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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 October 2026 | Viewed by 12118

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 250 words) can be sent to the Editorial Office for assessment.

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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Published Papers (7 papers)

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Research

Jump to: Review

13 pages, 5029 KB  
Article
A Simple and Visual Colorimetric Aptasensor Based on AuNPs for the Rapid Detection of Sulfamethazine in Environmental Samples
by Luwei Chai, Yarong Wang, Shuang Jiang, Xue Wang, Yong Xie and Tao Le
Biosensors 2026, 16(2), 103; https://doi.org/10.3390/bios16020103 - 5 Feb 2026
Viewed by 728
Abstract
Sulfamethazine (SMZ) is widely used in livestock production, and its residues can enter water and soil environments, posing potential risks to human health and ecosystems. This study focuses on environmental samples and constructs an AuNP-based colorimetric aptasensor using the SMZ1S aptamer for the [...] Read more.
Sulfamethazine (SMZ) is widely used in livestock production, and its residues can enter water and soil environments, posing potential risks to human health and ecosystems. This study focuses on environmental samples and constructs an AuNP-based colorimetric aptasensor using the SMZ1S aptamer for the rapid visual detection of SMZ. Under optimized conditions, the aptasensor showed a wide linear range from 0.05 to 0.4 µg/mL and a limit of detection of 0.039 µg/mL. Molecular dynamics simulations have demonstrated that the aptamer’s binding to SMZ is stable, providing a theoretical basis for the high selectivity of the aptasensor. Spike-and-recovery experiments yielded recoveries of 87.3–105.5%, 88.6–102.8%, and 87.5–103.4% for SMZ in lake water, tap water, and soil samples, respectively, with relative standard deviations of 5.9–8.3%, 8.0–10.6%, and 4.8–9.6%, showing good agreement with high-performance liquid chromatography (HPLC) results (R2 ≥ 0.981). Overall, the proposed aptasensor provides a simple and effective approach for rapid detection of SMZ in environmental samples. Full article
(This article belongs to the Special Issue Aptamer-Based Sensing: Designs and Applications)
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15 pages, 4766 KB  
Article
Electrochemical/Colorimetric Dual-Mode Aptasensor Based on CuZr-MOF and Fe3O4@ZIF-8 for Detection of Malathion in Vegetables
by Kaili Liu, Jiwei Dong, Youkai Wang, Jiashuai Sun, Peisen Li, Yemin Guo and Xia Sun
Biosensors 2026, 16(2), 101; https://doi.org/10.3390/bios16020101 - 4 Feb 2026
Viewed by 590
Abstract
In on-site rapid detection, the electrochemical method boasts high sensitivity and rapid response capabilities, while the colorimetric method can provide intuitive visual readings suitable for on-site screening. Therefore, this study developed an innovative dual-mode electrochemical/colorimetric aptasensor for the accurate detection of malathion (MAL) [...] Read more.
In on-site rapid detection, the electrochemical method boasts high sensitivity and rapid response capabilities, while the colorimetric method can provide intuitive visual readings suitable for on-site screening. Therefore, this study developed an innovative dual-mode electrochemical/colorimetric aptasensor for the accurate detection of malathion (MAL) in vegetables. The sensor combines magnetic Fe3O4@ZIF-8-DNA composites and CuZr-MOF-cDNA probes, enabling simultaneous detection of the target through electrochemical reactions and colorimetric changes. The introduction of CuZr-MOF not only enhances the sensor’s conductivity but also significantly amplifies the electrochemical signal through its catalytic properties. The magnetic Fe3O4@ZIF-8-DNA composite facilitates solid–liquid separation under an external magnetic field. When the target MAL is present, the aptamer binds to the target, causing the CuZr-MOF-cDNA probes to release from the composite, altering the number of free probes in the supernatant and generating varying intensities of colorimetric signals. Meanwhile, the MAL captured in the precipitate by the aptamer is quantitatively detected through electrochemical methods. Experimental results demonstrate that as the target concentration increases, the colorimetric signal intensifies while the electrochemical signal weakens, showing a good linear relationship between the two. The aptasensor’s limit of detection (LOD) for colorimetric and electrochemical modes was 1.57 × 10−11 M and 4.76 × 10−11 M, respectively, with recoveries ranging from 87.71% to 107.68% and relative standard deviations between 3.23% and 10.75%. This method exhibits high sensitivity, excellent selectivity, and strong reliability, providing a novel technique for the accurate quantification of MAL in vegetables, particularly suited for on-site rapid detection. Full article
(This article belongs to the Special Issue Aptamer-Based Sensing: Designs and Applications)
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16 pages, 3740 KB  
Article
The Role of Surfactants in Stabilizing Fluorescence Anisotropy for Protein–Aptamer Binding Affinity Measurements
by Bhagya R. Samarakoon, Susan L. Bilderback and Rebecca J. Whelan
Biosensors 2025, 15(12), 801; https://doi.org/10.3390/bios15120801 - 6 Dec 2025
Cited by 1 | Viewed by 1221
Abstract
Fluorescence Anisotropy (FA) is a sensitive and efficient technique for quantifying biomolecular interactions, offering advantages such as minimal sample requirements and elimination of separation of bound from unbound species. Thus, it is well suited for aptamer–protein binding affinity studies. However, accurately determining equilibrium [...] Read more.
Fluorescence Anisotropy (FA) is a sensitive and efficient technique for quantifying biomolecular interactions, offering advantages such as minimal sample requirements and elimination of separation of bound from unbound species. Thus, it is well suited for aptamer–protein binding affinity studies. However, accurately determining equilibrium dissociation constants (KD) in FA requires low concentrations of fluorescently labeled aptamers to prevent ligand depletion. A significant challenge arises at low aptamer concentrations due to an unexpected and physically nonmeaningful increase in apparent anisotropy, which impairs accurate data fitting. This anomalous increase in apparent anisotropy may arise from non-specific adsorption of aptamers to surfaces. In this study, we investigated the use of non-ionic surfactants to mitigate these effects and stabilize the anisotropy signal at low aptamer concentrations using the thrombin aptamer as a model system. We evaluated the impact of varying concentrations of two surfactants (Tween 20 and Triton X-100) on plots of anisotropy as a function of aptamer concentration and determined aptamer–protein binding affinities. Addition of 0.1% Tween 20 corrects the anomalous increase in anisotropy at low aptamer concentrations, enabling the use of aptamer concentrations as low as 5 nM in binding assays. Triton X-100 was less effective. By incorporating optimized concentrations of Tween 20, we demonstrated improved assay reproducibility and accuracy in KD determination, expanding the dynamic range of usable aptamer concentrations in FA-based binding affinity studies. Similar benefits were observed with the clinically relevant aptamer s10yh2 and human serum albumin. These findings provide a practical strategy for enhancing the robustness of FA measurements and may be applicable to other aptamer–target systems and high-throughput assay formats. Full article
(This article belongs to the Special Issue Aptamer-Based Sensing: Designs and Applications)
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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
Cited by 1 | Viewed by 1413
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
Cited by 1 | Viewed by 1702
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
Cited by 6 | Viewed by 3031
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

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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
Cited by 4 | Viewed by 2480
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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