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Ravi Kumara GS, Pandith A, Seo YJ. Highly fluorescent morpholine naphthalimide deoxyuridine nucleotide for the detection of miRNA 24-3P through rolling circle amplification. Analyst 2021; 145:4777-4781. [PMID: 32478340 DOI: 10.1039/d0an00723d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this study we synthesized the nucleotide dUrkTP, a highly fluorescent naphthalimide deoxyuridine triphosphate that undergoes aggregation-induced emission (AIE). We incorporated and extended dUrkTP during the primer extension of DNA mediated by DNA polymerase, and also in the rolling circle amplification of DNA mediated by Phi29 polymerase. Accordingly, we could use this fluorescent nucleotide for the detection of microRNA 24-3P, a biomarker of porcine reproductive and respiratory syndrome virus. The direct labeling system obtained during rolling circle DNA amplification exhibited increased fluorescence, due to AIE of the dUrkTP residue upon gel formation, thereby allowing the detection of miRNA 24-3P. This direct labeling system facilitated the simple and inexpensive detection of miRNA 24-3P with high sensitivity (limit of detection: 3.58 fM) and selectivity.
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Affiliation(s)
| | - Anup Pandith
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, South Korea.
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, South Korea.
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2
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Yang Z, Hu Q, Qin L, Zhu S, Qiu L, Su Y, Jin J. RNase H amplified RNA probe and graphene oxide system for highly sensitive detection of (CAG)n DNA repeat sequences. NANOTECHNOLOGY 2019; 30:465502. [PMID: 31426052 DOI: 10.1088/1361-6528/ab3c8b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Huntington's disease is a chronic progressive neurodegeneration which is caused by CAG repeat sequences expanding in the huntingtin gene. There is currently no disease-modifying treatment for the disease, and its progression can only be slowed down before the onset of symptoms. A novel fluorescent platform which contains an RNA probe and graphene oxide for detection of the biomarker of Huntington's disease, CAG repeat sequences, was constructed in this investigation. In addition, RNase H was employed in the fluorescent system to enhance the sensitivity of the detection capability. The fluorescent signal was increased through the cyclic amplified reaction, which results from RNase H, specifically digestion of the RNA strand in the complement of the RNA-DNA duplex. The designed measurement method can detect CAG repeat sequences with a detection limit of 108 pM (R2 = 0.968) under which we optimized assay conditions. Furthermore, the detection limit is approximately 18 times lower than the traditional DNA and graphene oxide detection method without assistance of RNase H. Additionally, the probing platform also shows stronger ability to discriminate between the fluorescence of the target sequence and that of other non-target sequences. The results of our studies demonstrate that the RNase H amplified RNA probe and graphene oxide system exhibited excellent sensitivity and selectivity to the target of CAG repeats sequences.
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Le BH, Nguyen TVT, Joo HN, Seo YJ. Large-Stokes-shift-based folded DNA probing systems targeting DNA and miRNA 21 with signal amplification. Bioorg Med Chem 2018; 26:4881-4885. [DOI: 10.1016/j.bmc.2018.08.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/21/2022]
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4
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Le BH, Seo YJ. Transcription of Unnatural Fluorescent Nucleotides and their Application with Graphene Oxide for the Simple and Direct Detection of miRNA. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences; Chonbuk National University; Jeonju 561-756 South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences; Chonbuk National University; Jeonju 561-756 South Korea
- Department of Chemistry; Chonbuk National University; Jeonju 561-756 South Korea
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [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: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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Le BH, Seo YJ. Highly sensitive MicroRNA 146a detection using a gold nanoparticle-based CTG repeat probing system and isothermal amplification. Anal Chim Acta 2017; 999:155-160. [PMID: 29254567 DOI: 10.1016/j.aca.2017.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/10/2017] [Accepted: 11/09/2017] [Indexed: 12/13/2022]
Abstract
We have developed a gold nanoparticle (AuNP)-based CTG repeat probing system displaying high quenching capability and combined it with isothermal amplification for the detection of miRNA 146a. This method of using a AuNP-based CTG repeat probing system with isothermal amplification allowed the highly sensitive (14 aM) and selective detection of miRNA 146a. A AuNP-based CTG repeat probing system having a hairpin structure and a dTF fluorophore exhibited highly efficient quenching because the CTG repeat-based stable hairpin structure imposed a close distance between the AuNP and the dTF residue. A small amount of miRNA 146a induced multiple copies of the CAG repeat sequence during rolling circle amplification; the AuNP-based CTG repeat probing system then bound to the complementary multiple-copy CAG repeat sequence, thereby inducing a structural change from a hairpin to a linear structure with amplified fluorescence. This AuNP-based CTG probing system combined with isothermal amplification could also discriminate target miRNA 146a from one- and two-base-mismatched miRNAs (ORN 1 and ORN 2, respectively). This simple AuNP-based CTG probing system, combined with isothermal amplification to induce a highly sensitive change in fluorescence, allows the detection of miRNA 146a with high sensitivity (14 aM) and selectivity.
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Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea; Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea.
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Nguyen TVT, Le BH, Seo YJ. Highly fluorescence quenching graphene oxide-based oligodeoxynucleotide hairpin systems for probing CNG DNA repeat sequences. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.07.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Xie YS, Zhang XL, Xie K, Zhao Y, Wu H, Yang J. Chiral-aminoquinoline-based fluorescent pH probe with large stokes shift for bioimaging. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 179:51-57. [PMID: 28214676 DOI: 10.1016/j.saa.2017.02.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
The aminoquinoline derivatives, (R)- and (S)-2-phenyl-2-(quinolin-6-ylamino)ethan-1-ol (R-PEO and S-PEO), were synthesized by a tandem one-pot three-step CN coupling method where Smiles rearrangement was the key procedure. The selected compound R-PEO showed a significant fluorescence enhancement with a turn-on ratio over 98-fold and enabled the real time determination of proton concentration in acidic solution. The fluorescence intensity of R-PEO exhibited strong pH-dependent performance with a large Stokes shift (115nm) and responded linearly to minor pH change within the range of 3.8-6.0. With the help of 1H NMR spectrum, we also confirmed the protonation of the quinoline unit should be the proposed reaction. Compared with the conjugated acid of N-hexylquinolin-6-amine (NQA), the conjugated acid of R-PEO shows significant planar intramolecular charge transfer (PICT) character. Furthermore, biological imaging proved that R-PEO probe can be used to monitor the pH change of S. cerevisiae in vivo.
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Affiliation(s)
- Yong-Sheng Xie
- The School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Xin-Ling Zhang
- The School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Kun Xie
- The School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Yanmei Zhao
- The School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Huan Wu
- The School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404100, China
| | - Jidong Yang
- The School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404100, China.
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Joo HN, Van Thi Nguyen T, Chae HK, Seo YJ. pH-Dependant fluorescence switching of an i-motif structure incorporating an isomeric azobenzene/pyrene fluorophore. Bioorg Med Chem Lett 2017; 27:2415-2419. [PMID: 28416130 DOI: 10.1016/j.bmcl.2017.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/01/2017] [Accepted: 04/04/2017] [Indexed: 12/28/2022]
Abstract
In this study, we synthesized an Azo-py phosphoramidite, featuring azobenzene and pyrene units, as a novel fluorescent and isomeric (trans- and cis-azobenzene units) material, which we incorporated in an i-motif DNA sequence. We then monitored the structural dynamics and changes in fluorescence as the modified DNA sequences transformed from single strands at pH 7 to i-motif quadruplex structures at pH 3. After incorporating Azo-py into the 4A loop position of an i-motif sequence, dramatic changes in fluorescence occurred as the DNA structures changed from single-strands to i-motif quadruplex structures. Interestingly, the cis form of Azo-py induced a more stable i-motif structure than did the trans form, as confirmed from circular dichroism spectra and melting temperature data. The absorption and fluorescence signals of these Azo-py-incorporated i-motif systems exhibited switchable and highly correlated signaling patterns. Such isomeric structures based on Azo-py might find potential applications in biology, where control over stable i-motif quadruplex structures might be performed with switchable fluorescence signaling.
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Affiliation(s)
- Han Na Joo
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea
| | - Thuy Van Thi Nguyen
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, South Korea
| | - Hyeon Kyeong Chae
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea; Department of Bioactive Material Sciences, Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, South Korea.
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Nguyen TVT, Seo YJ. Highly sensitive fluorescent sensor targeting CuCl2 based on thiophene attached anthracene compound (TA). Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.01.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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11
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Lee JW, Son YS, Hwang JY, Park Y, Hwang GT. pH-Responsive quencher-free molecular beacon systems containing 2′-deoxyuridine units labeled with fluorene derivatives. Org Biomol Chem 2017; 15:7165-7172. [DOI: 10.1039/c7ob01703k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
pH-Responsive oligodeoxynucleotides only exhibited dramatic increases in fluorescence upon duplex formation with their fully matched target DNAs.
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Affiliation(s)
- Ji Won Lee
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Ye-Seul Son
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Jun Yeon Hwang
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Yoojin Park
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology
- Pohang 37673
- Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
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Junager NPL, Kongsted J, Astakhova K. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes. SENSORS 2016; 16:s16081173. [PMID: 27472344 PMCID: PMC5017339 DOI: 10.3390/s16081173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 01/08/2023]
Abstract
Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.
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Affiliation(s)
- Nina P L Junager
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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Joo HN, Seo YJ. Single excitation three color folded DNA probe for SNP typing. Bioorg Med Chem Lett 2015; 25:5286-90. [PMID: 26453008 DOI: 10.1016/j.bmcl.2015.09.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/07/2015] [Accepted: 09/18/2015] [Indexed: 11/15/2022]
Abstract
A single fluorophore based multi-color emission probing system has been developed in the current work. dA(py) was used as the fluorophore, which was incorporated at the end of folded oligonucleotide with increasing number. Depending on the number of dA(py) three different color emissions were observed, viz. blue, green and red. These interesting color patterns were further used for the SNP typing of DNA. Every folded oligonucleotide with different number of dA(py)s could discriminate the full matched target sequence from one base mismatched and two base mismatched sequences. Furthermore, this probing system has a simple structure and also exhibited large Stokes shifted signal for discriminating the target DNA.
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Affiliation(s)
- Han Na Joo
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea; Department of Bioactive Material Sciences, Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, South Korea.
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