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Chemosensors
Special Issues
State of the Art in Nucleic Acid Detection
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State of the Art in Nucleic Acid Detection

A special issue of Chemosensors (ISSN 2227-9040). This special issue belongs to the section "Analytical Methods, Instrumentation and Miniaturization".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 13758

Special Issue Editors

Dr. Chaoxing Liu

E-Mail Website
Guest Editor
Department of Chemistry, University of California, Riverside, CA 92521, USA
Interests: DNA modifications; epigenetics; nucleic acid chemistry; DNA sequencing; DNA probe; cancer
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Michela Alessandra Denti

E-Mail Website
Guest Editor
Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università degli Studi di Trento, Via Sommarive 9, 38123 Trento, Italy
Interests: RNA biology; RNA biomarkers; nucleic acids sensors; biosensors; medical biotechnology
Prof. Dr. Hyun Gyu Park

E-Mail Website
Guest Editor
Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
Interests: nucleic acid bioengineering; microarray technology for genetic diagnosis; electrochemical technology for genetic diagnosis; genetic engineering & nanobiotechnology for disease diagnostics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nucleic acids are gene code, which contain not only canonical nucleobases such as guanine (G), cytosine (C), adenine (A), and thymine (T), but also modified or damaged bases including 5-methylcytosine, N6-Methyladenosine, 8-oxoguanine, 5-hydroxyluracil, and abasic sites. Nucleic acids (DNA and RNA) are also considered biomarkers for many diseases, and tools of therapeutical intervention (antisense oligonucleotides, siRNAs, mRNA vaccines). Epigenetic DNA modification, epitranscriptomic RNA modification, single-nucleotide polymorphism, or specific DNA and RNA fragments detection give us a lot of information for the diagnosis of diseases, such as cancer and COVID-19 nucleic acid detection. The detection of these DNA and RNA modifications, mutations, or specific DNA and RNA fragments is fundamental to the understanding of life development and disease therapy. However, due to the low amounts of these DNA and RNA modifications in the whole genome and transcriptome, detection technologies are still performing poorly, which represents a significant knowledge gap. In this research area, many multi-pronged approaches have been developed, encompassing mass-spectrometry-based analytical chemistry, synthetic organic chemistry, biochemistry, and molecular biology. Addressing this critical knowledge gap will facilitate humans’ long-term goal of diagnosis and treatment of diseases. Especially in the current situation, COVID-19 is evoking an imminent threat to global health security with unprecedented devastating challenges to humankind. Considering its significance, there is an immense and urgent need for the development of fast, lower-cost, sensitive, and reliable detection methods for nucleic acid, especially molecular diagnostics for COVID-19.

The aim of this Issue of “State of the Art in Nucleic Acid Detection” is to highlight the recent development of nucleic acid detection of DNA and RNA modifications, mutations or specific nucleic acid biomarkers. Authors are invited to submit work exploring methods including mass spectrometry, chemical probes, nucleic acid sensors, DNA sequencing, electrochemical, optical, lab-on-a chip devices, clinic kits, molecular diagnostic methods, advanced and automated sensing platforms, bioassays, and detection systems for nucleic acid detection. Both review articles and research papers are welcome.

Dr. Chaoxing Liu
Prof. Dr. Michela Alessandra Denti
Prof. Dr. Hyun Gyu Park
Guest Editors

If you want to learn more information or need any advice, you can contact the Special Issue Editor Tammy Zhang via <[email protected]> directly.

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. Chemosensors 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 2700 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 acids
  • epigenetics
  • epitranscriptomics
  • RNA biomarkers
  • RNA theraputics
  • DNA modification
  • biomarker
  • molecular diagnostics
  • COVID-19

Published Papers (5 papers)

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Research

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16 pages, 2937 KiB  
Article
An Integrated, Real-Time Convective PCR System for Isolation, Amplification, and Detection of Nucleic Acids
by Guijun Miao, Meng Guo, Ke Li, Xiangzhong Ye, Michael G. Mauk, Shengxiang Ge, Ningshao Xia, Duli Yu and Xianbo Qiu
Chemosensors 2022, 10(7), 271; https://doi.org/10.3390/chemosensors10070271 - 11 Jul 2022
Cited by 4 | Viewed by 2088
Abstract
Convective PCR (CPCR) can perform rapid nucleic acid amplification by inducing thermal convection to continuously, cyclically driving reagent between different zones of the reactor for spatially separate melting, annealing, and extending in a capillary tube with constant heating temperatures at different locations. CPCR [...] Read more.
Convective PCR (CPCR) can perform rapid nucleic acid amplification by inducing thermal convection to continuously, cyclically driving reagent between different zones of the reactor for spatially separate melting, annealing, and extending in a capillary tube with constant heating temperatures at different locations. CPCR is promoted by incorporating an FTA membrane filter into the capillary tube, which constructs a single convective PCR reactor for both sample preparation and amplification. To simplify fluid control in sample preparation, lysed sample or wash buffer is driven through the membrane filter through centrifugation. A movable resistance heater is used to heat the capillary tube for amplification, and meanwhile, a smartphone camera is adopted to monitor in situ fluorescence signal from the reaction. Different from other existing CPCR systems with the described simple, easy-to-use, integrated, real-time microfluidic CPCR system, rapid nucleic acid analysis can be performed from sample to answer. A couple of critical issues, including wash scheme and reaction temperature, are analyzed for optimized system performance. It is demonstrated that influenza A virus with the reasonable concentration down to 1.0 TCID50/mL can be successfully detected by the integrated microfluidic system within 45 min. Full article
(This article belongs to the Special Issue State of the Art in Nucleic Acid Detection)
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13 pages, 2643 KiB  
Article
Isothermal Amplification and Lateral Flow Nucleic Acid Test for the Detection of Shiga Toxin-Producing Bacteria for Food Monitoring
by Sabrina Petrucci, Emre Dikici, Sylvia Daunert and Sapna K. Deo
Chemosensors 2022, 10(6), 210; https://doi.org/10.3390/chemosensors10060210 - 2 Jun 2022
Cited by 5 | Viewed by 2095
Abstract
Foodborne bacteria have persisted as a significant threat to public health and to the food and agriculture industry. Due to the widespread impact of these pathogens, there has been a push for the development of strategies that can rapidly detect foodborne bacteria on-site. [...] Read more.
Foodborne bacteria have persisted as a significant threat to public health and to the food and agriculture industry. Due to the widespread impact of these pathogens, there has been a push for the development of strategies that can rapidly detect foodborne bacteria on-site. Shiga toxin-producing E. coli strains (such as E. coli O157:H7, E. coli O121, and E. coli O26) from contaminated food have been a major concern. They carry genes stx1 and/or stx2 that produce two toxins, Shiga toxin 1 and Shiga toxin 2, which are virulent proteins. In this work, we demonstrate the development of a rapid test based on an isothermal recombinase polymerase amplification reaction for two Shiga toxin genes in a single reaction. Results of the amplification reaction are visualized simultaneously for both Shiga toxins on a single lateral flow paper strip. This strategy targets the DNA encoding Shiga toxin 1 and 2, allowing for broad detection of any Shiga toxin-producing bacterial species. From sample to answer, this method can achieve results in approximately 35 min with a detection limit of 10 CFU/mL. This strategy is sensitive and selective, detecting only Shiga toxin-producing bacteria. There was no interference observed from non-pathogenic or pathogenic non-Shiga toxin-producing bacteria. A detection limit of 10 CFU/mL for Shiga toxin-producing E. coli was also obtained in a food matrix. This strategy is advantageous as it allows for timely identification of Shiga toxin-related contamination for quick initial food contamination assessments. Full article
(This article belongs to the Special Issue State of the Art in Nucleic Acid Detection)
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17 pages, 2194 KiB  
Article
The Usefulness of Autoradiography for DNA Repair Proteins Activity Detection in the Cytoplasm towards Radiolabeled Oligonucleotides Containing 5′,8-Cyclo-2′-deoxyadenosine
by Karolina Boguszewska, Bolesław T. Karwowski and Julia Kaźmierczak-Barańska
Chemosensors 2022, 10(6), 204; https://doi.org/10.3390/chemosensors10060204 - 28 May 2022
Viewed by 1913
Abstract
Autoradiography of 32P-radiolabeled oligonucleotides is one of the most precise detection methods of DNA repair processes. In this study, autoradiography allowed assessing the activity of proteins in the cytoplasm involved in DNA repair. The cytoplasm is the site of protein biosynthesis but [...] Read more.
Autoradiography of 32P-radiolabeled oligonucleotides is one of the most precise detection methods of DNA repair processes. In this study, autoradiography allowed assessing the activity of proteins in the cytoplasm involved in DNA repair. The cytoplasm is the site of protein biosynthesis but is also a target cellular compartment of synthetic therapeutic oligonucleotide (STO) delivery. The DNA-based drugs may be impaired by radiation-induced lesions, such as clustered DNA lesions (CDL) and/or 5′,8-cyclo-2′-deoxypurines (cdPu). CDL and cdPu may appear in the sequence of STO after irradiation and subsequently impair DNA repair, as shown in previous studies. Hence, the interesting questions are (1) is it safe to combine STO treatment with radiotherapy; (2) are repair proteins active in the cytoplasm; and (3) is their activity different in the cytoplasm than in the nucleus? This unique study examined whether the proteins involved in the DNA repair are affected by the CDL while they are still present in the cytoplasm of xrs5, BJ, and XPC cells. Double-stranded oligonucleotides with bi-stranded CDL were used (containing AP site in one strand and a (5′S) or (5′R) 5′,8-cyclo-2′-deoxyadenosine (cdA) in the other strand located 1 or 4 bp in both directions). The results have shown that the proteins involved in the repair were active in the cytoplasm, but less than in the nucleus. The general trends aligned for cytoplasm and nucleus—lesions located in the 5′-end direction inhibited the course of DNA repair. The combination of STO with radiotherapy should be applied carefully, as unrepaired lesions within STO may impair their therapeutic efficiency. Full article
(This article belongs to the Special Issue State of the Art in Nucleic Acid Detection)
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13 pages, 1964 KiB  
Article
Carbon Electrodes with Gold Nanoparticles for the Electrochemical Detection of miRNA 21-5p
by Verónica Morgado Serrano, Inês Simões Patrício Silva, Ana Rita Cardoso and Maria Goreti Ferreira Sales
Chemosensors 2022, 10(5), 189; https://doi.org/10.3390/chemosensors10050189 - 19 May 2022
Cited by 6 | Viewed by 3263
Abstract
Extracellular vesicles are involved in many physiological and pathological activities. They transport miRNAs to recipient cells during their role in intercellular communication, making them emerging biomarkers of many diseases. Interest in exosomal miRNAs has grown after they have shown numerous advantages as biomarkers [...] Read more.
Extracellular vesicles are involved in many physiological and pathological activities. They transport miRNAs to recipient cells during their role in intercellular communication, making them emerging biomarkers of many diseases. Interest in exosomal miRNAs has grown after they have shown numerous advantages as biomarkers for diagnosis, prognosis, and evaluation of cancer treatment. This work describes the development of a biosensor for the detection of 21-5p miRNA in human serum using screen-printed carbon electrodes modified with gold nanoparticles fabricated in situ, an innovative approach to avoid the use of more expensive gold substrates that provide better analytical outputs. The several variables involved in the assembly of the biosensor were optimized by univariant mode. Under the best conditions, the biosensor showed a linear response from 0.010 fM to 10 pM, with a limit of detection (LOD) of 4.31 aM. The sensitivity was 0.3718 relative Ω per decade concentration in buffered saline solutions, and the standard deviation of the blank is 2.94 Ω. A linear response was also obtained when human serum samples were tested with miRNA 21-5p. Interference from similar miRNA and miss-match miRNA sequences was evaluated and good selectivity for miRNA 21-5p was observed. Overall, the device proposed is an alternative approach to gold substrates, which typically result in more sensitive systems and lower LODs, which compares favorably to current gold-based biosensors for the targeted miRNA. This design may be further extended to other nucleic acids. Full article
(This article belongs to the Special Issue State of the Art in Nucleic Acid Detection)
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Review

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17 pages, 1629 KiB  
Review
SARS-CoV-2 Detection Methods
by Alexandra Lino, Marita A. Cardoso, Helena M. R. Gonçalves and Paula Martins-Lopes
Chemosensors 2022, 10(6), 221; https://doi.org/10.3390/chemosensors10060221 - 11 Jun 2022
Cited by 11 | Viewed by 3256
Abstract
A fast and highly specific detection of COVID-19 infections is essential in managing the virus dissemination networks. The most relevant technologies developed for SARS-CoV-2 detection, along with their advantages and limitations, will be presented and fully explored. Additionally, some of the newest and [...] Read more.
A fast and highly specific detection of COVID-19 infections is essential in managing the virus dissemination networks. The most relevant technologies developed for SARS-CoV-2 detection, along with their advantages and limitations, will be presented and fully explored. Additionally, some of the newest and emerging COVID-19 diagnosis tools, such as biosensing platforms, will also be introduced. Considering the extreme relevance that all these technologies assume in pandemic control, it is of the utmost relevance to have an intrinsic knowledge of the parameters that need to be taken into consideration before choosing the most adequate test for a particular situation. Moreover, the new variants of the virus and their potential impact on the detection method’s effectiveness will be discussed. In order to better manage the pandemic, it is essential to maintain continuous research into the SARS-CoV-2 genome and updated genomic surveillance at the global level. This will allow for timely detection of new mutations and viral variants, which may affect the performance of COVID-19 detection tests. Full article
(This article belongs to the Special Issue State of the Art in Nucleic Acid Detection)
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