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Asa TA, Seo YJ. I-motif sensor for the fluorometric detection of Monkeypox. Analyst 2024. [PMID: 39058361 DOI: 10.1039/d4an00947a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
In this study, we developed an isothermal fluorometric diagnostic method for DNA virus-generating disorders such as Mpox. Our results showed that the release of a large number of protons during multiplex-LAMP markedly lowered the pH level, which transformed the retinoblastoma (Rb) linear ssDNA into i-motifs. Consequently, thiazole orange (TO; a fluorometric probe sensitive to the i-motif) boosted the signal-on fluorescence because of its ability to bind selectively to i-motifs. This multiplex-LAMP/i-motif-TO system enabled simultaneous detection aimed at numerous potential targets with remarkable sensitivity (1.47 pg per mL) and efficiency (30 minutes). Our method is expected to enable DNA-virus-related diseases to be efficiently and accurately assessed.
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Affiliation(s)
- Tasnima Alam Asa
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
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2
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Liu ST, Chen JS, Liu XP, Mao CJ, Jin BK. A photoelectrochemical biosensor based on b-TiO 2/CdS:Eu/Ti 3C 2 heterojunction for the ultrasensitive detection of miRNA-21. Talanta 2023; 253:123601. [PMID: 36126520 DOI: 10.1016/j.talanta.2022.123601] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/26/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
A novel photoelectrochemical (PEC) biosensor based on b-TiO2/CdS:Eu/Ti3C2 heterojunction was developed for ultrasensitive determination of miRNA-21. In this device, the b-TiO2/CdS:Eu/Ti3C2 heterojunction with excellent energy level arrangement effectively facilitated photoelectric conversion efficiency and accelerated the separation of the photogenerated electron hole pairs, which because that the structure of heterojunction overcomes the drawbacks of single material, such as narrow light absorption range, wide band gap, short carrier lifetime, etc., improves light utilization, extends the lifetime of photogenerated electron hole pairs, and promotes electron transfer. Herein, hairpin DNA1 (H1) decorated on the b-TiO2/CdS:Eu/Ti3C2 electrode surface by Cd-S bonds, after H2/miRNA-21 heterduplex was introduced, the strand-displacement reaction (SDR) was triggered between H1 and H2/miRNA-21, accordingly, miRNA-21 was discharged from the H2/miRNA-21 heterduplex, forming the H1/H2 duplex, and the reuse of miRNA-21 was realized. As a signal amplification factor, the signal amplification factor H3-CdSe was hybridized with H1/H2 duplex, which greatly enhanced the sensitivity of the PEC biosensor. Under optimal conditions, the designed PEC biosensor displayed outstanding sensitivity, selectivity and stability with a wide liner range from 1.0 μM to 10.0 fM and a low detection limit of 3.3 fM. The preparation of the optoelectronic material affords a new direction for the progress of heterojunction photovoltaic materials and the construction of the proposed biosensor also provides a new thought for the PEC detection of human miRNA-21 with superior performance. Simultaneously, the established biosensor exhibiting tremendous possibility for detecting other biomarkers and biomolecules in clinical diagnosis fields.
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Affiliation(s)
- Shen-Ting Liu
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials of Anhui Province, Key Laboratory of Functional Inorganic Materials of Anhui Province, School of Chemistry & Chemical Engineering, Anhui University, Hefei, 230601, PR China
| | - Jing-Shuai Chen
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials of Anhui Province, Key Laboratory of Functional Inorganic Materials of Anhui Province, School of Chemistry & Chemical Engineering, Anhui University, Hefei, 230601, PR China
| | - Xing-Pei Liu
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials of Anhui Province, Key Laboratory of Functional Inorganic Materials of Anhui Province, School of Chemistry & Chemical Engineering, Anhui University, Hefei, 230601, PR China.
| | - Chang-Jie Mao
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials of Anhui Province, Key Laboratory of Functional Inorganic Materials of Anhui Province, School of Chemistry & Chemical Engineering, Anhui University, Hefei, 230601, PR China.
| | - Bao-Kang Jin
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials of Anhui Province, Key Laboratory of Functional Inorganic Materials of Anhui Province, School of Chemistry & Chemical Engineering, Anhui University, Hefei, 230601, PR China
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Alom KM, Ravi Kumara GS, Seo YJ. 22AG G-quadruplex RNA/QnMorpholine-mediated fluorimetric detection of miR-21. Anal Biochem 2022; 656:114879. [PMID: 36084699 DOI: 10.1016/j.ab.2022.114879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022]
Abstract
Herein we report a simple ligation/transcription-mediated system, using a 22AG G-quadruplex RNA secondary structure and a fluorescence-inducing QnMorpholine probe, for the detection of miR-21. In the presence of the target miR-21, two oligonucleotide probes (promoter and reporter) were ligated, thereby transcribing the 22AG RNA sequence, a complement of the reporter probe. In contrast, in the absence of this target-induced ligation, the reporter complement could not be transcribed to produce the 22AG RNA sequence. Subsequent addition of the QnMorpholine probe resulted in binding with the 22AG G-quadruplex RNA, thereby generating high fluorescence; no fluorescence occurred in the absence of this secondary structure. Hence, the presence of miR-21 was evidenced by a target-induced high-intensity signal. This simple one-pot fluorimetric system, which could detect miR-21 of up to 3.08 femtomolar in less than 30 min, holds promise as a diagnostic tool for selective and sensitive miRNA detection.
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Affiliation(s)
- Kazi Morshed Alom
- Department of Chemistry, Jeonbuk National University, Jeonju, 561-756, Republic of Korea
| | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju, 561-756, Republic of Korea.
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Alom KM, Kumara GSR, Seo YJ. Unnatural nucleotide-based rkDNA probe combined with graphene oxide for detection of alkaline phosphatase activity. Bioorg Med Chem Lett 2022; 64:128694. [PMID: 35314327 DOI: 10.1016/j.bmcl.2022.128694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/18/2022]
Abstract
In this study we developed a fluorescent double-stranded DNA, incorporating an unnatural dUrk nucleotide, that we used as a probe for the detection of alkaline phosphatase (ALP) based on enzymatic cleavage of the non-fluorescent complementary strand. Primer extension performed using the unnatural nucleotide triphosphate dUrkTP and the natural deoxynucleotide triphosphates dATP, dCTP, and dGTP provided a simple fluorescent DNA strand that hybridized with the 5́-monophosphate non-fluorescent complementary strand. When applying the 5́-phosphate recognition and cleavage properties of lambda exonuclease (λ-exo), this probe could bind to graphene oxide (GO) and quench the fluorescence (in the absence of ALP) or not bind to GO and retain its fluorescence (in the presence of ALP). We obtained strongly fluorescent DNA strands through simple incorporation of multiple A sites in the complementary sequence, thereby increasing the number of dUrk residues during primer extension. This unnatural nucleotide-based rkDNA probing system exhibited high fluorescence differentiation for discriminating the status of ALP. This rkDNA-GO probing system appears to be a promising tool for monitoring the activity of disease-associated enzymes.
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Affiliation(s)
- Kazi Morshed Alom
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, Republic of Korea
| | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, Republic of Korea.
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Choi MH, Seo YJ. Rapid and highly sensitive hairpin structure-mediated colorimetric detection of miRNA. Anal Chim Acta 2021; 1176:338765. [PMID: 34399900 DOI: 10.1016/j.aca.2021.338765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 01/15/2023]
Abstract
Herein, we report a novel hairpin structure-mediated diagnostic method for the simple and rapid colorimetric detection of miRNA through the sensing of pyrophosphate. When the hairpin structure of the template DNA (h-Probe) was hybridized with the primer, the DNA primer extension mediated by nPfu special enzyme was blocked. However, this h-Probe was extended using nPfu special enzyme, upon the structural change of the template DNA, from a hairpin to a linear structure, in the presence of the target miRNA. The miRNA-hybridized template DNA sequence was cleaved by a duplex-specific nuclease (DSN), which cleaved the DNA from the RNA-DNA hybrid, thereby allowing the target miRNA to be recycled. Primer extension using nPfu special enzyme produced pyrophosphate when nucleotide triphosphate was incorporated into the DNA; this pyrophosphate was sensed in terms of a color change, from pink to colorless, when using pp Probe, a probe developed previously by our group. This novel system for the colorimetric detection of target miRNA operated with high sensitivity (LOD = 132 aM) and selectivity, with the whole detection process requiring only 30 min. Furthermore, this system could also detect miRNA fluorimetrically with similar sensitivity (LOD = 105 aM), highlighting the dual-sensing properties of pp Probe. This unique, extremely simple, and rapid system for the detection of miRNA through a highly sensitive color change would presumably be useful in applications requiring point-of-care detection.
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Affiliation(s)
- Moon Hyeok Choi
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea.
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Ravi Kumara GS, Seo YJ. Polymerase-mediated synthesis of p-vinylaniline-coupled fluorescent DNA for the sensing of nucleolin protein- c-myc G-quadruplex interactions. Org Biomol Chem 2021; 19:5788-5793. [PMID: 34085078 DOI: 10.1039/d1ob00863c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this paper we report the synthesis of two deoxyuridine derivatives (dUCN2, dUPy)-featuring p-vinylaniline-based fluorophores linked through a propargyl unit at the 5' position-that function as molecular rotors. This probing system proved to be useful for the sensing of gene regulation arising from interactions between this G-quadruplex and nucleolin.
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Affiliation(s)
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
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Choi MH, Lee J, Seo YJ. Combined recombinase polymerase amplification/rkDNA-graphene oxide probing system for detection of SARS-CoV-2. Anal Chim Acta 2021; 1158:338390. [PMID: 33863409 PMCID: PMC7973912 DOI: 10.1016/j.aca.2021.338390] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 01/07/2023]
Abstract
The development of rapid, highly sensitive, and selective methods for the diagnosis of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) should help to prevent the spread of this pandemic virus. In this study, we combined recombinase polymerase amplification (RPA), as a means of isothermal DNA amplification, with an rkDNA-graphene oxide (GO) probe system to allow the rapid detection of SARS-CoV-2 with high sensitivity and selectivity. We used in situ enzymatic synthesis to prepare an rkDNA probe that was complementary to an RPA-amplified sequence of the target N-gene of SARS-CoV-2. The fluorescence of this rkDNA was perfectly quenched in the presence of GO. When the quenched rkDNA-GO system was added to the RPA-amplified sequence of the target SARS-CoV-2, the fluorescence recovered dramatically. The combined RPA/rkDNA-GO system exhibited extremely high selectivity (discrimination factor: 17.2) and sensitivity (LOD = 6.0 aM) for the detection of SARS-CoV-2. The total processing time was only 1.6 h. This combined RPA/rkDNA-GO system appears to be a very efficient and simple method for the point-of-care detection of SARS-CoV-2.
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Affiliation(s)
- Moon Hyeok Choi
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Jaehyeon Lee
- Department of Laborotory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, 54896, South Korea
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea.
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