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Molecular Recognition and Biosensing
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Molecular Recognition and Biosensing

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 20 May 2026 | Viewed by 14463

Special Issue Editor

Dr. Longjiao Zhu

E-Mail Website
Guest Editor
Department of Nutrition and Health, China Agricultural University, No. 10, Tianxiu Road, Beijing 100193, China
Interests: functional nucleic acids; nanomaterial; food safety; nutrition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular recognition, a fundamental process in biology and chemistry, involves the specific interaction between a receptor and its ligand. This interaction is crucial for biological processes such as cell signaling, immune response, and metabolic regulation. Biosensing, on the other hand, utilizes biological components or systems to detect and quantify analytes of interest. Biosensors, which integrate molecular recognition elements with signal transduction mechanisms, have found widespread applications in healthcare, environmental monitoring, food safety, and security.

Recent advancements in nanotechnology have significantly enhanced the capabilities of biosensors. Nanomaterials, such as gold nanoparticles and nanozymes, offer unique properties that can improve the sensitivity, selectivity, and stability of biosensors. For instance, gold nanoparticles can enhance the fluorescence resonance energy transfer process, enabling highly sensitive nucleic acid detection. Similarly, defective nanozymes with catalase-mimicking characteristics have shown promising results in tetracycline degradation.

Despite the significant progress made in molecular recognition and biosensing, several challenges remain. These include the scalability of production processes, the reproducibility of results, and the integration of biosensors into practical applications. To address these shortcomings, research focus on the points below are welcomed in this Special Issue:

  • Development of Novel Molecular Recognition Elements (such as aptamers and peptide nucleic acids);
  • Integration of Nanotechnology;
  • Multimodal Biosensing;
  • Real-Time Monitoring and Point-of-Care Diagnostics;
  • Enhanced Sensitivity and Specificity;
  • Miniaturization and Integration;
  • Multifunctionality and Versatility;
  • Developing Robust and Scalable Production Methods;
  • Improving Reproducibility and Standardization;
  • Exploring New Applications and Environments.

Dr. Longjiao Zhu
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • molecular recognition
  • biosensor
  • nanomaterials
  • aptamer
  • nucleic acids
  • sensitivity

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Published Papers (5 papers)

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Research

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14 pages, 2217 KB  
Article
Creation of an Engineered Oxygen-Insensitive L-Glutamate Oxidase for the Application of Electrochemical L-Glutamate Sensors
by Mika Hatada, Shouhei Takamatsu, Ryutaro Asano, Kazunori Ikebukuro, Wakako Tsugawa and Koji Sode
Int. J. Mol. Sci. 2026, 27(6), 2831; https://doi.org/10.3390/ijms27062831 - 20 Mar 2026
Viewed by 337
Abstract
L-glutamate (L-Glu) is the primary excitatory neurotransmitter in the mammalian central nervous system. Developing a real-time monitoring system is essential to understanding the onset and progression of related conditions. However, the absence of an L-Glu dehydrogenase that is insensitive to oxygen limits the [...] Read more.
L-glutamate (L-Glu) is the primary excitatory neurotransmitter in the mammalian central nervous system. Developing a real-time monitoring system is essential to understanding the onset and progression of related conditions. However, the absence of an L-Glu dehydrogenase that is insensitive to oxygen limits the development of oxygen-independent electrochemical enzymatic sensors. Additionally, the most commonly used L-Glu-specific oxidase requires site-specific proteolytic post-translational modifications in specific host microorganisms, which makes protein engineering difficult. To address these issues, L-Glu oxidase derived from Streptomyces mobaraensis (SmEOx), which does not require post-translational modifications, was engineered to function as a dehydrogenase. Residues crucial for the oxidative half reaction with oxygen in SmEOx were identified, and mutagenesis studies were conducted. Mutant SmEOx variants with suppressed oxidase activity and improved dye-mediated dehydrogenase activity compared to the wild-type enzyme were successfully obtained. The ratio of dehydrogenase activity to oxidase activity (Dh/Ox) increased ~2900-fold in mutant M117I and ~6700-fold in mutant M117F/K400N compared to wild-type recombinant SmEOx. The resulting virtually L-Glu dehydrogenases (vEDHs) were modified with a redox mediator and evaluated using transient open-circuit potential (OCP)-based L-Glu measurements. As a result, the vEDH (M117F/K400N mutant)-immobilized electrode enabled electrochemical L-Glu detection under ambient oxygen without the need for an external electron mediator, unlike the wild-type enzyme. The created vEDH, together with the OCP sensor developed using it, paves the way for future development of miniaturized, real-time L-Glu monitoring systems with high temporal and spatial resolution. Full article
(This article belongs to the Special Issue Molecular Recognition and Biosensing)
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15 pages, 1142 KB  
Article
Experimental Study and Molecular Modeling of Antibody Interactions with Different Fluoroquinolones
by Yulia I. Meteleshko, Maria G. Khrenova, Nadezhda A. Byzova, Shen Xing, Hongtao Lei, Anatoly V. Zherdev, Boris B. Dzantiev and Olga D. Hendrickson
Int. J. Mol. Sci. 2025, 26(24), 11862; https://doi.org/10.3390/ijms262411862 - 9 Dec 2025
Viewed by 674
Abstract
Antibodies against low-molecular-weight compounds exhibit cross-reactivities (CRs) with their structural analogs, varying by orders of magnitude for different substances. This variability limits the informativeness of antibody applications as analytical reagents and for other aims when samples contain several members of the same family, [...] Read more.
Antibodies against low-molecular-weight compounds exhibit cross-reactivities (CRs) with their structural analogs, varying by orders of magnitude for different substances. This variability limits the informativeness of antibody applications as analytical reagents and for other aims when samples contain several members of the same family, their derivatives, or partial degradation products. Therefore, there is a demand to find some criteria for understanding the relationships between the structural characteristics of antigens of a given chemical class and their immunochemical activity. This study presents an experimental and theoretical investigation of the properties of a monoclonal antibody (MAb) against the S-stereoisomer of gatifloxacin, a member of the widely used (fluoro)quinolone (FQ) family of antibiotics, characterized by high structural diversity. The aim was to determine FQs that form complexes with MAb and suggest a methodology to predict their CRs in silico. For this, the interaction of MAb with 26 FQs was studied using the enzyme-linked immunosorbent assay and presented as CR values to the target antigen. The most pronounced CRs were observed for lomefloxacin, sarafloxacin, and ciprofloxacin. Molecular dynamics (MD) simulations were performed to identify differences in analyte interactions at the MAb antigen-binding site, which determines binding affinity. It has been shown that molecular docking fails to discriminate cross-reactive from non-cross-reactive compounds because FQs have similar cores. Therefore, advanced analysis of MD trajectories was carried out. It allowed for clarification of the dynamic features of analyte–antibody interactions responsible for binding. It was shown by the dynamical network analysis that the sum of betweenness centrality between a node corresponding to the quinolone ring and nodes representing MAb amino acids is higher for cross-reactive haptens. The found regularities can be transferred to other analyte–antibody systems as a binary classifier that discriminates cross-reactive and non-cross-reactive compounds. Full article
(This article belongs to the Special Issue Molecular Recognition and Biosensing)
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18 pages, 1478 KB  
Article
Design and Characterization of Aptamers to Antibiotic Kanamycin with Improved Affinity
by Alexey V. Samokhvalov, Oksana G. Maksimenko, Anatoly V. Zherdev and Boris B. Dzantiev
Int. J. Mol. Sci. 2025, 26(22), 11234; https://doi.org/10.3390/ijms262211234 - 20 Nov 2025
Cited by 1 | Viewed by 1030
Abstract
Aptamers are promising synthetic molecular receptors that bind to specific targets by adopting a unique tertiary structure. However, their selection using standard SELEX protocols often does not allow the achievement of high affinity to the targets. Due to the lack and difficulty of [...] Read more.
Aptamers are promising synthetic molecular receptors that bind to specific targets by adopting a unique tertiary structure. However, their selection using standard SELEX protocols often does not allow the achievement of high affinity to the targets. Due to the lack and difficulty of obtaining data on the 3D structure of aptamers and their complexes, the design of known aptamers based on simple rules and software is in demand. The presented work considers the comparative characterization and design of DNA aptamers specific to the antibiotic kanamycin based on complementary interactions and structural motifs (bulges, mismatches, loops) predicted by NUPACK, RNAfold, and UNAFold software. The design included the elimination of non-functional parts of the aptamers and the stabilization of the kanamycin-binding loop. Seven novel aptamers, chosen based on these predictions, were synthesized, and their affinities were measured using an isothermal titration calorimetry technique. The prediction of end stem and hairpin loop structures was confirmed by comparison with circular dichroism data. As a result of sequential design with truncation of unnecessary nucleotides, a novel optimal 42-base-long aptamer was designed and demonstrated a dissociation constant of 109 ± 15 nM, which is 4.7-fold lower than the initial preparation (470 ± 40 nM) and overcomes all known aptamers to kanamycin. Full article
(This article belongs to the Special Issue Molecular Recognition and Biosensing)
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Review

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27 pages, 3956 KB  
Review
Advances in MXene-Based Electrochemical Sensors for Multiplexed Detection in Biofluids
by Meiqing Yang, Congkai Xie and Haozi Lu
Int. J. Mol. Sci. 2025, 26(11), 5368; https://doi.org/10.3390/ijms26115368 - 3 Jun 2025
Cited by 15 | Viewed by 4090
Abstract
Detection of multiple analytes in biofluids is of significance for early disease diagnosis, effective treatment monitoring, and accurate prognostic assessment. Electrochemical sensors have emerged as a promising tool for the multiplexed detection of biofluids due to their low cost, high sensitivity, and rapid [...] Read more.
Detection of multiple analytes in biofluids is of significance for early disease diagnosis, effective treatment monitoring, and accurate prognostic assessment. Electrochemical sensors have emerged as a promising tool for the multiplexed detection of biofluids due to their low cost, high sensitivity, and rapid response. Two-dimensional transition metal carbon/nitride MXene, which has the advantages of a large specific surface area, good electrical conductivity, and abundant surface functional groups, has received increasing attention in the electrochemical sensing field. This paper systematically reviews the advances of MXene-based electrochemical sensors for multiplexed detection in biofluids, emphasizing the design of MXene-based electrode materials as well as the strategies for distinguishing multiple signals during simultaneous electrochemical analysis. In addition, this paper critically analyzes the existing challenges of MXene-based electrochemical sensors for multiplexed detection of biofluids and proposes future development directions for this field. The ultimate goal is to improve biofluid multiplexed detection technology for clinical medical applications. Full article
(This article belongs to the Special Issue Molecular Recognition and Biosensing)
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33 pages, 8513 KB  
Review
Graphene Nanopore Fabrication and Applications
by Qijiao Sun, Min Dai, Junjie Hong, Silu Feng, Chengyong Wang and Zhishan Yuan
Int. J. Mol. Sci. 2025, 26(4), 1709; https://doi.org/10.3390/ijms26041709 - 17 Feb 2025
Cited by 11 | Viewed by 7439
Abstract
Graphene is a revolutionary material with excellent optical, electrical and mechanical properties and has garnered significant attention in the realm of nanopore technology. Devices incorporating graphene nanopores leverage the material’s atomic thickness to enhance detection precision in solid-state nanopores. These nanopores exhibit high [...] Read more.
Graphene is a revolutionary material with excellent optical, electrical and mechanical properties and has garnered significant attention in the realm of nanopore technology. Devices incorporating graphene nanopores leverage the material’s atomic thickness to enhance detection precision in solid-state nanopores. These nanopores exhibit high spatial resolution and ion selectivity, making them promising sensors for biomolecular detection. Additionally, their unique characteristics suggest their considerable potential for applications in material separation and osmotic power generation. In recent years, several literature reviews on graphene nanopores have been published; however, some have not fully addressed certain important aspects, such as the depth of theoretical analysis, the extent of coverage on technological advancements, and the exploration of potential applications. This paper reviews current fabrication methods, including “top-down” etching and “bottom-up” synthesis, highlighting their advantages and limitations. We also summarize diverse applications of graphene nanopores, such as in biomolecule detection and water desalination. Our findings emphasize the need for a deeper exploration of these aspects, advancing the field by showcasing the broader potential of graphene nanopores in addressing various technological challenges. Full article
(This article belongs to the Special Issue Molecular Recognition and Biosensing)
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