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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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Lee SY, Hong SW, Yeo H, Hwang GT. The linkers in fluorene-labeled 2′-deoxyuridines affect fluorescence discriminating phenomena upon duplex formation. RSC Adv 2020; 10:18853-18859. [PMID: 35518342 PMCID: PMC9053879 DOI: 10.1039/d0ra01651a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/08/2020] [Indexed: 11/29/2022] Open
Abstract
Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers—UF (without linker), UFL (with ethynyl linker), and UDF (with diethynyl linker)—have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the fluorescence emission properties upon duplex formation with fully matched and single-base-mismatched targets. Here, we describe the influence of the linkers on the emission behavior, the intramolecular electron transfer between the fluorene moiety and the uracil base after photoexcitation, and the structural stability upon duplex formation. The probe containing the UFL residue (with an ethynyl linker) and cytosine residues as flanking bases exhibited the greatest fluorescence turn-on selective behavior toward the perfectly matched target. Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the emission properties upon duplex formations.![]()
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Affiliation(s)
- So Young Lee
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Seung Woo Hong
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Hyeonuk Yeo
- Department of Chemistry Education
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
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Colorimetric determination of cytosine-rich ssDNA by silver(I)-modulated glucose oxidase-catalyzed growth of gold nanoparticles. Mikrochim Acta 2019; 186:467. [PMID: 31240491 DOI: 10.1007/s00604-019-3591-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Abstract
A colorimetric assay is described for determination of cytosine-rich ssDNA at physiological pH values. The working principle is based on (a) Ag(I) ion-induced formation of an i-motif structure, and (b) glucose oxidase-controlled growth of gold nanoparticles (AuNPs). The combination between Ag+ and cytosine-rich DNA can modulate the generation of H2O2 resulting from enzyme catalyzed glucose oxidation. Depending on the amount of H2O2 formed, the solution containing the AuNPs will turn red in the presence of cytosine-rich ssDNA but blue in the absence of such DNA if Ag+ is added before the formation of the red AuNPs. Upon addition of C-DNA at different concentrations, the peak shift (Δλ) of the AuNP solution relative to the SPR peak position (560 nm) in the absence of C-DNA is taken as the signal readout. The method shows a good linear response toward C-DNA over the range 10-200 nM with a detection limit of 2.7 nM. It may also be performed visually. The photometric assay is highly sensitive, specific, and rapid. The method is particularly attractive in terms of applications such as in human serum analysis, a colorimetric logic gate, and the calculation of binding constants for the interaction between Ag+ and glucose oxidase (GOx), and between Ag+ and cytosine-rich ssDNAs. Graphical abstract Schematic presentation of colorimetric detection of cytosine (C)-rich ssDNA (C-DNA) based on the modulation of the glucose oxidase (GOx)-catalyzed growth of gold nanoparticles (AuNPs) with Ag+ as the enzyme inhibitor.
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Lee HJ, Go GH, Ro JJ, Kim BH. Detection of cofilin mRNA by hybridization-sensitive double-stranded fluorescent probes. RSC Adv 2018; 8:7514-7517. [PMID: 35539109 PMCID: PMC9078427 DOI: 10.1039/c7ra13349a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Abstract
We have developed hybridization-sensitive fluorescent oligonucleotide probes that, in the presence of quencher strands, undergo efficient fluorescence quenching through the formation of partial DNA/DNA duplexes.
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Affiliation(s)
- Ha Jung Lee
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Gui Han Go
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Jong Jin Ro
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Byeang Hyean Kim
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of 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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Nim-Anussornkul D, Vilaivan T. Synthesis and optical properties of pyrrolidinyl peptide nucleic acid bearing a base discriminating fluorescence nucleobase 8-(pyrene-1-yl)-ethynyladenine. Bioorg Med Chem 2017; 25:6388-6397. [PMID: 29111370 DOI: 10.1016/j.bmc.2017.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/06/2017] [Accepted: 10/12/2017] [Indexed: 12/29/2022]
Abstract
A combination of fluorophore and nucleobase through a π-conjugated rigid linker integrates the base pairing and the fluorescence change into a single event. Such base discriminating fluorophore can change its fluorescence as a direct response to the base pairing event and therefore have advantages over tethered labels or base surrogates lacking the hydrogen-bonding ability. 8-(Pyrene-1-yl)ethynyl-adenine (APyE) has been extensively used as fluorescence labels in DNA and LNA, but it showed little discrimination between different nucleobases. Herein we investigated the synthesis, base pairing ability and optical properties of APyE in pyrrolidinyl peptide nucleic acid - a DNA mimic that shows much stronger affinity and specificity towards DNA than natural oligonucleotides. The APyE in PNA pairs specifically with thymine in the DNA strand, and resulted in 1.5-5.2-fold enhanced and blue-shifted fluorescence emission. Fluorescence quenching was observed in the presence of mismatched base or abasic site directly opposite to the APyE. The behavior of APyE in acpcPNA is distinctively different from DNA whereby a fluorescence was increased selectively upon duplex formation with complementary DNA and therefore emphasizing the unique advantages of using PNA as alternative oligonucleotide probes. Applications as color-shifting probe for detection of trinucleotide repeats in DNA were demonstrated, and the performance of the probe was further improved by combination with reduced graphene oxide as an external nanoquencher.
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Affiliation(s)
- Duangrat Nim-Anussornkul
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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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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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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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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Fluorescent Oligonucleotides Containing a 2-Ethynylfluorene- or 2-Ethynylfluorenone-labeled 2′-Deoxyguanosine Unit: Fluorescence Changes upon Duplex Formation. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Shibata T, Nakatani K. Fluorescence Probe for Detecting CCG Trinucleotide Repeat DNA Expansion and Slip-Out. Chembiochem 2016; 17:1685-8. [DOI: 10.1002/cbic.201600200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Tomonori Shibata
- Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1, Mihogaoka Ibaraki 567-0047 Japan
| | - Kazuhiko Nakatani
- Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1, Mihogaoka Ibaraki 567-0047 Japan
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12
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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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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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Kim KT, Heo W, Joo T, Kim BH. Photophysical and structural investigation of a PyA-modified adenine cluster: its potential use for fluorescent DNA probes exhibiting distinct emission color changes. Org Biomol Chem 2015; 13:8470-8. [DOI: 10.1039/c5ob01159k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A PyA-modified adenine cluster, exhibiting a large Stokes shift based on interstrand stacking interactions of adenines, was investigated and exploited as signaling parts of fluorescent DNA probes.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Wooseok Heo
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Taiha Joo
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Byeang Hyean Kim
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- 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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