Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

Jeddi, Iman; Saiz, Leonor

doi:10.1038/s41598-021-88796-2

Cited by 11 publications

(2 citation statements)

References 36 publications

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“…This not only impacts their conformation but also enhances the comprehension of DNA-aptamer interactions with the PDA surface. However, previous experimental and computational studies have demonstrated that the orientation or conformation of a tethered biorecognition element on a biosensor surface can alter upon immobilization, significantly affecting the biosensor’s performance ( Wong and Pettitt, 2004 ; Jeddi and Saiz, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

DNA aptamer-functionalized PDA nanoparticles: from colloidal chemistry to biosensor applications

Zaw,

Noon Shean Aye,

Daduang

et al. 2024

Front. Bioeng. Biotechnol.

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Polydopamine nanoparticles (PDA NPs) are widely utilized in the field of biomedical science for surface functionalization because of their unique characteristics, such as simple and low-cost preparation methods, good adhesive properties, and ability to incorporate amine and oxygen-rich chemical groups. However, challenges in the application of PDA NPs as surface coatings on electrode surfaces and in conjugation with biomolecules for electrochemical sensors still exist. In this work, we aimed to develop an electrochemical interface based on PDA NPs conjugated with a DNA aptamer for the detection of glycated albumin (GA) and to study DNA aptamers on the surfaces of PDA NPs to understand the aptamer-PDA surface interactions using molecular dynamics (MD) simulation. PDA NPs were synthesized by the oxidation of dopamine in Tris buffer at pH 10.5, conjugated with DNA aptamers specific to GA at different concentrations (0.05, 0.5, and 5 μM), and deposited on screen-printed carbon electrodes (SPCEs). The charge transfer resistance of the PDA NP-coated SPCEs decreased, indicating that the PDA NP composite is a conductive bioorganic material. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) confirmed that the PDA NPs were spherical, and dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR), and Raman spectroscopy data indicated the successful conjugation of the aptamers on the PDA NPs. The as-prepared electrochemical interface was employed for the detection of GA. The detection limit was 0.17 μg/mL. For MD simulation, anti-GA aptamer through the 5′terminal end in a single-stranded DNA-aptamer structure and NH2 linker showed a stable structure with its axis perpendicular to the PDA surface. These findings provide insights into improved biosensor design and have demonstrated the potential for employing electrochemical PDA NP interfaces in point-of-care applications.

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Section: Resultsmentioning

confidence: 99%

DNA aptamer-functionalized PDA nanoparticles: from colloidal chemistry to biosensor applications

Zaw,

Noon Shean Aye,

Daduang

et al. 2024

Front. Bioeng. Biotechnol.

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“…Besides the choice of the chemical conjugation route, aptamer immobilization should also be tailored in terms of the surface coverage density and orientation to achieve the proper functional folding of the aptamers [ 100 , 101 , 102 ]. Proper aptamer density on a surface is crucial for achieving sufficient binding sites for the target, while minimizing steric hindrance and electrostatic repulsion between neighboring aptamers.…”

Section: Aptasensorsmentioning

confidence: 99%

Aptasensors versus immunosensors—Which will prevail?

Arshavsky‐Graham

Heuer

Xin

et al. 2022

Engineering in Life Sciences

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Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.

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Molecular dynamics simulation and experiment study on a displacement-based electrochemical dual-signal response of interfacial kanamycin aptamer probe

Xiang,

Liu,

Han

et al. 2024

Applied Surface Science

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Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

Cited by 11 publications

References 36 publications

DNA aptamer-functionalized PDA nanoparticles: from colloidal chemistry to biosensor applications

DNA aptamer-functionalized PDA nanoparticles: from colloidal chemistry to biosensor applications

Aptasensors versus immunosensors—Which will prevail?

Molecular dynamics simulation and experiment study on a displacement-based electrochemical dual-signal response of interfacial kanamycin aptamer probe

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