An electrochemical impedimetric sensing platform based on a peptide aptamer identified by high-throughput molecular docking for sensitive l-arginine detection

He, Yumin; Zhou, Li; Deng, Lei; Feng, Zemeng; Cao, Zhong; Yin, Yan

doi:10.1016/j.bioelechem.2020.107634

Cited by 40 publications

(13 citation statements)

References 48 publications

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“…He et al (2020) introduced an electrochemical aptasensor for the sensitive monitoring of l ‐arginine by using the hybrid method, including MD simulation and molecular docking. The potential interaction between the peptide aptamers and l ‐arginine was predicted by using molecular docking.…”

Section: Computational Methods As a Complement Of Experimental Technimentioning

confidence: 99%

Recent advances in computational methods for biosensor design

Khoshbin

Housaindokht

Izadyar

et al. 2020

Biotech & Bioengineering

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Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost‐effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast‐growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.

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Section: Computational Methods As a Complement Of Experimental Technimentioning

confidence: 99%

Recent advances in computational methods for biosensor design

Khoshbin

Housaindokht

Izadyar

et al. 2020

Biotech & Bioengineering

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“…Up to now, various researches have been performed a lot of research regarding the molecular dynamic and docking simulation to investigate the behavior of protein, aptamer, ligands, and peptides in the atomic scale [30,31]. In 2021, He et al [32] performed molecular docking simulations for an electrochemical impedimetric sensing platform based on a peptide aptamer, and they found the binding capacity of peptide aptamers by molecular docking and demonstrated that docking was an effective tool to screen peptide aptamers for amino acid-binding capacity.…”

Section: Introductionmentioning

confidence: 99%

[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein

Asadzadeh

Moosavi

Alexandrakis

et al. 2021

BioMed Research International

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Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for selecting the aptamer candidate with the highest binding strength to a target. We combine information from the binding free energy calculations, molecular docking, and molecular dynamics simulations to investigate the interactions of both aptamers with TNF-α. The results reveal that the RNA aptamer has a more stable structure relative to the DNA aptamer. Interaction of aptamers with TNF-α does not have any negative effect on its structure. The results of molecular docking and molecular dynamics simulations suggest that the RNA aptamer has a stronger interaction with the protein. Also, these findings illustrate that basic residues of TNF-α establish more atomic contacts with the aptamers compared to acidic or pH-neutral ones. Furthermore, binding energy calculations show that the interaction of the RNA aptamer with TNF-α is thermodynamically more favorable. In total, the findings of this study indicate that the RNA aptamer is a more suitable candidate for using as an apta-biosensor of TNF-α and, therefore, of greater potential use for the diagnosis of blood infections. Also, this study provides more information about aptamer-protein interactions and increases our understanding of this phenomenon.

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“…Furthermore, GNPs are more biocompatible, easier to bioconjugate, and less toxic than QDs [61]. Feng et al fabricated an electrochemical impedance spectroscopy (EIS)-based biosensor for L-Arg detection, which exhibited acceptable performance in the linear range of 0.1 pM-0.1 mM with a detection limit of 0.01 pM [62].…”

Section: Aptamer-based Biosensorsmentioning

confidence: 99%

A Review on Biosensors and Recent Development of Nanostructured Materials-Enabled Biosensors

Naresh

Lee

2021

Sensors

930

427

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A biosensor is an integrated receptor-transducer device, which can convert a biological response into an electrical signal. The design and development of biosensors have taken a center stage for researchers or scientists in the recent decade owing to the wide range of biosensor applications, such as health care and disease diagnosis, environmental monitoring, water and food quality monitoring, and drug delivery. The main challenges involved in the biosensor progress are (i) the efficient capturing of biorecognition signals and the transformation of these signals into electrochemical, electrical, optical, gravimetric, or acoustic signals (transduction process), (ii) enhancing transducer performance i.e., increasing sensitivity, shorter response time, reproducibility, and low detection limits even to detect individual molecules, and (iii) miniaturization of the biosensing devices using micro-and nano-fabrication technologies. Those challenges can be met through the integration of sensing technology with nanomaterials, which range from zero- to three-dimensional, possessing a high surface-to-volume ratio, good conductivities, shock-bearing abilities, and color tunability. Nanomaterials (NMs) employed in the fabrication and nanobiosensors include nanoparticles (NPs) (high stability and high carrier capacity), nanowires (NWs) and nanorods (NRs) (capable of high detection sensitivity), carbon nanotubes (CNTs) (large surface area, high electrical and thermal conductivity), and quantum dots (QDs) (color tunability). Furthermore, these nanomaterials can themselves act as transduction elements. This review summarizes the evolution of biosensors, the types of biosensors based on their receptors, transducers, and modern approaches employed in biosensors using nanomaterials such as NPs (e.g., noble metal NPs and metal oxide NPs), NWs, NRs, CNTs, QDs, and dendrimers and their recent advancement in biosensing technology with the expansion of nanotechnology.

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An electrochemical impedimetric sensing platform based on a peptide aptamer identified by high-throughput molecular docking for sensitive l-arginine detection

Cited by 40 publications

References 48 publications

Recent advances in computational methods for biosensor design

Recent advances in computational methods for biosensor design

[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein

A Review on Biosensors and Recent Development of Nanostructured Materials-Enabled Biosensors

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