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Biomedicines
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Nucleic Acid Based Sensing for Biomedical Applications
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Nucleic Acid Based Sensing for Biomedical Applications

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Biomedical Engineering and Materials".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 19118

Special Issue Editor

Dr. Natalia Komarova

E-Mail Website
Guest Editor
Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia
Interests: aptamer; SELEX; in vitro evolution; DNAzymes; biosensors; sensing technologies; next generation sequencing

Special Issue Information

Dear Colleagues,

Nucleic acids have great potential for use in sensing technologies. This Special Issue is focused on the application of nucleic acids for the development of biosensors aimed at diagnostics and medicinal purposes. Different types of nucleic acid entities like aptamers, nucleic acid reporters and switches, and DNA/RNAzymes can serve as receptor layers of biosensors. Complementary interactions, molecular beacons, nucleic acid amplification reactions, and catalytic activity of nucleic acids provide the means for signal amplification and detection. We invite the authors to submit research articles as well as specialized reviews dedicated to the development of novel nucleic acid-based receptors against the targets of physiological or medicinal significance, the design and characterization of original sensing schemes, and sensing platforms and biosensors employing nucleic acids with the potential for application in diagnostics and medicinal research.

Dr. Natalia Komarova
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. Biomedicines 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 2600 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

  • aptamers
  • DNAzymes
  • RNAzymes
  • nucleic acid probes
  • molecular beacons
  • receptors
  • biomarkers
  • biosensors
  • signal amplification

Published Papers (5 papers)

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Research

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12 pages, 2116 KiB  
Article
A Miniaturized System for Rapid, Isothermal Detection of SARS-CoV-2 in Human and Environmental Samples
by Jake Staples, Athanasia-Maria Dourou, Irene Liampa, Calvin Sjaarda, Emily Moslinger, Henry Wong, Prameet M. Sheth, Stilianos Arhondakis and Ravi Prakash
Biomedicines 2023, 11(7), 2038; https://doi.org/10.3390/biomedicines11072038 - 20 Jul 2023
Viewed by 1909
Abstract
We report a small-footprint cost-effective isothermal rapid DNA amplification system, with integrated microfluidics for automated sample analysis and detection of SARS-CoV-2 in human and environmental samples. Our system measures low-level fluorescent signals in real-time during amplification, while maintaining the desired assay temperature on [...] Read more.
We report a small-footprint cost-effective isothermal rapid DNA amplification system, with integrated microfluidics for automated sample analysis and detection of SARS-CoV-2 in human and environmental samples. Our system measures low-level fluorescent signals in real-time during amplification, while maintaining the desired assay temperature on a low power, portable system footprint. A unique soft microfluidic chip design was implemented to mitigate thermocapillary effects and facilitate optical alignment for automated image capture and signal analysis. The system-on-board prototype, coupled with the LAMP primers designed by BioCoS, was sensitive enough to detect large variations in viral loads of SARS-CoV-2 corresponding to a threshold cycle range of 16 to 39. Furthermore, tested samples consisted of a broad range of viral strains and lineages identified in Canada during 2021–2022. Clinical specimens were collected and tested at the Kingston Health Science Centre using a clinically validated PCR assay, and variants were determined using whole genome sequencing. Full article
(This article belongs to the Special Issue Nucleic Acid Based Sensing for Biomedical Applications)
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13 pages, 2537 KiB  
Article
Urinary MicroRNA Sensing Using Electrochemical Biosensor to Evaluate Colorectal Cancer Progression
by Sow-Neng Pang, Yu-Lun Lin, Yueh-Er Chiou, Wai-Hung Leung and Wen-Hui Weng
Biomedicines 2022, 10(6), 1434; https://doi.org/10.3390/biomedicines10061434 - 17 Jun 2022
Cited by 1 | Viewed by 1720
Abstract
Research in cancer diagnostics has recently established its footing and significance in the biosensor sphere, emphasizing the idea of a unique probe design used as a sensor and actuator, to identify the presence of protein, DNA, RNA, or miRNA. The fluorescein isothiocyanate (FITC) [...] Read more.
Research in cancer diagnostics has recently established its footing and significance in the biosensor sphere, emphasizing the idea of a unique probe design used as a sensor and actuator, to identify the presence of protein, DNA, RNA, or miRNA. The fluorescein isothiocyanate (FITC) probe and biotinylated probe are designed for a two-pronged approach to the detection of the urinary miR-21 and miR-141, both of which have demonstrated significance in the development and progression of colorectal cancer, a leading cause of mortality and morbidity. The remainder of the apparatus is composed of a modified screen-printed carbon electrode (SPCE), to which the probes adhere, that transduces signals via the redox reaction between H2O2 and HRP, measured with chronoamperometry and cyclic voltammetry. The precise nature of our ultra-non-invasive biosensor makes for a highly sensitive and practical cancer detector, concluded by the significance when establishing disease presence (miR-21 p-value = 0.0176, miR-141 p-value = 0.0032), disease follow-up (miR-21 p-value = 0.00154, miR141 p-value < 0.0005), and even disease severity. This article hopes to emphasize the potential of an additional clinical tool for the management of colorectal cancer. Full article
(This article belongs to the Special Issue Nucleic Acid Based Sensing for Biomedical Applications)
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Review

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22 pages, 1446 KiB  
Review
Design and Prediction of Aptamers Assisted by In Silico Methods
by Su Jin Lee, Junmin Cho, Byung-Hoon Lee, Donghwan Hwang and Jee-Woong Park
Biomedicines 2023, 11(2), 356; https://doi.org/10.3390/biomedicines11020356 - 26 Jan 2023
Cited by 11 | Viewed by 6733
Abstract
An aptamer is a single-stranded DNA or RNA that binds to a specific target with high binding affinity. Aptamers are developed through the process of systematic evolution of ligands by exponential enrichment (SELEX), which is repeated to increase the binding power and specificity. [...] Read more.
An aptamer is a single-stranded DNA or RNA that binds to a specific target with high binding affinity. Aptamers are developed through the process of systematic evolution of ligands by exponential enrichment (SELEX), which is repeated to increase the binding power and specificity. However, the SELEX process is time-consuming, and the characterization of aptamer candidates selected through it requires additional effort. Here, we describe in silico methods in order to suggest the most efficient way to develop aptamers and minimize the laborious effort required to screen and optimise aptamers. We investigated several methods for the estimation of aptamer-target molecule binding through conformational structure prediction, molecular docking, and molecular dynamic simulation. In addition, examples of machine learning and deep learning technologies used to predict the binding of targets and ligands in the development of new drugs are introduced. This review will be helpful in the development and application of in silico aptamer screening and characterization. Full article
(This article belongs to the Special Issue Nucleic Acid Based Sensing for Biomedical Applications)
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23 pages, 4130 KiB  
Review
Aptamer-Based Biosensors for the Colorimetric Detection of Blood Biomarkers: Paving the Way to Clinical Laboratory Testing
by Anna Davydova and Mariya Vorobyeva
Biomedicines 2022, 10(7), 1606; https://doi.org/10.3390/biomedicines10071606 - 06 Jul 2022
Cited by 10 | Viewed by 2840
Abstract
Clinical diagnostics for human diseases rely largely on enzyme immunoassays for the detection of blood biomarkers. Nevertheless, antibody-based test systems have a number of shortcomings that have stimulated a search for alternative diagnostic assays. Oligonucleotide aptamers are now considered as promising molecular recognizing [...] Read more.
Clinical diagnostics for human diseases rely largely on enzyme immunoassays for the detection of blood biomarkers. Nevertheless, antibody-based test systems have a number of shortcomings that have stimulated a search for alternative diagnostic assays. Oligonucleotide aptamers are now considered as promising molecular recognizing elements for biosensors (aptasensors) due to their high affinity and specificity of target binding. At the moment, a huge variety of aptasensors have been engineered for the detection of various analytes, especially disease biomarkers. However, despite their great potential and excellent characteristics in model systems, only a few of these aptamer-based assays have been translated into practice as diagnostic kits. Here, we will review the current progress in the engineering of aptamer-based colorimetric assays as the most suitable format for clinical lab diagnostics. In particular, we will focus on aptasensors for the detection of blood biomarkers of cardiovascular, malignant, and neurodegenerative diseases along with common inflammation biomarkers. We will also analyze the main obstacles that have to be overcome before aptamer test systems can become tantamount to ELISA for clinical diagnosis purposes. Full article
(This article belongs to the Special Issue Nucleic Acid Based Sensing for Biomedical Applications)
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19 pages, 2324 KiB  
Review
Nanomaterial-Based Fluorescence Resonance Energy Transfer (FRET) and Metal-Enhanced Fluorescence (MEF) to Detect Nucleic Acid in Cancer Diagnosis
by Jin-Ha Choi, Taehyeong Ha, Minkyu Shin, Sang-Nam Lee and Jeong-Woo Choi
Biomedicines 2021, 9(8), 928; https://doi.org/10.3390/biomedicines9080928 - 31 Jul 2021
Cited by 23 | Viewed by 5016
Abstract
Nucleic acids, including DNA and RNA, have received prodigious attention as potential biomarkers for precise and early diagnosis of cancers. However, due to their small quantity and instability in body fluids, precise and sensitive detection is highly important. Taking advantage of the ease-to-functionality [...] Read more.
Nucleic acids, including DNA and RNA, have received prodigious attention as potential biomarkers for precise and early diagnosis of cancers. However, due to their small quantity and instability in body fluids, precise and sensitive detection is highly important. Taking advantage of the ease-to-functionality and plasmonic effect of nanomaterials, fluorescence resonance energy transfer (FRET) and metal-enhanced fluorescence (MEF)-based biosensors have been developed for accurate and sensitive quantitation of cancer-related nucleic acids. This review summarizes the recent strategies and advances in recently developed nanomaterial-based FRET and MEF for biosensors for the detection of nucleic acids in cancer diagnosis. Challenges and opportunities in this field are also discussed. We anticipate that the FRET and MEF-based biosensors discussed in this review will provide valuable information for the sensitive detection of nucleic acids and early diagnosis of cancers. Full article
(This article belongs to the Special Issue Nucleic Acid Based Sensing for Biomedical Applications)
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