Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA.
Identifieur interne : 000130 ( Main/Exploration ); précédent : 000129; suivant : 000131Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA.
Auteurs : Po-Jung Jimmy Huang [Canada] ; Woohyun J. Moon [Canada] ; Juewen Liu [Canada]Source :
- Biochemistry [ 1520-4995 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : ARN, Oligonucléotides phosphorothioates.
- métabolisme : ADN catalytique, ARN, Fer, Iode, Oligonucléotides phosphorothioates.
- Conformation d'acide nucléique, Humains.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Phosphorothioate Oligonucleotides, RNA.
- chemical , metabolism : DNA, Catalytic, Iodine, Iron, Phosphorothioate Oligonucleotides, RNA.
- Humans, Nucleic Acid Conformation.
Abstract
Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I2) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the Rp and Sp stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I2 also required Na+, consistent with the property of Ce13d and confirming the similar role of I2 as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I2 detection. With EDTA for masking metal ions, I2 was selectively detected down to 4.7 nM. Oxidation of I- with Fe3+ produced I2 in situ, allowing detection of Fe3+ down to 78 nM. By harnessing nonelectrostatic interactions, such as the I2/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.
DOI: 10.1021/acs.biochem.8b00900
PubMed: 30272443
Affiliations:
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Moon</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 </wicri:regionArea><wicri:noRegion>Ontario N2L 3G1 </wicri:noRegion></affiliation></author><author><name sortKey="Liu, Juewen" sort="Liu, Juewen" uniqKey="Liu J" first="Juewen" last="Liu">Juewen Liu</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 </wicri:regionArea><wicri:noRegion>Ontario N2L 3G1 </wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30272443</idno><idno type="pmid">30272443</idno><idno type="doi">10.1021/acs.biochem.8b00900</idno><idno type="wicri:Area/Main/Corpus">000199</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000199</idno><idno type="wicri:Area/Main/Curation">000199</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000199</idno><idno type="wicri:Area/Main/Exploration">000199</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA.</title><author><name sortKey="Jimmy Huang, Po Jung" sort="Jimmy Huang, Po Jung" uniqKey="Jimmy Huang P" first="Po-Jung" last="Jimmy Huang">Po-Jung Jimmy Huang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 </wicri:regionArea><wicri:noRegion>Ontario N2L 3G1 </wicri:noRegion></affiliation></author><author><name sortKey="Moon, Woohyun J" sort="Moon, Woohyun J" uniqKey="Moon W" first="Woohyun J" last="Moon">Woohyun J. Moon</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 </wicri:regionArea><wicri:noRegion>Ontario N2L 3G1 </wicri:noRegion></affiliation></author><author><name sortKey="Liu, Juewen" sort="Liu, Juewen" uniqKey="Liu J" first="Juewen" last="Liu">Juewen Liu</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 </wicri:regionArea><wicri:noRegion>Ontario N2L 3G1 </wicri:noRegion></affiliation></author></analytic><series><title level="j">Biochemistry</title><idno type="eISSN">1520-4995</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA, Catalytic (metabolism)</term><term>Humans (MeSH)</term><term>Iodine (metabolism)</term><term>Iron (metabolism)</term><term>Nucleic Acid Conformation (MeSH)</term><term>Phosphorothioate Oligonucleotides (chemistry)</term><term>Phosphorothioate Oligonucleotides (metabolism)</term><term>RNA (chemistry)</term><term>RNA (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN catalytique (métabolisme)</term><term>ARN (composition chimique)</term><term>ARN (métabolisme)</term><term>Conformation d'acide nucléique (MeSH)</term><term>Fer (métabolisme)</term><term>Humains (MeSH)</term><term>Iode (métabolisme)</term><term>Oligonucléotides phosphorothioates (composition chimique)</term><term>Oligonucléotides phosphorothioates (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Phosphorothioate Oligonucleotides</term><term>RNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA, Catalytic</term><term>Iodine</term><term>Iron</term><term>Phosphorothioate Oligonucleotides</term><term>RNA</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>ARN</term><term>Oligonucléotides phosphorothioates</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN catalytique</term><term>ARN</term><term>Fer</term><term>Iode</term><term>Oligonucléotides phosphorothioates</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term><term>Nucleic Acid Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Conformation d'acide nucléique</term><term>Humains</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I<sub>2</sub>) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the R<sub>p</sub> and S<sub>p</sub> stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I<sub>2</sub> also required Na<sup>+</sup>, consistent with the property of Ce13d and confirming the similar role of I<sub>2</sub> as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I<sub>2</sub> detection. With EDTA for masking metal ions, I<sub>2</sub> was selectively detected down to 4.7 nM. Oxidation of I<sup>-</sup> with Fe<sup>3+</sup> produced I<sub>2</sub> in situ, allowing detection of Fe<sup>3+</sup> down to 78 nM. By harnessing nonelectrostatic interactions, such as the I<sub>2</sub>/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30272443</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>30</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1520-4995</ISSN><JournalIssue CitedMedium="Internet"><Volume>58</Volume><Issue>5</Issue><PubDate><Year>2019</Year><Month>02</Month><Day>05</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA.</ArticleTitle><Pagination><MedlinePgn>422-429</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/acs.biochem.8b00900</ELocationID><Abstract><AbstractText>Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I<sub>2</sub>) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the R<sub>p</sub> and S<sub>p</sub> stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I<sub>2</sub> also required Na<sup>+</sup>, consistent with the property of Ce13d and confirming the similar role of I<sub>2</sub> as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I<sub>2</sub> detection. With EDTA for masking metal ions, I<sub>2</sub> was selectively detected down to 4.7 nM. Oxidation of I<sup>-</sup> with Fe<sup>3+</sup> produced I<sub>2</sub> in situ, allowing detection of Fe<sup>3+</sup> down to 78 nM. By harnessing nonelectrostatic interactions, such as the I<sub>2</sub>/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jimmy Huang</LastName><ForeName>Po-Jung</ForeName><Initials>PJ</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Moon</LastName><ForeName>Woohyun J</ForeName><Initials>WJ</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Juewen</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0001-5918-9336</Identifier><AffiliationInfo><Affiliation>Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>10</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biochemistry</MedlineTA><NlmUniqueID>0370623</NlmUniqueID><ISSNLinking>0006-2960</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021881">DNA, Catalytic</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D054735">Phosphorothioate Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>63231-63-0</RegistryNumber><NameOfSubstance UI="D012313">RNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>9679TC07X4</RegistryNumber><NameOfSubstance UI="D007455">Iodine</NameOfSubstance></Chemical><Chemical><RegistryNumber>E1UOL152H7</RegistryNumber><NameOfSubstance UI="D007501">Iron</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D021881" MajorTopicYN="N">DNA, Catalytic</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007455" MajorTopicYN="N">Iodine</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007501" MajorTopicYN="N">Iron</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054735" MajorTopicYN="N">Phosphorothioate Oligonucleotides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012313" MajorTopicYN="N">RNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>10</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>10</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>10</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30272443</ArticleId><ArticleId IdType="doi">10.1021/acs.biochem.8b00900</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country></list><tree><country name="Canada"><noRegion><name sortKey="Jimmy Huang, Po Jung" sort="Jimmy Huang, Po Jung" uniqKey="Jimmy Huang P" first="Po-Jung" last="Jimmy Huang">Po-Jung Jimmy Huang</name></noRegion><name sortKey="Liu, Juewen" sort="Liu, Juewen" uniqKey="Liu J" first="Juewen" last="Liu">Juewen Liu</name><name sortKey="Moon, Woohyun J" sort="Moon, Woohyun J" uniqKey="Moon W" first="Woohyun J" last="Moon">Woohyun J. 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