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Biosensors
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Aptamer-Based Sensing: Designs and Applications
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Aptamer-Based Sensing: Designs and Applications

A special issue of Biosensors (ISSN 2079-6374). This special issue belongs to the section "Biosensor Materials".

Deadline for manuscript submissions: 15 December 2025 | Viewed by 4436

Special Issue Editor

Prof. Dr. Tao Le

E-Mail Website
Guest Editor
Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing 401331, China
Interests: aptasensor; nanocomposite; biosensor; pathogen detection; immune sensing; food safety

Special Issue Information

Dear Colleagues,

Aptamers are short, single-stranded oligonucleotides that can bind to specific targets with high affinity and specificity. Their unique properties make them valuable tools in various fields, including diagnostics, therapeutics, and environmental monitoring. This Special Issue will focus on the latest advancements in aptamer-based sensing technologies, exploring innovative designs, applications, and methodologies.

We invite researchers to submit original research articles and reviews that address, but are not limited to, the following topics:

  • Biomedical diagnosis, including disease marker detection, early cancer diagnosis, infectious disease detection, etc.;
  • Food safety detecting, involving the detection of harmful substances in food, pollutants, and pathogens;
  • Environmental monitoring, including the detection of harmful substances in water quality, air, and soil;
  • Combination of nanomaterials and sensing technology, specifically studying the application of nanomaterials in enhancing aptasensor performance;
  • Development of new sensing technology, such as electrochemical sensing, fluorescence sensing, surface-enhanced Raman scattering (SERS), etc.;
  • Basic research and theoretical exploration, including aptamer screening and structure and function research.

We look forward to your contributions to this exciting Special Issue!

Prof. Dr. Tao Le
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biosensors is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • aptamer
  • aptasensor
  • DNA
  • RNA
  • screening
  • point of care
  • SELEX
  • diagnostics

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

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Research

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23 pages, 3461 KB  
Article
Plasmonic Nanosensors for EGFR Detection: Optimizing Aptamer-Based Competitive Displacement Assays
by Alexandra Falamas, Andra-Sorina Tatar, Sanda Boca and Cosmin Farcău
Biosensors 2025, 15(10), 699; https://doi.org/10.3390/bios15100699 - 15 Oct 2025
Abstract
This study presents a comparative investigation of plasmonic sensing platforms based on colloidal gold nanoparticle (AuNP) suspensions and gold film over nanosphere (AuFoN) solid substrates for the detection of epidermal growth factor receptor (EGFR), an essential biomarker and therapeutic target in oncology. The [...] Read more.
This study presents a comparative investigation of plasmonic sensing platforms based on colloidal gold nanoparticle (AuNP) suspensions and gold film over nanosphere (AuFoN) solid substrates for the detection of epidermal growth factor receptor (EGFR), an essential biomarker and therapeutic target in oncology. The strategy relies on fluorescence emission modulation of an Atto647N-labeled DNA oligomer competitively bound to an EGFR-specific aptamer. Our results demonstrate that the colloidal AuNPs can function as competitive binding sensors, leading to fluorescence quenching upon fluorophore attachment to the surface of the NPs and partial fluorescence recovery due to EGFR-induced displacement of the fluorophore–aptamer complex. This specificity was confirmed by reversed binding experiments. However, the system proved highly sensitive to the experimental design: excessive washing (centrifugation) led to unspecific aggregation and signal loss, while reduced washing steps improved signal retention and revealed EGFR-induced fluorophore displacement into the supernatant. On the contrary, film-based substrates exhibited strong initial fluorescence, but failed to retain the fluorophore–aptamer complex after washing, resulting in fluorescence decay independent of EGFR incubation. This indicates that AuFoN lacked the binding stability necessary for specific displacement-based sensing. These findings highlight that while colloidal AuNPs can support competitive binding detection, their reproducibility is limited by colloidal stability and protocol sensitivity, whereas AuFoN substrates require improved surface functionalization strategies. The study emphasizes the critical role of surface chemistry, aptamer–fluorophore affinity, and washing protocols in determining the success or failure of plasmon-enhanced aptamer-based biosensing systems and suggests opportunities for improving specificity and robustness in future designs. Full article
(This article belongs to the Special Issue Aptamer-Based Sensing: Designs and Applications)
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19 pages, 5463 KB  
Article
PEI-Fe3O4/PTA-AuNPs Hybrid System for Rapid DNA Extraction and Colorimetric LAMP Detection of E. faecium
by Muniyandi Maruthupandi, Haang Seok Choi and Nae Yoon Lee
Biosensors 2025, 15(9), 601; https://doi.org/10.3390/bios15090601 - 12 Sep 2025
Viewed by 1032
Abstract
This study introduces a novel nucleic acid testing (NAT) protocol that integrates rapid deoxyribonucleic acid (DNA) extraction, isothermal amplification, and visual detection to enable efficient analysis of opportunistic pathogens. Polyethylenimine-functionalized iron oxide (PEI-Fe3O4) nanoparticles were prepared by combining PEI, [...] Read more.
This study introduces a novel nucleic acid testing (NAT) protocol that integrates rapid deoxyribonucleic acid (DNA) extraction, isothermal amplification, and visual detection to enable efficient analysis of opportunistic pathogens. Polyethylenimine-functionalized iron oxide (PEI-Fe3O4) nanoparticles were prepared by combining PEI, acting as a stabilizing agent, with iron salt, which was utilized as the metal ion precursor by the ultrasonication-assisted co-precipitation method, and characterized for structural, optical, and magnetic properties. PEI-Fe3O4 exhibited cationic and anionic behavior in response to pH variations, enhancing adaptability for DNA binding and release. PEI-Fe3O4 enabled efficient extraction of E. faecium DNA within 10 min at 40 °C, yielding 17.4 ng/µL and achieving an extraction efficiency of ~59% compared to a commercial kit (29.5 ng/µL). The extracted DNA was efficiently amplified by loop-mediated isothermal amplification (LAMP) at 65 °C for 45 min. Pyrogallol-rich poly(tannic acid)-stabilized gold nanoparticles (PTA-AuNPs) served as colorimetric probes for direct visual detection of the DNA amplified using LAMP. The magnetic-nanogold (PEI-Fe3O4/PTA-AuNPs) hybrid system achieved a limit of quantification of 1 fg/µL. To facilitate field deployment, smartphone-based RGB analysis enabled quantitative and equipment-free readouts. Overall, the PEI-Fe3O4/PTA-AuNPs hybrid system used in NAT offers a rapid, cost-effective, and portable solution for DNA detection, making the system suitable for microbial monitoring. Full article
(This article belongs to the Special Issue Aptamer-Based Sensing: Designs and Applications)
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16 pages, 3231 KB  
Article
Aptamer-Conjugated Magnetic Nanoparticles Integrated with SERS for Multiplex Salmonella Detection
by Fan Sun, Kun Pang, Keke Yang, Li Zheng, Mengmeng Wang, Yufeng Wang, Qiang Chen, Zihong Ye, Pei Liang and Xiaoping Yu
Biosensors 2025, 15(7), 464; https://doi.org/10.3390/bios15070464 - 19 Jul 2025
Viewed by 1477
Abstract
Salmonella is a rapidly spreading and widespread zoonotic infectious disease that poses a serious threat to the safety of both poultry and human lives. Therefore, the timely detection of Salmonella in foods and animals has become an urgent need for food safety. This [...] Read more.
Salmonella is a rapidly spreading and widespread zoonotic infectious disease that poses a serious threat to the safety of both poultry and human lives. Therefore, the timely detection of Salmonella in foods and animals has become an urgent need for food safety. This work describes the construction of an aptamer-based sensor for Salmonella detection, using Fe3O4 magnetic beads and Ag@Au core–shell nanoparticles-embedded 4-mercaptobenzoic acid (4MBA). Leveraging the high affinity between biotin and streptavidin, aptamers were conjugated to Fe3O4 magnetic beads. These beads were then combined with Ag@4MBA@Au nanoparticles functionalized with complementary aptamers through hydrogen bonding and π-π stacking interactions, yielding a SERS-based aptamer sensor with optimized Raman signals from 4MBA. When target bacteria are present, aptamer-conjugated magnetic beads exhibit preferential binding to the bacteria, leading to a decrease in the surface-enhanced Raman scattering (SERS) signal. And it was used for the detection of five different serotypes of Salmonella, respectively, and the results showed that the aptamer sensor exhibited a good linear relationship between the concentration range of 102–108 CFU/mL and LOD is 35.51 CFU/mL. The SERS aptasensor was utilized for the detection of spiked authentic samples with recoveries between 94.0 and 100.4%, which proved the usability of the method and helped to achieve food safety detection. Full article
(This article belongs to the Special Issue Aptamer-Based Sensing: Designs and Applications)
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Review

Jump to: Research

22 pages, 8351 KB  
Review
Recent Progress in DNA Biosensors: Target-Specific and Structure-Guided Signal Amplification
by Jae Eon Lee and Seung Pil Pack
Biosensors 2025, 15(8), 476; https://doi.org/10.3390/bios15080476 - 23 Jul 2025
Viewed by 1210
Abstract
Deoxyribonucleic acid (DNA) is not only a fundamental biological molecule but also a versatile material for constructing sensitive and specific biosensing platforms. Its ability to undergo sequence-specific hybridization via Watson–Crick base pairing enables both precise target recognition and the programmable construction of nanoscale [...] Read more.
Deoxyribonucleic acid (DNA) is not only a fundamental biological molecule but also a versatile material for constructing sensitive and specific biosensing platforms. Its ability to undergo sequence-specific hybridization via Watson–Crick base pairing enables both precise target recognition and the programmable construction of nanoscale structures. The demand for ultrasensitive detection increases in fields such as disease diagnostics, therapeutics, and other areas, and the inherent characteristics of DNA have driven the development of a wide range of signal amplification strategies. Among these, polymerase chain reaction (PCR), rolling circle amplification (RCA), and loop-mediated isothermal amplification (LAMP) represent powerful target-based methods that enzymatically increase the concentration of nucleic acid targets, thereby boosting detection sensitivity. In parallel, structure-based strategies leverage the nanoscale spatial programmability of DNA to construct functional architectures with high precision. DNA can be used as a scaffold, such as DNA nanostructures, to organize sensing elements and facilitate signal transduction. It can also function as a probe, like aptamers, to recognize targets with high affinity. These versatilities enable the creation of highly sophisticated sensing platforms that integrate molecular recognition and signal amplification. Driven by DNA nano-assembly capability, both target-based and structure-based approaches are driving the advancement of highly sensitive, selective, and adaptable diagnostic technologies. This review highlights recent developments in DNA nano-assembly-driven amplification strategies. Full article
(This article belongs to the Special Issue Aptamer-Based Sensing: Designs and Applications)
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