez, Jorge L.; Palma, Matteo

doi:10.1039/d0tb01291b

Cited by 15 publications

(9 citation statements)

References 48 publications

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“…Moreover, the present insights and methodologies can be useful for understanding molecular interactions. For instance, biomolecular recognition events using DNA aptasensors [ 16 ], and the interaction between single molecules positioned near a functional surface [ 96 , 97 ] could be investigated. Finally, our experimental and modeling methodology can be useful for investigating the interaction of molecular components tethered to soft matter systems based on polymers such as in the emerging fields of RNA [ 98 ] and protein [ 99 ] origami.…”

Section: Discussionmentioning

confidence: 99%

“…Although nature uses proteins as templates to orchestrate the directional arrangement of molecules [ 13 ], scientists have harnessed DNA as a programmable polymer [ 1 ], with specific self-assembly via Watson-Crick hydrogen base-pairing rules, to fabricate templates of nanometric spacing. Single molecules and single nanoparticles have been spatially arranged using DNA for applications including tissue engineering [ 14 ], cellular delivery [ 15 ], single molecule biosensing [ 16 , 17 ], nanomemories [ 18 ], nanophotonics [ 19 , 20 , 21 ], and excitonics [ 22 , 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

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Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Cervantes-Salguero

Biaggne

Youngsman

et al. 2022

IJMS

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Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Cervantes-Salguero

Biaggne

Youngsman

et al. 2022

IJMS

Self Cite

View full text Add to dashboard Cite

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“…Today, based on defined physicochemical properties, aptasensors are commonly classified into electrochemical, optical, and mass-sensitive aptasensors (Figure 4). Particularly, aptasensor platforms that employ solid supports during sensing provide an opportunity for the measurement of analytes in real time [75,[143][144][145]. In addition, current aptasensor developments pursue simultaneous measurement of multiple aptamer targets (multiplexing) as well as miniaturization.…”

Section: Aptamer-based Biosensors For Diagnostic Applications To Mpsmentioning

confidence: 99%

Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications

et al. 2023

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Many biological processes (physiological or pathological) are relevant to membrane proteins (MPs), which account for almost 30% of the total of human proteins. As such, MPs can serve as predictive molecular biomarkers for disease diagnosis and prognosis. Indeed, cell surface MPs are an important class of attractive targets of the currently prescribed therapeutic drugs and diagnostic molecules used in disease detection. The oligonucleotides known as aptamers can be selected against a particular target with high affinity and selectivity by iterative rounds of in vitro library evolution, known as Systematic Evolution of Ligands by EXponential Enrichment (SELEX). As an alternative to antibodies, aptamers offer unique features like thermal stability, low-cost, reuse, ease of chemical modification, and compatibility with various detection techniques. Particularly, immobilized-aptamer sensing platforms have been under investigation for diagnostics and have demonstrated significant value compared to other analytical techniques. These “aptasensors” can be classified into several types based on their working principle, which are commonly electrochemical, optical, or mass-sensitive. In this review, we review the studies on aptamer-based MP-sensing technologies for diagnostic applications and have included new methodological variations undertaken in recent years.

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“…Small DNA strands protruding from each unit, called sticky ends, allow the selective binding of units via DNA base pairing. Whereas using large and relatively robust DNA units, such as DNA origami, provide abundant space per unit for molecular arrangement and functionality [8,9,[12][13][14][15][16]21,22], small units provide simplicity and a large quantity of units per volume as they are composed of a few addressable DNA strands [3,20,[23][24][25][26][27]. The addressability of such strands may provide a high density of functional moieties per unit in a large nanosheet, which can help with promoting adhesion to surfaces.…”

Section: Introductionmentioning

confidence: 99%

Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization

et al. 2023

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DNA is programmed to hierarchically self-assemble into superstructures spanning from nanometer to micrometer scales. Here, we demonstrate DNA nanosheets assembled out of a rationally designed flexible DNA unit (F-unit), whose shape resembles a Feynman diagram. F-units were designed to self-assemble in two dimensions and to display a high DNA density of hydrophobic moieties. oxDNA simulations confirmed the planarity of the F-unit. DNA nanosheets with a thickness of a single DNA duplex layer and with large coverage (at least 30 μm × 30 μm) were assembled from the liquid phase at the solid/liquid interface, as unambiguously evidenced by atomic force microscopy imaging. Interestingly, single-layer nanodiscs formed in solution at low DNA concentrations. DNA nanosheet superstructures were further assembled at liquid/liquid interfaces, as demonstrated by the fluorescence of a double-stranded DNA intercalator. Moreover, the interfacial mechanical properties of the nanosheet superstructures were measured as a response to temperature changes, demonstrating the control of interfacial shear mechanics based on DNA nanostructure engineering. The rational design of the F-unit, along with the presented results, provide an avenue toward the controlled assembly of reconfigurable/responsive nanosheets and membranes at liquid/liquid interfaces, to be potentially used in the characterization of biomechanical processes and materials transport.

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Single-molecule DNA origami aptasensors for real-time biomarker detection

Abstract: Here we report the use of DNA nanostructures as platforms to monitor aptamers inherent conformational changes upon analyte binding, with single-molecule resolution and real-time capability. An aptasensor designed to sense...

Cited by 15 publications

References 48 publications

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications

Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization

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