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Biosensors
Special Issues
Design and Application of Novel Nucleic Acid Probe
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Design and Application of Novel Nucleic Acid Probe

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

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 5866

Special Issue Editors

Dr. Chiuan-Chian Chiou

E-Mail Website
Guest Editor
Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
Interests: nucleic acid probe; label-free probe; DNA nanostructure; aptasensor
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Kou-Chen Liu

E-Mail Website
Guest Editor
Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan, Taiwan
Interests: nucleic acid probe; label-free probe; DNA nanostructure; aptasensor

Special Issue Information

Dear Colleagues,

Nucleic acid-based biosensors are becoming popular in food, environmental, and healthcare applications, as nucleic acids are relatively easy to design and have a variety of different interactions with their targets. The success of nucleic acid-based biosensor is highly dependent on the design of nucleic acid probes. This Special Issue welcomes papers that analyze novel nucleic acid probe design and application. The probes can have intra-molecular or inter-molecular interaction with sequence-specific Watson–Crick hydrogen bonding or Hoogsteen hydrogen bonding, or non-specific hydrophobic interaction. The probes can be labeled or label free. The probes can either reveal a detectable signal or trigger a downstream reaction or conformational switch. Therefore, probes that have or can interact with their targets to form structures, such as triple helix, G-quadruplex, i-motif, aptamer, or self-assembled nanostructure, are within the scope. We welcome the application of these novel probes in the detection of different targets, including other nucleic acid sequences, proteins, small molecules, extracellular vesicles, or even cells.

Dr. Chiuan-Chian Chiou
Prof. Dr. Kou-Chen Liu
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

  • nucleic acid probe
  • label-free probe
  • triplex forming oligonucleotides (TFOs)
  • G-quadruplex
  • i-motif
  • aptamer/aptasensor
  • DNA nanostructure
  • hoogsteen hydrogen bonding
  • conformational switch

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Published Papers (3 papers)

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Research

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19 pages, 3040 KiB  
Article
Identification of Podoplanin Aptamers by SELEX for Protein Detection and Inhibition of Platelet Aggregation Stimulated by C-Type Lectin-like Receptor 2
by Hui-Ju Tsai, Kai-Wen Cheng, Jou-Chen Li, Tsai-Xiang Ruan, Ting-Hsin Chang, Jin-Ru Wang and Ching-Ping Tseng
Biosensors 2024, 14(10), 464; https://doi.org/10.3390/bios14100464 - 27 Sep 2024
Viewed by 1513
Abstract
Tumor cell-induced platelet aggregation (TCIPA) is a mechanism for the protection of tumor cells in the bloodstream and the promotion of tumor progression and metastases. The platelet C-type lectin-like receptor 2 (CLEC-2) can bind podoplanin (PDPN) on a cancer cell surface to facilitate [...] Read more.
Tumor cell-induced platelet aggregation (TCIPA) is a mechanism for the protection of tumor cells in the bloodstream and the promotion of tumor progression and metastases. The platelet C-type lectin-like receptor 2 (CLEC-2) can bind podoplanin (PDPN) on a cancer cell surface to facilitate TCIPA. Selective blockage of PDPN-mediated platelet–tumor cell interaction is a plausible strategy for inhibiting metastases. In this study, we aimed to screen for aptamers, which are the single-stranded DNA oligonucleotides that form a specific three-dimensional structure, bind to specific molecular targets with high affinity and specificity, bind to PDPN, and interfere with PDPN/CLEC-2 interactions. The systematic evolution of ligands by exponential enrichment (SELEX) was employed to enrich aptamers that recognize PDPN. The initial characterization of ssDNA pools enriched by SELEX revealed a PDPN aptamer designated as A1 displaying parallel-type G-quadruplexes and long stem-and-loop structures and binding PDPN with a material with a dissociation constant (Kd) of 1.3 ± 1.2 nM. The A1 aptamer recognized both the native and denatured form of PDPN. Notably, the A1 aptamer was able to quantitatively detect PDPN proteins in Western blot analysis. The A1 aptamer could interfere with the interaction between PDPN and CLEC-2 and inhibit PDPN-induced platelet aggregation in a concentration-dependent manner. These findings indicated that the A1 aptamer is a candidate for the development of biosensors in detecting the levels of PDPN expression. The action by A1 aptamer could result in the prevention of tumor cell metastases, and if so, could become an effective pharmacological agent in treating cancer patients. Full article
(This article belongs to the Special Issue Design and Application of Novel Nucleic Acid Probe)
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11 pages, 2335 KiB  
Article
Introducing Triplex Forming Oligonucleotide into Loop-Mediated Isothermal Amplification for Developing a Lateral Flow Biosensor for Streptococci Detection
by Wei Chang, Po-Hao Chou, Cai-Tong Wu, Jheng-Da Song, Kun-Nan Tsai and Chiuan-Chian Chiou
Biosensors 2024, 14(5), 257; https://doi.org/10.3390/bios14050257 - 17 May 2024
Cited by 1 | Viewed by 2093
Abstract
Loop-mediated isothermal amplification (LAMP) technology is extensively utilized for the detection of infectious diseases owing to its rapid processing and high sensitivity. Nevertheless, conventional LAMP signaling methods frequently suffer from a lack of sequence specificity. This study integrates a triplex-forming oligonucleotide (TFO) probe [...] Read more.
Loop-mediated isothermal amplification (LAMP) technology is extensively utilized for the detection of infectious diseases owing to its rapid processing and high sensitivity. Nevertheless, conventional LAMP signaling methods frequently suffer from a lack of sequence specificity. This study integrates a triplex-forming oligonucleotide (TFO) probe into the LAMP process to enhance sequence specificity. This TFO-LAMP technique was applied for the detection of Group B Streptococcus (GBS). The TFO probe is designed to recognize a specific DNA sequence, termed the TFO targeting sequence (TTS), within the amplified product, facilitating detection via fluorescent instrumentation or lateral flow biosensors. A screening method was developed to identify TFO sequences with high affinity to integrate TFO into LAMP, subsequently incorporating a selected TTS into an LAMP primer. In the TFO-LAMP assay, a FAM-labeled TFO is added to target the TTS. This TFO can be captured by an anti-FAM antibody on lateral flow test strips, thus creating a nucleic acid testing biosensor. The efficacy of the TFO-LAMP assay was confirmed through experiments with specimens spiked with varying concentrations of GBS, demonstrating 85% sensitivity at 300 copies and 100% sensitivity at 30,000 copies. In conclusion, this study has successfully developed a TFO-LAMP technology that offers applicability in lateral flow biosensors and potentially other biosensor platforms. Full article
(This article belongs to the Special Issue Design and Application of Novel Nucleic Acid Probe)
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Review

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16 pages, 3203 KiB  
Review
Advances in Genotyping Detection of Fragmented Nucleic Acids
by Qian Liu, Yun Chen and Hao Qi
Biosensors 2024, 14(10), 465; https://doi.org/10.3390/bios14100465 - 28 Sep 2024
Viewed by 1550
Abstract
Single nucleotide variant (SNV) detection is pivotal in various fields, including disease diagnosis, viral screening, genetically modified organism (GMO) identification, and genotyping. However, detecting SNVs presents significant challenges due to the fragmentation of nucleic acids caused by cellular apoptosis, molecular shearing, and physical [...] Read more.
Single nucleotide variant (SNV) detection is pivotal in various fields, including disease diagnosis, viral screening, genetically modified organism (GMO) identification, and genotyping. However, detecting SNVs presents significant challenges due to the fragmentation of nucleic acids caused by cellular apoptosis, molecular shearing, and physical degradation processes such as heating. Fragmented nucleic acids often exhibit variable lengths and inconsistent breakpoints, complicating the accurate detection of SNVs. This article delves into the underlying causes of nucleic acid fragmentation and synthesizes the strengths and limitations of next-generation sequencing technology, high-resolution melting curves, molecular probes, and CRISPR-based approaches for SNV detection in fragmented nucleic acids. By providing a detailed comparative analysis, it seeks to offer valuable insights for researchers working to overcome the challenges of SNV detection in fragmented samples, ultimately advancing the accurate and efficient detection of single nucleotide variants across diverse applications. Full article
(This article belongs to the Special Issue Design and Application of Novel Nucleic Acid Probe)
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