Biophysical properties and thermal stability of oligonucleotides of RNA containing 7,8-dihydro-8-hydroxyadenosine.
Identifieur interne : 001621 ( PubMed/Checkpoint ); précédent : 001620; suivant : 001622Biophysical properties and thermal stability of oligonucleotides of RNA containing 7,8-dihydro-8-hydroxyadenosine.
Auteurs : Ana M. Chauca-Diaz ; Yu Jung Choi ; Marino J E. ResendizSource :
- Biopolymers [ 1097-0282 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- analogues et dérivés : Adénosine.
- ARN, Adénosine, Conformation d'acide nucléique, Dichroïsme circulaire, Oligonucléotides.
English descriptors
- KwdEn :
- MESH :
- chemical , analogs & derivatives : Adenosine.
- chemical , chemistry : Adenosine, Oligonucleotides, RNA.
- Circular Dichroism, Nucleic Acid Conformation.
Abstract
Circular dichroism (CD) was used to assess the stabilization/destabilization imposed by oxidative lesion 7,8-dihydro-8-hydroxyadenosine (8-oxoA) on strands of RNA with different structural motifs. RNA:RNA homoduplex destabilization was observed in a position dependent manner using 10-mers as models that displayed differences between 12.7 and 15.1°C. We found that increasing the number of modifications resulted in depressed Tm values of about 12-15°C per lesion. The same effect was observed on RNA:DNA heteroduplex samples. We also tested the effects of this lesion in short hairpins containing the tetraloop UUCX (X = A, 8-oxoA). We found that the stem was hypersensitive to substitution of A by 8-oxoA and that it destabilized the structure by >23°C. Concomitant substitution at the stem and loop prevented formation of this secondary structure or lead to other less-stable hairpins. Incorporation of this lesion at the first base of the loop had no effect on either structure. Overall, we found that the effects of 8-oxoA on RNA structure are position dependent and that its stabilization may vary from sharp decreases to small increments, in some cases, leading to the formation of other more/less stable structures. These structural changes may have larger biological implications, particularly if the oxidatively modified RNA persists, thus leading to changes in RNA reactivity and function.
DOI: 10.1002/bip.22579
PubMed: 25363418
Affiliations:
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Resendiz</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25363418</idno><idno type="pmid">25363418</idno><idno type="doi">10.1002/bip.22579</idno><idno type="wicri:Area/PubMed/Corpus">001802</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001802</idno><idno type="wicri:Area/PubMed/Curation">001802</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001802</idno><idno type="wicri:Area/PubMed/Checkpoint">001621</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001621</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Biophysical properties and thermal stability of oligonucleotides of RNA containing 7,8-dihydro-8-hydroxyadenosine.</title><author><name sortKey="Chauca Diaz, Ana M" sort="Chauca Diaz, Ana M" uniqKey="Chauca Diaz A" first="Ana M" last="Chauca-Diaz">Ana M. Chauca-Diaz</name><affiliation><nlm:affiliation>Department of Chemistry, University of Colorado Denver, Science Building, 1151 Arapahoe St, Denver, CO, 80204.</nlm:affiliation><wicri:noCountry code="subField">80204</wicri:noCountry></affiliation></author><author><name sortKey="Choi, Yu Jung" sort="Choi, Yu Jung" uniqKey="Choi Y" first="Yu Jung" last="Choi">Yu Jung Choi</name></author><author><name sortKey="Resendiz, Marino J E" sort="Resendiz, Marino J E" uniqKey="Resendiz M" first="Marino J E" last="Resendiz">Marino J E. Resendiz</name></author></analytic><series><title level="j">Biopolymers</title><idno type="eISSN">1097-0282</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adenosine (analogs & derivatives)</term><term>Adenosine (chemistry)</term><term>Circular Dichroism</term><term>Nucleic Acid Conformation</term><term>Oligonucleotides (chemistry)</term><term>RNA (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ()</term><term>Adénosine ()</term><term>Adénosine (analogues et dérivés)</term><term>Conformation d'acide nucléique</term><term>Dichroïsme circulaire</term><term>Oligonucléotides ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analogs & derivatives" xml:lang="en"><term>Adenosine</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Adenosine</term><term>Oligonucleotides</term><term>RNA</term></keywords><keywords scheme="MESH" qualifier="analogues et dérivés" xml:lang="fr"><term>Adénosine</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Circular Dichroism</term><term>Nucleic Acid Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN</term><term>Adénosine</term><term>Conformation d'acide nucléique</term><term>Dichroïsme circulaire</term><term>Oligonucléotides</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Circular dichroism (CD) was used to assess the stabilization/destabilization imposed by oxidative lesion 7,8-dihydro-8-hydroxyadenosine (8-oxoA) on strands of RNA with different structural motifs. RNA:RNA homoduplex destabilization was observed in a position dependent manner using 10-mers as models that displayed differences between 12.7 and 15.1°C. We found that increasing the number of modifications resulted in depressed Tm values of about 12-15°C per lesion. The same effect was observed on RNA:DNA heteroduplex samples. We also tested the effects of this lesion in short hairpins containing the tetraloop UUCX (X = A, 8-oxoA). We found that the stem was hypersensitive to substitution of A by 8-oxoA and that it destabilized the structure by >23°C. Concomitant substitution at the stem and loop prevented formation of this secondary structure or lead to other less-stable hairpins. Incorporation of this lesion at the first base of the loop had no effect on either structure. Overall, we found that the effects of 8-oxoA on RNA structure are position dependent and that its stabilization may vary from sharp decreases to small increments, in some cases, leading to the formation of other more/less stable structures. These structural changes may have larger biological implications, particularly if the oxidatively modified RNA persists, thus leading to changes in RNA reactivity and function.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25363418</PMID><DateCompleted><Year>2016</Year><Month>05</Month><Day>23</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1097-0282</ISSN><JournalIssue CitedMedium="Internet"><Volume>103</Volume><Issue>3</Issue><PubDate><Year>2015</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Biopolymers</Title><ISOAbbreviation>Biopolymers</ISOAbbreviation></Journal><ArticleTitle>Biophysical properties and thermal stability of oligonucleotides of RNA containing 7,8-dihydro-8-hydroxyadenosine.</ArticleTitle><Pagination><MedlinePgn>167-74</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/bip.22579</ELocationID><Abstract><AbstractText>Circular dichroism (CD) was used to assess the stabilization/destabilization imposed by oxidative lesion 7,8-dihydro-8-hydroxyadenosine (8-oxoA) on strands of RNA with different structural motifs. RNA:RNA homoduplex destabilization was observed in a position dependent manner using 10-mers as models that displayed differences between 12.7 and 15.1°C. We found that increasing the number of modifications resulted in depressed Tm values of about 12-15°C per lesion. The same effect was observed on RNA:DNA heteroduplex samples. We also tested the effects of this lesion in short hairpins containing the tetraloop UUCX (X = A, 8-oxoA). We found that the stem was hypersensitive to substitution of A by 8-oxoA and that it destabilized the structure by >23°C. Concomitant substitution at the stem and loop prevented formation of this secondary structure or lead to other less-stable hairpins. Incorporation of this lesion at the first base of the loop had no effect on either structure. Overall, we found that the effects of 8-oxoA on RNA structure are position dependent and that its stabilization may vary from sharp decreases to small increments, in some cases, leading to the formation of other more/less stable structures. These structural changes may have larger biological implications, particularly if the oxidatively modified RNA persists, thus leading to changes in RNA reactivity and function.</AbstractText><CopyrightInformation>© 2014 The Authors. Biopolymers Published by Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chauca-Diaz</LastName><ForeName>Ana M</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Colorado Denver, Science Building, 1151 Arapahoe St, Denver, CO, 80204.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Choi</LastName><ForeName>Yu Jung</ForeName><Initials>YJ</Initials></Author><Author ValidYN="Y"><LastName>Resendiz</LastName><ForeName>Marino J E</ForeName><Initials>MJ</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P30 CA046934</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>P30CA046934</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biopolymers</MedlineTA><NlmUniqueID>0372525</NlmUniqueID><ISSNLinking>0006-3525</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>29851-57-8</RegistryNumber><NameOfSubstance UI="C036009">8-oxoadenosine</NameOfSubstance></Chemical><Chemical><RegistryNumber>63231-63-0</RegistryNumber><NameOfSubstance UI="D012313">RNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>K72T3FS567</RegistryNumber><NameOfSubstance UI="D000241">Adenosine</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000241" MajorTopicYN="N">Adenosine</DescriptorName><QualifierName UI="Q000031" MajorTopicYN="Y">analogs & derivatives</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002942" MajorTopicYN="N">Circular Dichroism</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009841" MajorTopicYN="N">Oligonucleotides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012313" MajorTopicYN="N">RNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">8-oxoadenosine</Keyword><Keyword MajorTopicYN="N">RNA structural changes</Keyword><Keyword MajorTopicYN="N">circular dichroism</Keyword><Keyword MajorTopicYN="N">nucleic acid stability</Keyword><Keyword MajorTopicYN="N">oxidative damage of RNA</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>09</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>10</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>10</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>11</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>11</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>5</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25363418</ArticleId><ArticleId 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Chauca-Diaz</name><name sortKey="Choi, Yu Jung" sort="Choi, Yu Jung" uniqKey="Choi Y" first="Yu Jung" last="Choi">Yu Jung Choi</name><name sortKey="Resendiz, Marino J E" sort="Resendiz, Marino J E" uniqKey="Resendiz M" first="Marino J E" last="Resendiz">Marino J E. Resendiz</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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