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Tao Y, Zheng Y, Zhai Q, Wei D. Recent advances in the development of small molecules targeting RNA G-quadruplexes for drug discovery. Bioorg Chem 2021; 110:104804. [PMID: 33740677 DOI: 10.1016/j.bioorg.2021.104804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Extensive evidence indicates that RNA G-quadruplexes have associated with some important cellular events. Investigation of RNA G-quadruplexes is thus vital to revealing their biofunctions. Several small molecules have been developed to target RNA G-quadruplexes to date. Some of the small molecules showed significantly light-up fluorescence signals upon binding to RNA G-quadruplexes, while some of them regulated the biofunctions of RNA G-quadruplexes. In this mini-review, the small molecules divided into four kinds are expounded which focused mainly on their structural features and biological activities. Moreover, we raised the current challenges and promising prospects. This mini-review might contribute to exploiting more sophisticated small molecules targeting RNA G-quadruplexes with high specificity based on the reported chemical structural features.
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Affiliation(s)
- Yanfei Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingge Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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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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3
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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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Le BH, Seo YJ. Direct incorporation and extension of a fluorescent nucleotide through rolling circle DNA amplification for the detection of microRNA 24-3P. Bioorg Med Chem Lett 2018; 28:2035-2038. [PMID: 29709251 DOI: 10.1016/j.bmcl.2018.04.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 12/27/2022]
Abstract
We designed and synthesized several fluorescent nucleotides from thiophene, anthracene and pyrene, which have different sizes, and screened their incorporation and extension capability during the rolling circle amplification of DNA. The thiophene-based fluorescent nucleotide (dUthioTP) could highly incorporate and extended into the rolling circle DNA product, while other fluorescent nucleotides (dUanthTP, and dUpyrTP) could not. This dUthioTP fluorescent nucleotide could be used for the detection of miRNA 24-3P, which is related PRRSV. This direct labeling system during rolling circle DNA amplification exhibited an increased fluorescence signal showing gel formation for the detection of miRNA 24-3P. This direct labeling system is a very simple and cost-efficient method for the detection miRNA 24-3P and also exhibited highly sensitive and selective detection properties.
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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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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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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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7
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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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Le BH, Koo JC, Joo HN, Seo YJ. Diverse size approach to incorporate and extend highly fluorescent unnatural nucleotides into DNA. Bioorg Med Chem 2017; 25:3591-3596. [PMID: 28501432 DOI: 10.1016/j.bmc.2017.03.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 11/28/2022]
Abstract
We have prepared a series of size-diverse unnatural nucleotides containing fluorescent (dApyrTP, dUpyrTP, dUantTP, dUthiTP) and quencher (dUazoTP) units, as well as nucleotides presenting small functional groups (dAethTP, dAoctTP, dUethTP, dUiodTP), all based on deoxyadenosine and deoxyuridine, and examined their suitability for use in enzymatic incorporation and extension into DNA. We observed a size-dependence of the incorporation and extension capability (following the order dUiodTP=dUethTP=dUthiTP>dUazoTP>dUpyrTP>dUantTP) during primer extension. This result was supported by circular dichroism (CD) spectra, which revealed a trend in the different B-form DNA structures depending on the size of the unit at the 5-position of the deoxyuridine (dUiodTP>dUethTP>dUthiTP>dUpyrTP), obtained from the PCR products. Interestingly, dUthiTP could be incorporated and extended into long DNA strands during primer extension and even PCR amplification, with CD spectroscopy confirming a stable secondary B-form duplex DNA structure. We observed full-length extension products even when combining dUthiTP with a template containing 24 continuous dA units during the primer extension. Thus, we believe that dUthiTP is a promising fluorescent nucleotide for a diverse range of biological applications requiring multiple incorporation and extension directly without disruption of B-form DNA structures.
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Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Chonbuk National University, Jeonju 54896, South Korea
| | - Ja Choon Koo
- Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 54896, South Korea
| | - Han Na Joo
- Department of Chemistry, Chonbuk National University, Jeonju 54896, South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences, Chonbuk National University, Jeonju 54896, South Korea; Department of Chemistry, Chonbuk National University, Jeonju 54896, 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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10
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Na Joo H, huy Le B, Jun Seo Y. Azo-pyrene–based fluorescent sensor of reductive cleavage of isomeric azo functional group. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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11
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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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Kim IS, Seo YJ. TT Dimerization and Its Effect on Human Telomere G-Quadruplex Formation. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- In Sun Kim
- 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; Chonbuk National University; Jeonju 561-756 South Korea
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13
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Joo HN, Seo YJ. Using gold aggregation to probe the inhibition and destruction of the G-quadruplex structure by TT-dimerization. Bioorg Med Chem Lett 2015; 25:2434-7. [PMID: 25908518 DOI: 10.1016/j.bmcl.2015.03.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/11/2015] [Accepted: 03/24/2015] [Indexed: 11/29/2022]
Abstract
Thrombin binding G-quadruplex oligonucleotide containing two TT-dimer fragments and a gold attachment (ODN G1-G) was designed and synthesized with the aim of understanding the TT-dimer effect in G-quadruplex formation. Our results showed that TT-dimer mutation induced by UV light inhibits the formation of and even destroys the G-quadruplex structure, as confirmed by UV, CD and melting temperature measurements. The structural change resulting from TT-dimer formation with DNA was additionally probed and was found to be accompanied by significant gold aggregation that was observed in the form of a signal change from red to blue.
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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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Joo HN, Seo YJ. A multiplex fluorophore molecular beacon: detection of the target sequence using large Stokes shift and multiple emission signal properties. Chem Commun (Camb) 2015; 51:2939-42. [DOI: 10.1039/c4cc08854a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a multiplex fluorophore molecular beacon (mfMB) with fluorophores located at its end to produce unique FRET (Fluorescence Resonance Energy Transfer). It exhibited diverse fluorescence properties depending on the mixing pattern, such as large Stokes shift emission and multiple colors.
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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
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16
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Azo compounds with different sized fluorophores and characterization of their photophysical properties based on trans to cis conformational change. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.07.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Kim IS, Seo YJ. Probe development for detection of TERRA 1 intramolecular G-quadruplex formation using a fluorescent adenosine derivative. Bioorg Med Chem Lett 2014; 24:1589-91. [PMID: 24513043 DOI: 10.1016/j.bmcl.2014.01.068] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/09/2014] [Accepted: 01/22/2014] [Indexed: 01/20/2023]
Abstract
We developed a probing system to detect the intramolecular G-quadruplex of telomeric repeat-containing RNA (TERRA 1). We used a fluorescent adenosine derivative rA(py) as a fluorophore and incorporated it into the dangling position of the parallel-type G-quadruplex sequence of TERRA 1. The rA(py)-modified G-quadruplex structure exhibited a strong fluorescence emission signal, while the emission signals of the single-strand and duplex structures were much lower.
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Affiliation(s)
- In Sun Kim
- 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.
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Lee DG, Kim IS, Park JW, Seo YJ. Multiplex fluorophore systems on DNA with new diverse fluorescence properties and ability to sense the hybridization dynamics. Chem Commun (Camb) 2014; 50:7273-6. [DOI: 10.1039/c4cc01378f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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