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Biosensors
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DNA Molecular Engineering-Based Biosensors
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DNA Molecular Engineering-Based Biosensors

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

Deadline for manuscript submissions: 31 October 2025 | Viewed by 5739

Special Issue Editor

Dr. Yifan Lyu

E-Mail Website
Guest Editor
College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
Interests: DNA dynamic nanotechnology; DNA self-assembly nanostructure; artificial cell; single-molecule imaging; bioanalysis

Special Issue Information

Dear Colleagues,

Bioanalysis of important biotargets offers an effective means to understand the operational mechanisms of spatiotemporal biological systems. There is an urgent need to develop novel biosensors and bioanalysis strategies with high sensitivity, high precision, and high intelligence through molecular engineering design. Benefitting from the obvious advantages of DNA molecules, such as the predictability of DNA hybridizations and the scaling-up ability of DNA strand displacement reactions, DNA nanotechnology provides a flexible and programmable platform for molecular engineering. Through rational molecular design, DNA molecules can be constructed into a series of DNA reaction networks and DNA nanostructures with specific functions involving molecular computing, logic control, mechanical motion and intelligent signal transduction. By combining DNA molecular engineering with biosensing strategies, numerous DNA molecular engineering-based biosensors have been reported in recent years and have showed great potential in bioapplications. However, due to the complexity of biological systems, there are still some challenges when designing DNA molecular engineering-based biosensors. With the development of biology and biomedicine, more and more important biological targets should be detected and various bioenvironments should be considered. In addition, we hope that our sensors will continue to become more sensitive, more selective, cheaper, smaller, and easy to use.

This Special Issue aims to gather original articles and reviews showing research advances, molecular design, innovative applications, new challenges and future perspectives regarding DNA molecular engineering-based biosensors.

If you would be interested in submitting a contribution, or if you have any questions, please contact me.

Dr. Yifan Lyu
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

  • biosensors
  • DNA nanotechnology
  • molecular diagnosis
  • bioimaging
  • bioanalysis
  • functional nucleic acid
  • aptamers

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Published Papers (4 papers)

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Research

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14 pages, 6839 KiB  
Article
Analysis of Colorectal Cancer Gene Mutations and Application of Long Blocker Displacement Amplification Technology for High-Throughput Mutation Detection
by Ping Lu, Xinglei Su, Sirui Leong, Xuehao Xiu, Ping Song, Junjie Peng and Yunpei Si
Biosensors 2025, 15(5), 308; https://doi.org/10.3390/bios15050308 - 12 May 2025
Viewed by 171
Abstract
Genetic mutation detection for colorectal cancer (CRC) is crucial for precision diagnosis and treatment, yet current methods often suffer from challenges such as low sensitivity, time consumption, and high costs. In our preliminary bioinformatic analysis of 751 CRC cases from The Cancer Genome [...] Read more.
Genetic mutation detection for colorectal cancer (CRC) is crucial for precision diagnosis and treatment, yet current methods often suffer from challenges such as low sensitivity, time consumption, and high costs. In our preliminary bioinformatic analysis of 751 CRC cases from The Cancer Genome Atlas and 131 Chinese patient samples, APC, TP53, and KRAS were identified as the most frequently mutated genes. Among them, KRAS missense mutations emerged as key diagnostic biomarkers. In this study, we applied a fluorescence-based long block displacement amplification (LBDA) sensing method for the rapid, high-throughput, and cost-effective detection of KRAS genetic mutations. In the LBDA system, SYBR Green dye binds to the amplified double-stranded DNA, generating a fluorescence signal that directly reflects the abundance of mutant types (MTs). This real-time signal output enables the enrichment and sensitive detection of MTs, establishing LBDA as an efficient biosensing platform for KRAS genotyping. Using this technique, a detection limit of 0.08% variant allele frequency was achieved with 20 ng of synthetic DNA input. To evaluate clinical performance, the LBDA method was applied to 118 tissue samples from 59 CRC patients, including tumor and matched peritumoral tissues. For 59 CRC tumor samples, LBDA successfully identified KRAS mutations in 37.29% of cases, closely matching results (42.37%) obtained by next-generation sequencing and achieving 88% sensitivity and 100% specificity. In conclusion, this study presents a rapid and cost-effective mutation detection method based on optical biosensing, offering strong potential for advancing personalized CRC diagnosis and treatment. Full article
(This article belongs to the Special Issue DNA Molecular Engineering-Based Biosensors)
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16 pages, 5366 KiB  
Article
Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations
by Kaitlin Bullard, Deborah Okyere, Shelbi J. Foster, Asmaa A. Sadoon, Jiali Li, Jingyi Chen and Yong Wang
Biosensors 2025, 15(5), 272; https://doi.org/10.3390/bios15050272 - 26 Apr 2025
Viewed by 267
Abstract
Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics [...] Read more.
Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg2+ ions at different concentrations. The simulations show that Mg2+ ions reduce the fluctuations of DNA strands, enhance base-pairing, and stabilize bent DNA molecules. The computational results are further verified by both melting curve experiments and ensemble FRET measurements, highlighting the mechanical instability and sensitivity of bent DNA molecules. Full article
(This article belongs to the Special Issue DNA Molecular Engineering-Based Biosensors)
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14 pages, 2123 KiB  
Article
Development of a Modular miRNA-Responsive Biosensor for Organ-Specific Evaluation of Liver Injury
by Xinxin Zhang, Tingting Wang, Xiangqing Fan, Meixia Wang, Zhixi Duan, Fang He, Hong-Hui Wang and Zhihong Li
Biosensors 2024, 14(9), 450; https://doi.org/10.3390/bios14090450 - 20 Sep 2024
Viewed by 1639
Abstract
MicroRNAs (miRNAs) are increasingly being considered essential diagnostic biomarkers and therapeutic targets for multiple diseases. In recent years, researchers have emphasized the need to develop probes that can harness extracellular miRNAs as input signals for disease diagnostics. In this study, we introduce a [...] Read more.
MicroRNAs (miRNAs) are increasingly being considered essential diagnostic biomarkers and therapeutic targets for multiple diseases. In recent years, researchers have emphasized the need to develop probes that can harness extracellular miRNAs as input signals for disease diagnostics. In this study, we introduce a novel miRNA-responsive biosensor (miR-RBS) designed to achieve highly sensitive and specific detection of miRNAs, with a particular focus on targeted organ-specific visualization. The miR-RBS employs a Y-structured triple-stranded DNA probe (Y-TSDP) that exhibits a fluorescence-quenched state under normal physiological conditions. The probe switches to an activated state with fluorescence signals in the presence of high miRNA concentrations, enabling rapid and accurate disease reporting. Moreover, the miR-RBS probe had a modular design, with a fluorescence-labeled strand equipped with a functional module that facilitates specific binding to organs that express high levels of the target receptors. This allowed the customization of miRNA detection and cell targeting using aptameric anchors. In a drug-induced liver injury model, the results demonstrate that the miR-RBS probe effectively visualized miR-122 levels, suggesting it has good potential for disease diagnosis and organ-specific imaging. Together, this innovative biosensor provides a versatile tool for the early detection and monitoring of diseases through miRNA-based biomarkers. Full article
(This article belongs to the Special Issue DNA Molecular Engineering-Based Biosensors)
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Review

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24 pages, 13029 KiB  
Review
DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications
by Chunran Ma, Shiquan Li, Yuqi Zeng and Yifan Lyu
Biosensors 2024, 14(5), 236; https://doi.org/10.3390/bios14050236 - 8 May 2024
Cited by 1 | Viewed by 2783
Abstract
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular [...] Read more.
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed. Full article
(This article belongs to the Special Issue DNA Molecular Engineering-Based Biosensors)
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