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Novel Amplex Red Oxidases Based on Noncanonical DNA Structures: Property Studies and Applications in MicroRNA Detection
G-triplex has recently been identified as a new secondary structure in G-rich sequences. However, its functions and biological roles remain largely unknown. This study first developed two kinds of Amplex Red oxidases, which were based on relatively new G-triplex structure and a common G-quadruplex o...
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Published in: | Analytical chemistry (Washington) 2014-03, Vol.86 (6), p.2925-2930 |
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creator | Wang, Shaoru Fu, Boshi Wang, Jiaqi Long, Yuelin Zhang, Xiaoe Peng, Shuang Guo, Pu Tian, Tian Zhou, Xiang |
description | G-triplex has recently been identified as a new secondary structure in G-rich sequences. However, its functions and biological roles remain largely unknown. This study first developed two kinds of Amplex Red oxidases, which were based on relatively new G-triplex structure and a common G-quadruplex one. A collection of DNA binding assays including circular dichroism (CD) spectroscopy, a CD melting assay, and a UV titration study were used to determine the G-triplex structure of G3 oligomer. The low intrinsic oxidative activity of hemin was significantly enhanced using G-triplex or G-quadruplex. Only one key guanine deletion from the G3 oligomer or G4 one could result in a much decreased Amplex Red oxidation activity. To the best of our knowledge, this is the first case reporting direct use of air as the oxidant for fluorescence generation based on DNAzyme strategies. Further mechanism studies demonstrated an involvement of on-site H2O2 generation from O2 and water and a following oxidation of Amplex Red to resorufin, causing a fluorescence enhancement. Furthermore, the newly developed oxidases have been effectively used in microRNA detection, using only one biotin-labeled probe and one small-molecule substrate. The conjugation of a target DNA to the G-triplex- or G-quadruplex-forming sequence enabled one to produce G-triplex or G-quadruplex by endonuclease in the presence of a slight amount of miRNA and amplify the signal of fluorescence from the oxidation of Amplex Red. Our findings of novel Amplex Red oxidases could potentially be used in a wide range of applications. |
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However, its functions and biological roles remain largely unknown. This study first developed two kinds of Amplex Red oxidases, which were based on relatively new G-triplex structure and a common G-quadruplex one. A collection of DNA binding assays including circular dichroism (CD) spectroscopy, a CD melting assay, and a UV titration study were used to determine the G-triplex structure of G3 oligomer. The low intrinsic oxidative activity of hemin was significantly enhanced using G-triplex or G-quadruplex. Only one key guanine deletion from the G3 oligomer or G4 one could result in a much decreased Amplex Red oxidation activity. To the best of our knowledge, this is the first case reporting direct use of air as the oxidant for fluorescence generation based on DNAzyme strategies. Further mechanism studies demonstrated an involvement of on-site H2O2 generation from O2 and water and a following oxidation of Amplex Red to resorufin, causing a fluorescence enhancement. Furthermore, the newly developed oxidases have been effectively used in microRNA detection, using only one biotin-labeled probe and one small-molecule substrate. The conjugation of a target DNA to the G-triplex- or G-quadruplex-forming sequence enabled one to produce G-triplex or G-quadruplex by endonuclease in the presence of a slight amount of miRNA and amplify the signal of fluorescence from the oxidation of Amplex Red. Our findings of novel Amplex Red oxidases could potentially be used in a wide range of applications.</description><identifier>ISSN: 0003-2700</identifier><identifier>EISSN: 1520-6882</identifier><identifier>DOI: 10.1021/ac402535a</identifier><identifier>PMID: 24564683</identifier><identifier>CODEN: ANCHAM</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>Analytical chemistry ; Assaying ; Biosensing Techniques ; Circular Dichroism ; Deoxyribonucleic acid ; Dichroism ; DNA ; DNA - chemistry ; Fluorescence ; MicroRNAs - analysis ; Nucleic Acid Conformation ; Oligomers ; Oxidase ; Oxidation ; Oxidoreductases - chemistry ; Ribonucleic acid ; Ribonucleic acids ; RNA ; Spectrometry, Mass, Electrospray Ionization ; Spectrophotometry, Ultraviolet</subject><ispartof>Analytical chemistry (Washington), 2014-03, Vol.86 (6), p.2925-2930</ispartof><rights>Copyright © 2014 American Chemical Society</rights><rights>Copyright American Chemical Society Mar 18, 2014</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a409t-6ac026a189ea3f1cc3c8e7f3e30475672a98357bea0a00124d83798c175a82653</citedby><cites>FETCH-LOGICAL-a409t-6ac026a189ea3f1cc3c8e7f3e30475672a98357bea0a00124d83798c175a82653</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24564683$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Shaoru</creatorcontrib><creatorcontrib>Fu, Boshi</creatorcontrib><creatorcontrib>Wang, Jiaqi</creatorcontrib><creatorcontrib>Long, Yuelin</creatorcontrib><creatorcontrib>Zhang, Xiaoe</creatorcontrib><creatorcontrib>Peng, Shuang</creatorcontrib><creatorcontrib>Guo, Pu</creatorcontrib><creatorcontrib>Tian, Tian</creatorcontrib><creatorcontrib>Zhou, Xiang</creatorcontrib><title>Novel Amplex Red Oxidases Based on Noncanonical DNA Structures: Property Studies and Applications in MicroRNA Detection</title><title>Analytical chemistry (Washington)</title><addtitle>Anal. Chem</addtitle><description>G-triplex has recently been identified as a new secondary structure in G-rich sequences. However, its functions and biological roles remain largely unknown. This study first developed two kinds of Amplex Red oxidases, which were based on relatively new G-triplex structure and a common G-quadruplex one. A collection of DNA binding assays including circular dichroism (CD) spectroscopy, a CD melting assay, and a UV titration study were used to determine the G-triplex structure of G3 oligomer. The low intrinsic oxidative activity of hemin was significantly enhanced using G-triplex or G-quadruplex. Only one key guanine deletion from the G3 oligomer or G4 one could result in a much decreased Amplex Red oxidation activity. To the best of our knowledge, this is the first case reporting direct use of air as the oxidant for fluorescence generation based on DNAzyme strategies. Further mechanism studies demonstrated an involvement of on-site H2O2 generation from O2 and water and a following oxidation of Amplex Red to resorufin, causing a fluorescence enhancement. Furthermore, the newly developed oxidases have been effectively used in microRNA detection, using only one biotin-labeled probe and one small-molecule substrate. The conjugation of a target DNA to the G-triplex- or G-quadruplex-forming sequence enabled one to produce G-triplex or G-quadruplex by endonuclease in the presence of a slight amount of miRNA and amplify the signal of fluorescence from the oxidation of Amplex Red. Our findings of novel Amplex Red oxidases could potentially be used in a wide range of applications.</description><subject>Analytical chemistry</subject><subject>Assaying</subject><subject>Biosensing Techniques</subject><subject>Circular Dichroism</subject><subject>Deoxyribonucleic acid</subject><subject>Dichroism</subject><subject>DNA</subject><subject>DNA - chemistry</subject><subject>Fluorescence</subject><subject>MicroRNAs - analysis</subject><subject>Nucleic Acid Conformation</subject><subject>Oligomers</subject><subject>Oxidase</subject><subject>Oxidation</subject><subject>Oxidoreductases - chemistry</subject><subject>Ribonucleic acid</subject><subject>Ribonucleic acids</subject><subject>RNA</subject><subject>Spectrometry, Mass, Electrospray Ionization</subject><subject>Spectrophotometry, Ultraviolet</subject><issn>0003-2700</issn><issn>1520-6882</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><recordid>eNqN0U9rFTEQAPAgin2tHvwCEhBBD6uTZPNnvT3b2hbqq1Q9L9PsPNiyL9kmu9p-e1NeW0QPesnA8JsJM8PYCwHvBEjxHn0NUiuNj9hCaAmVcU4-ZgsAUJW0ADtsN-dLACFAmKdsR9ba1MapBfu5ij9o4MvNONA1P6eOn133HWbK_GN5Ox4DX8XgMcTQexz4wWrJv05p9tOcKH_gX1IcKU03JTl3fSnD0PHlOA5FT30MmfeBf-59iuel8oAm8rfpZ-zJGodMz-_iHvv-6fDb_nF1enZ0sr88rbCGZqoMepAGhWsI1Vp4r7wju1akoLbaWImNU9peEAKW8WTdOWUb54XV6KTRao-92fYdU7yaKU_tps-ehgEDxTm3wjRSKeka8W9aNquMbSz8BwVnrJOiLvTVH_QyzimUmYsSYKTT1hX1dqvKnnJOtG7H1G8w3bQC2tsbtw83LvblXcf5YkPdg7w_agGvtwB9_u23vxr9AkX0qlY</recordid><startdate>20140318</startdate><enddate>20140318</enddate><creator>Wang, Shaoru</creator><creator>Fu, Boshi</creator><creator>Wang, Jiaqi</creator><creator>Long, Yuelin</creator><creator>Zhang, Xiaoe</creator><creator>Peng, Shuang</creator><creator>Guo, Pu</creator><creator>Tian, Tian</creator><creator>Zhou, Xiang</creator><general>American Chemical Society</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7U5</scope><scope>7U7</scope><scope>7U9</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20140318</creationdate><title>Novel Amplex Red Oxidases Based on Noncanonical DNA Structures: Property Studies and Applications in MicroRNA Detection</title><author>Wang, Shaoru ; 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Chem</addtitle><date>2014-03-18</date><risdate>2014</risdate><volume>86</volume><issue>6</issue><spage>2925</spage><epage>2930</epage><pages>2925-2930</pages><issn>0003-2700</issn><eissn>1520-6882</eissn><coden>ANCHAM</coden><abstract>G-triplex has recently been identified as a new secondary structure in G-rich sequences. However, its functions and biological roles remain largely unknown. This study first developed two kinds of Amplex Red oxidases, which were based on relatively new G-triplex structure and a common G-quadruplex one. A collection of DNA binding assays including circular dichroism (CD) spectroscopy, a CD melting assay, and a UV titration study were used to determine the G-triplex structure of G3 oligomer. The low intrinsic oxidative activity of hemin was significantly enhanced using G-triplex or G-quadruplex. Only one key guanine deletion from the G3 oligomer or G4 one could result in a much decreased Amplex Red oxidation activity. To the best of our knowledge, this is the first case reporting direct use of air as the oxidant for fluorescence generation based on DNAzyme strategies. Further mechanism studies demonstrated an involvement of on-site H2O2 generation from O2 and water and a following oxidation of Amplex Red to resorufin, causing a fluorescence enhancement. Furthermore, the newly developed oxidases have been effectively used in microRNA detection, using only one biotin-labeled probe and one small-molecule substrate. The conjugation of a target DNA to the G-triplex- or G-quadruplex-forming sequence enabled one to produce G-triplex or G-quadruplex by endonuclease in the presence of a slight amount of miRNA and amplify the signal of fluorescence from the oxidation of Amplex Red. Our findings of novel Amplex Red oxidases could potentially be used in a wide range of applications.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>24564683</pmid><doi>10.1021/ac402535a</doi><tpages>6</tpages></addata></record> |
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subjects | Analytical chemistry Assaying Biosensing Techniques Circular Dichroism Deoxyribonucleic acid Dichroism DNA DNA - chemistry Fluorescence MicroRNAs - analysis Nucleic Acid Conformation Oligomers Oxidase Oxidation Oxidoreductases - chemistry Ribonucleic acid Ribonucleic acids RNA Spectrometry, Mass, Electrospray Ionization Spectrophotometry, Ultraviolet |
title | Novel Amplex Red Oxidases Based on Noncanonical DNA Structures: Property Studies and Applications in MicroRNA Detection |
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