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Biosensors
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Nucleic Acid Aptamer-Based Bioassays
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Nucleic Acid Aptamer-Based Bioassays

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

Deadline for manuscript submissions: closed (31 May 2025) | Viewed by 2771

Special Issue Editors

Dr. Jee-Woong Park

E-Mail Website
Guest Editor
Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu, Republic of Korea
Interests: aptamer; biosensor; SPR; molecular diagnosis; loop-mediated isothermal amplification; acoustophoresis
Special Issues, Collections and Topics in MDPI journals
Dr. Su Jin Lee

E-Mail
Guest Editor
Daegu Gyeongbuk Medical Innovation Foundation (K-MEDI hub), Daegu, Republic of Korea
Interests: aptamer; SELEX; aptamer based bioassays

Special Issue Information

Dear Colleagues,

Nucleic acid aptamer-based bioassays utilize the high specificity and affinity of DNA and RNA aptamers for a wide range of applications in diagnostics and environmental monitoring. These aptamers can be chemically synthesized with high precision and purity, making their production faster and more cost-effective compared to other molecules.

The Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is essential for identifying high-affinity aptamers, which are short, single-stranded DNA or RNA molecules.
Aptamer biosensors, or aptasensors, leverage these aptamers to detect various analytes with remarkable specificity and sensitivity. Electrochemical aptamer sensors are particularly notable for their robust and straightforward signal transduction, enabling the precise quantification of targets from small molecules to proteins and even whole cells.

A critical aspect of enhancing aptamer applications involves aptamer truncation, a process that shortens the aptamer while maintaining its binding affinity and specificity. This improves performance and reduces the cost of aptasensors. Predictive models and computational tools are vital in this optimization, simulating aptamer–target interactions to identify minimal functional sequences.

Research in this field focuses on combining efficient SELEX with advanced predictive algorithms or post-SELEX processes for truncation or engineering aptamers to develop efficient and cost-effective aptasensors, advancing innovative diagnostic tools in nucleic acid aptamer-based bioassays.

Dr. Jee-Woong Park
Dr. Su Jin Lee
Guest Editors

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

  • SELEX
  • aptamer biosensor
  • aptasensor
  • electrochemical aptamer sensor
  • aptamer truncation
  • prediction of aptamer

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Published Papers (2 papers)

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Review

45 pages, 7078 KB  
Review
Recent Advances in the Optimization of Nucleic Acid Aptamers and Aptasensors
by Yuan Wang and Mengyan Nie
Biosensors 2025, 15(10), 641; https://doi.org/10.3390/bios15100641 - 25 Sep 2025
Viewed by 990
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules that can bind to a target with high specificity and affinity, as screened by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). In recent years, SELEX technologies have been significantly advanced for the [...] Read more.
Nucleic acid aptamers are single-stranded DNA or RNA molecules that can bind to a target with high specificity and affinity, as screened by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). In recent years, SELEX technologies have been significantly advanced for the screening of aptamers for a variety of target molecules, cells, and even bacteria and viruses. By integrating recent advances of emerging technologies with SELEX, novel screening technologies for nucleic acid aptamers have emerged with improved screening efficiency, reduced production costs and enhanced aptamer performance for a wide range of applications in medical diagnostics, drug delivery, and environmental monitoring. Aptasensors utilize aptamers to detect a wide range of analytes, allowing for the accurate identification and determination of small molecules, proteins, and even whole cells with remarkable specificity and sensitivity. Further optimization of the aptasensor can be achieved by aptamer truncation, which not only maintains the high specificity and affinity of the aptamer binding with the target analytes, but also reduces the manufacturing cost. Predictive models also demonstrate the powerful capability of determination of the minimal functional sequences by simulation of aptamer–target interaction processes, thus effectively shortening the aptamer screening procedure and reducing the production costs. This paper summarizes the research progress of protein-targeted aptamer screening in recent years, introduces several typical aptasensors at present, discusses the optimization methods of aptasensors by combining efficient SELEX with advanced predictive algorithms or post-SELEX processes, as well as the challenges and opportunities faced by aptasensors. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamer-Based Bioassays)
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54 pages, 3531 KB  
Review
Designing the Future of Biosensing: Advances in Aptamer Discovery, Computational Modeling, and Diagnostic Applications
by Robert G. Jesky, Louisa H. Y. Lo, Ryan H. P. Siu and Julian A. Tanner
Biosensors 2025, 15(10), 637; https://doi.org/10.3390/bios15100637 - 24 Sep 2025
Viewed by 1343
Abstract
Recent advances in computational tools, particularly machine learning (ML), deep learning (DL), and structure-based modeling, are transforming aptamer research by accelerating discovery and enhancing biosensor development. This review synthesizes progress in predictive algorithms that model aptamer–target interactions, guide in silico sequence optimization, and [...] Read more.
Recent advances in computational tools, particularly machine learning (ML), deep learning (DL), and structure-based modeling, are transforming aptamer research by accelerating discovery and enhancing biosensor development. This review synthesizes progress in predictive algorithms that model aptamer–target interactions, guide in silico sequence optimization, and streamline design workflows for both laboratory and point-of-care diagnostic platforms. We examine how these approaches improve key aspects of aptasensor development, such as aptamer selection, sensing surface immobilization, signal transduction, and molecular architecture, which contribute to greater sensitivity, specificity, and real-time diagnostic capabilities. Particular attention is given to illuminating the technological and experimental advances in structure-switching aptamers, dual-aptamer systems, and applications in electrochemical, optical, and lateral flow platforms. We also discuss current challenges such as the standardization of datasets and interpretability of ML models and highlight future directions that will support the translation of aptamer-based biosensors into scalable, point-of-care and clinically deployable diagnostic solutions. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamer-Based Bioassays)
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