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Molecules
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Application of Nucleic Acid Probe in Analysis and Detection
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Application of Nucleic Acid Probe in Analysis and Detection

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Electrochemistry".

Deadline for manuscript submissions: closed (15 July 2022) | Viewed by 18718

Special Issue Editors

Prof. Dr. Zaisheng Wu

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Guest Editor
Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350117, China
Interests: nucleic acid probes; functional nucleic acid; nanomaterials; biosensors; drug delivery
Dr. Songbai Zhang

E-Mail Website
Guest Editor
College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde, China
Interests: nucleic acid probes; functional nucleic acid; biosensors; nanomaterials; drug delivery
Prof. Dr. Limin Lu

E-Mail Website
Guest Editor
College of Science, Jiangxi Agricultural University, Nanchang, China
Interests: nucleic acid probes; nanomaterials; biosensors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Beyond storing genetic information in organisms, nucleic acids have been widely used as probes in molecular biology, analytical chemistry, clinical medicine and even materials science in recent decades, which has greatly promoted the development of multiple disciplines. The narrow definition of a nucleic acid probe refers to a nucleic acid sequence with a label capable of hybridizing with the target gene and producing a detectable signal. Generalized nucleic acid probes include both detection probes that can provide both detectable signals and recognition elements for specifically hybridizing with nucleic acid sequences or binding to non-nucleic acid target molecules. Especially in the field of analytical chemistry, due to the successful screening of a large number of functional nucleic acids and the development of different signal transduction strategies in recent years, nucleic acid probes are enabling the highly sensitive and selective detection of a variety of target analytes. For example, the development of aptamers makes nucleic acid probes into selective recognition elements recognizing a large variety of species ranging from metal ions, small molecules, and proteins to even cells. The development of ribozymes gives nucleic acid probes the function of catalyzing the hydrolysis of RNAs. Moreover, the development of many colorimetric, fluorescent, electrochemical, electrochemiluminescent, Raman spectroscopic and other analytical techniques has greatly promoted the applications of nucleic acid probes in different areas, including environmental analysis, disease diagnostics, pharmaceutical screening, targeted disease therapy, bionanostructures and even combination with organic/inorganic materials. In addition, the applications of nucleic acid probes have expanded from in vitro to in vivo systems.

We invite original research articles related to the design, characterization, and application of nucleic acid probes against various target molecules, as well as review articles that summarize the recent advances or extensive achievements in a unique topic to potentially stimulate the continuing efforts. The potential topics include, but are not limited to:

  • Nucleic probes for biosensing or bioanalysis;
  • The design and application of new nucleic acid probes;
  • Nucleic acid probe-based signal-amplification methods;
  • Nucleic probes for disease diagnosis and treatment;
  • Nucleic acid probe-based nanomaterials and nanodevices;
  • The function and chemical modification of nucleic acid probes. 

Prof. Dr. Zaisheng Wu
Dr. Songbai Zhang
Prof. Dr. Limin Lu
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. Molecules is an international peer-reviewed open access semimonthly 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 acid probe
  • functional nucleic acids
  • biosensor
  • nanostructures
  • signal amplification
  • chemical modification
  • disease diagnosis and treatment

Published Papers (8 papers)

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Research

12 pages, 3033 KiB  
Article
DNA Interaction, DNA Photocleavage, Photocytotoxicity In Vitro, and Molecular Docking of Naphthyl-Appended Ruthenium Complexes
by Xia Hu, Qian Luo, Yao Qin, Yao Wu and Xue-Wen Liu
Molecules 2022, 27(12), 3676; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27123676 - 08 Jun 2022
Cited by 3 | Viewed by 1638
Abstract
With the development of metal-based drugs, Ru(II) compounds present potential applications of PDT (photodynamic therapy) and anticancer reagents. We herein synthesized two naphthyl-appended ruthenium complexes by the combination of the ligand with naphthyl and bipyridyl. The DNA affinities, photocleavage abilities, and photocytotoxicity were [...] Read more.
With the development of metal-based drugs, Ru(II) compounds present potential applications of PDT (photodynamic therapy) and anticancer reagents. We herein synthesized two naphthyl-appended ruthenium complexes by the combination of the ligand with naphthyl and bipyridyl. The DNA affinities, photocleavage abilities, and photocytotoxicity were studied by various spectral methods, viscosity measurement, theoretical computation method, gel electrophoresis, and MTT method. Two complexes exhibited strong interaction with calf thymus DNA by intercalation. Production of singlet oxygen (1O2) led to obvious DNA photocleavage activities of two complexes under 365 nm light. Furthermore, two complexes displayed obvious photocytotoxicity and low dark cytotoxicity towards Hela, A549, and A375 cells. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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12 pages, 2363 KiB  
Article
MXene–AuNP-Based Electrochemical Aptasensor for Ultra-Sensitive Detection of Chloramphenicol in Honey
by Jing Yang, Wei Zhong, Qi Yu, Jin Zou, Yansha Gao, Shuwu Liu, Songbai Zhang, Xiaoqiang Wang and Limin Lu
Molecules 2022, 27(6), 1871; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27061871 - 14 Mar 2022
Cited by 17 | Viewed by 3296
Abstract
A simple and label-free electrochemical aptasensor was developed for ultra-sensitive determination of chloramphenicol (CAP) based on a 2D transition of metal carbides (MXene) loaded with gold nanoparticles (AuNPs). The embedded AuNPs not only inhibit the aggregation of MXene sheets, but also improve the [...] Read more.
A simple and label-free electrochemical aptasensor was developed for ultra-sensitive determination of chloramphenicol (CAP) based on a 2D transition of metal carbides (MXene) loaded with gold nanoparticles (AuNPs). The embedded AuNPs not only inhibit the aggregation of MXene sheets, but also improve the quantity of active sites and electronic conductivity. The aptamers (Apts) were able to immobilize on the MXene–AuNP modified electrode surface through Au–S interaction. Upon specifically binding with CAP with high affinity, the CAP–Apt complexes produced low conductivity on the aptasensor surface, leading to a decreased electrochemical signal. The resulting current change was quantitatively correlated with CAP concentration. Under optimized experimental conditions, the constructed aptasensor exhibited a good linear relationship within a wide range of 0.0001–10 nM and with a low detection limit of 0.03 pM for CAP. Moreover, the developed aptasensor has been applied to the determination of CAP concentration in honey samples with satisfactory results. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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12 pages, 2729 KiB  
Article
Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection
by Yun Zhang, Xinao Ma, Jingtian Zhang, Feixian Luo, Wenshu Wang and Xiaojie Cui
Molecules 2021, 26(23), 7352; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26237352 - 03 Dec 2021
Cited by 8 | Viewed by 2341
Abstract
G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection [...] Read more.
G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection of nucleic acids. In this study, we developed a high-sensitivity biosensor targeting norovirus nucleic acids through rationally introducing a dimeric G-quadruplex structure into the DNAzyme. In this strategy, two separate molecular beacons each having a G-quadruplex-forming sequence embedded in the stem structure are brought together through hybridization with a target DNA strand, and thus forms a three-way junction architecture and allows a dimeric G-quadruplex to form, which, upon binding with hemin, has a synergistic enhancement of catalytic activities. This provides a high-sensitivity colorimetric readout by the catalyzing H2O2-mediated oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline -6-sulfonic acid) diammonium salt (ABTS). Up to 10 nM of target DNA can be detected through colorimetric observation with the naked eye using our strategy. Hence, our approach provides a non-amplifying, non-labeling, simple-operating, cost-effective colorimetric biosensing method for target nucleic acids, such as norovirus-conserved sequence detection, and highlights the further implication of higher-order multimerized G-quadruplex structures in the design of high-sensitivity biosensors. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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10 pages, 1690 KiB  
Article
Dual Catalytic Hairpin Assembly-Based Automatic Molecule Machine for Amplified Detection of Auxin Response Factor-Targeted MicroRNA-160
by Lei Wang, Xing Dai, Yujian Feng, Qiyang Zhao, Lin Liu, Chang Xue, Langtao Xiao and Ruozhong Wang
Molecules 2021, 26(21), 6432; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26216432 - 25 Oct 2021
Cited by 1 | Viewed by 1990
Abstract
MicroRNA160 plays a crucial role in plant development by negatively regulating the auxin response factors (ARFs). In this manuscript, we design an automatic molecule machine (AMM) based on the dual catalytic hairpin assembly (D-CHA) strategy for the signal amplification detection of miRNA160. The [...] Read more.
MicroRNA160 plays a crucial role in plant development by negatively regulating the auxin response factors (ARFs). In this manuscript, we design an automatic molecule machine (AMM) based on the dual catalytic hairpin assembly (D-CHA) strategy for the signal amplification detection of miRNA160. The detection system contains four hairpin-shaped DNA probes (HP1, HP2, HP3, and HP4). For HP1, the loop is designed to be complementary to miRNA160. A fragment of DNA with the same sequences as miRNA160 is separated into two pieces that are connected at the 3′ end of HP2 and 5′ end of HP3, respectively. In the presence of the target, four HPs are successively dissolved by the first catalytic hairpin assembly (CHA1), forming a four-way DNA junction (F-DJ) that enables the rearrangement of separated DNA fragments at the end of HP2 and HP3 and serving as an integrated target analogue for initiating the second CHA reaction, generating an enhanced fluorescence signal. Assay experiments demonstrate that D-CHA has a better performance compared with traditional CHA, achieving the detection limit as low as 10 pM for miRNA160 as deduced from its corresponding DNA surrogates. Moreover, non-target miRNAs, as well as single-base mutation targets, can be detected. Overall, the D-CHA strategy provides a competitive method for plant miRNAs detection. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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11 pages, 3200 KiB  
Article
Smartphone-Assisted Colorimetric Detection of Glutathione and Glutathione Reductase Activity in Human Serum and Mouse Liver Using Hemin/G-Quadruplex DNAzyme
by Yufen Lai, Mengyan Li, Xiaofei Liao and Li Zou
Molecules 2021, 26(16), 5016; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26165016 - 19 Aug 2021
Cited by 11 | Viewed by 2394
Abstract
Abnormal levels of reduced glutathione (GSH) and glutathione reductase (GR) are usually related to a variety of diseases, so it is of great significance to determine the GSH concentration and GR activity. We herein develop a smartphone-assisted colorimetric biosensor for the detection of [...] Read more.
Abnormal levels of reduced glutathione (GSH) and glutathione reductase (GR) are usually related to a variety of diseases, so it is of great significance to determine the GSH concentration and GR activity. We herein develop a smartphone-assisted colorimetric biosensor for the detection of GSH and GR activity in human serum and mouse liver using hemin/G-quadruplex DNAzyme. Firstly, an obvious color change from colorless to green can be observed, owing to the high peroxidase-like activity of hemin/G-quadruplex DNAzyme toward 2,2′-azino-bis(3-ethylbenzothiozoline-6-sulfonic acid) (ABTS). With the addition of GSH or GR, the H2O2-mediated oxidation of ABTS catalyzed by hemin/G-quadruplex DNAzyme is significantly inhibited, resulting in remarkable color fading. Therefore, the detection of GSH and GR activity can be achieved by observing the color transition or measuring the absorbance at 420 nm. The detection limit was estimated to be as low as 0.1 μM and 10 μU/mL for GSH and GR, respectively. More interestingly, the RGB values of the sensing system can be identified by the smartphone application (APP, color collect), which makes it an ideal format for on-site determination and point-of-care testing (POCT). In addition, the proposed method shows excellent selectivity and acceptable applicability for the determination of GSH concentration and GR activity in human serum samples and mouse liver tissues, which might hold great application potential in clinical diagnosis and drug screening. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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13 pages, 2205 KiB  
Article
Photoinduced DNA Cleavage and Photocytotoxic of Phenanthroline-Based Ligand Ruthenium Compounds
by Xia Hu, Ning-Yi Liu, Yuan-Qing Deng, Shan Wang, Ting Liu and Xue-Wen Liu
Molecules 2021, 26(11), 3471; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26113471 - 07 Jun 2021
Cited by 5 | Viewed by 1992
Abstract
The photophysical and biological properties of two new phenanthroline-based ligand ruthenium complexes were investigated in detail. Their DNA interaction modes were determined to be the intercalation mode using spectra titration and viscosity measurements. Under irradiation, obvious photo-reduced DNA cleavages were observed in the [...] Read more.
The photophysical and biological properties of two new phenanthroline-based ligand ruthenium complexes were investigated in detail. Their DNA interaction modes were determined to be the intercalation mode using spectra titration and viscosity measurements. Under irradiation, obvious photo-reduced DNA cleavages were observed in the two complexes via singlet oxygen generation. Furthermore, complex 2 showed higher DNA affinity, photocleavage activity, and singlet oxygen quantum yields than complex 1. The two complexes showed no toxicity towards tumor cells (HeLa, A549, and A375) in the dark. However, obvious photocytotoxicities were observed in the two complexes. Complex 2 exhibited large PIs (phototherapeutic indices) (ca. 400) towards HeLa cells. The study suggests that these complexes may act as DNA intercalators, DNA photocleavers, and photocytotoxic agents. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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9 pages, 7249 KiB  
Article
Label-Free Fluorescence Molecular Beacon Probes Based on G-Triplex DNA and Thioflavin T for Protein Detection
by Jun Xue, Jintao Yi and Hui Zhou
Molecules 2021, 26(10), 2962; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26102962 - 17 May 2021
Cited by 4 | Viewed by 2268
Abstract
Protein detection plays an important role in biological and biomedical sciences. The immunoassay based on fluorescence labeling has good specificity but a high labeling cost. Herein, on the basis of G-triplex molecular beacon (G3MB) and thioflavin T (ThT), we developed a simple and [...] Read more.
Protein detection plays an important role in biological and biomedical sciences. The immunoassay based on fluorescence labeling has good specificity but a high labeling cost. Herein, on the basis of G-triplex molecular beacon (G3MB) and thioflavin T (ThT), we developed a simple and label-free biosensor for protein detection. The biotin and streptavidin were used as model enzymes. In the presence of target streptavidin (SA), the streptavidin hybridized with G3MB-b (biotin-linked-G-triplex molecular beacon) perfectly and formed larger steric hindrance, which hindered the hydrolysis of probes by exonuclease III (Exo III). In the absence of target streptavidin, the exonuclease III successively cleaved the stem of G3MB-b and released the G-rich sequences which self-assembled into a G-triplex and subsequently activated the fluorescence signal of thioflavin T. Compared with the traditional G-quadruplex molecular beacon (G4MB), the G3MB only needed a lower dosage of exonuclease III and a shorter reaction time to reach the optimal detection performance, because the concise sequence of G-triplex was good for the molecular beacon design. Moreover, fluorescence experiment results exhibited that the G3MB-b had good sensitivity and specificity for streptavidin detection. The developed label-free biosensor provides a valuable and general platform for protein detection. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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10 pages, 5628 KiB  
Article
A Label-Free Fluorometric Glutathione Assay Based on a Conformational Switch of G-quadruplex
by Xi Zhou, Doudou Zhang, Ying Yan, Hailun He, Yukui Zhou and Changbei Ma
Molecules 2021, 26(9), 2743; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26092743 - 07 May 2021
Viewed by 1783
Abstract
In this paper, a label-free fluorescent method for glutathione (GSH) detection based on a thioflavin T/G-quadruplex conformational switch is developed. The sensing assay is fabricated depending on the virtue of mercury ions to form a thymine–thymine mismatch, which collapses the distance between two [...] Read more.
In this paper, a label-free fluorescent method for glutathione (GSH) detection based on a thioflavin T/G-quadruplex conformational switch is developed. The sensing assay is fabricated depending on the virtue of mercury ions to form a thymine–thymine mismatch, which collapses the distance between two ssDNA and directs the guanine-rich part to form an intra-strand asymmetric split G-quadruplex. The newly formed G-quadruplex efficiently reacts with thioflavin T and enhances the fluorescent intensity. In the presence of GSH, Hg2+ is absorbed, destroying the G-quadruplex formation with a significant decrease in fluorescence emission. The proposed fluorescent assay exhibits a linear range between 0.03–5 μM of GSH with a detection limit of 9.8 nM. Furthermore, the efficacy of this method is examined using human serum samples to detect GSH. Besides GSH, other amino acids are also investigated in standard samples, which display satisfactory sensitivity and selectivity. Above all, we develop a method with features including potentiality, facility, sensitivity, and selectivity for analyzing GSH for clinical diagnostics. Full article
(This article belongs to the Special Issue Application of Nucleic Acid Probe in Analysis and Detection)
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