Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases.
Identifieur interne : 002617 ( PubMed/Curation ); précédent : 002616; suivant : 002618Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases.
Auteurs : J. Sági [États-Unis] ; B. Hang ; B. SingerSource :
- Chemical research in toxicology [ 0893-228X ] ; 1999.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Oligonucleotides.
- Amino Acid Sequence, Chemical Phenomena, Chemistry, Physical, DNA Repair, In Situ Nick-End Labeling, Thermodynamics.
Abstract
We previously reported that 15-mer oligonucleotides with a central 1, N(6)-epsilonA were cleaved by alkylpurine-DNA N-glycosylase as a function of T(m), modulated by neighbor bases [Hang, B., Sági, J., and Singer, B. (1998) J. Biol. Chem. 273, 33406-33413]. This type of investigation has now been extended to cleavage by Escherichia coli endonuclease IV of a centrally placed synthetic AP site using both 15-mer and 35-mer duplexes. In 15-mers, the triplet sequences adjunct to the central AP site greatly affected the thermodynamic stability. The repair rate paralleled the thermal stability since endonuclease IV requires a double-stranded substrate. When the AP site-containing duplexes were 35-mers, there was also a general correlation between the thermostability and cleavage efficiency. However, the difference in the cleavage rates between different sequences was much less than with the 15-mers. Since the 35-mers were more than 96% annealed, this difference presumably results from local stability and structure adjacent to the AP site. These results suggest that under enzyme limiting conditions or overproduction of AP sites, sequence-dependent differential repair could occur in vivo.
DOI: 10.1021/tx990088y
PubMed: 10525266
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :002617
Links to Exploration step
pubmed:10525266Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases.</title>
<author><name sortKey="Sagi, J" sort="Sagi, J" uniqKey="Sagi J" first="J" last="Sági">J. Sági</name>
<affiliation wicri:level="1"><nlm:affiliation>Donner Laboratory, University of California, Berkeley, California 94720, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Donner Laboratory, University of California, Berkeley, California 94720</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Hang, B" sort="Hang, B" uniqKey="Hang B" first="B" last="Hang">B. Hang</name>
</author>
<author><name sortKey="Singer, B" sort="Singer, B" uniqKey="Singer B" first="B" last="Singer">B. Singer</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="1999">1999</date>
<idno type="RBID">pubmed:10525266</idno>
<idno type="pmid">10525266</idno>
<idno type="doi">10.1021/tx990088y</idno>
<idno type="wicri:Area/PubMed/Corpus">002617</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002617</idno>
<idno type="wicri:Area/PubMed/Curation">002617</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002617</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases.</title>
<author><name sortKey="Sagi, J" sort="Sagi, J" uniqKey="Sagi J" first="J" last="Sági">J. Sági</name>
<affiliation wicri:level="1"><nlm:affiliation>Donner Laboratory, University of California, Berkeley, California 94720, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Donner Laboratory, University of California, Berkeley, California 94720</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Hang, B" sort="Hang, B" uniqKey="Hang B" first="B" last="Hang">B. Hang</name>
</author>
<author><name sortKey="Singer, B" sort="Singer, B" uniqKey="Singer B" first="B" last="Singer">B. Singer</name>
</author>
</analytic>
<series><title level="j">Chemical research in toxicology</title>
<idno type="ISSN">0893-228X</idno>
<imprint><date when="1999" type="published">1999</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Chemical Phenomena</term>
<term>Chemistry, Physical</term>
<term>DNA Repair</term>
<term>In Situ Nick-End Labeling</term>
<term>Oligonucleotides (chemistry)</term>
<term>Thermodynamics</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Chimie physique</term>
<term>Méthode TUNEL</term>
<term>Oligonucléotides ()</term>
<term>Phénomènes chimiques</term>
<term>Réparation de l'ADN</term>
<term>Séquence d'acides aminés</term>
<term>Thermodynamique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Oligonucleotides</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Chemical Phenomena</term>
<term>Chemistry, Physical</term>
<term>DNA Repair</term>
<term>In Situ Nick-End Labeling</term>
<term>Thermodynamics</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Chimie physique</term>
<term>Méthode TUNEL</term>
<term>Oligonucléotides</term>
<term>Phénomènes chimiques</term>
<term>Réparation de l'ADN</term>
<term>Séquence d'acides aminés</term>
<term>Thermodynamique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">We previously reported that 15-mer oligonucleotides with a central 1, N(6)-epsilonA were cleaved by alkylpurine-DNA N-glycosylase as a function of T(m), modulated by neighbor bases [Hang, B., Sági, J., and Singer, B. (1998) J. Biol. Chem. 273, 33406-33413]. This type of investigation has now been extended to cleavage by Escherichia coli endonuclease IV of a centrally placed synthetic AP site using both 15-mer and 35-mer duplexes. In 15-mers, the triplet sequences adjunct to the central AP site greatly affected the thermodynamic stability. The repair rate paralleled the thermal stability since endonuclease IV requires a double-stranded substrate. When the AP site-containing duplexes were 35-mers, there was also a general correlation between the thermostability and cleavage efficiency. However, the difference in the cleavage rates between different sequences was much less than with the 15-mers. Since the 35-mers were more than 96% annealed, this difference presumably results from local stability and structure adjacent to the AP site. These results suggest that under enzyme limiting conditions or overproduction of AP sites, sequence-dependent differential repair could occur in vivo.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">10525266</PMID>
<DateCompleted><Year>2000</Year>
<Month>01</Month>
<Day>04</Day>
</DateCompleted>
<DateRevised><Year>2019</Year>
<Month>09</Month>
<Day>21</Day>
</DateRevised>
<Article PubModel="Print"><Journal><ISSN IssnType="Print">0893-228X</ISSN>
<JournalIssue CitedMedium="Print"><Volume>12</Volume>
<Issue>10</Issue>
<PubDate><Year>1999</Year>
<Month>Oct</Month>
</PubDate>
</JournalIssue>
<Title>Chemical research in toxicology</Title>
<ISOAbbreviation>Chem. Res. Toxicol.</ISOAbbreviation>
</Journal>
<ArticleTitle>Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases.</ArticleTitle>
<Pagination><MedlinePgn>917-23</MedlinePgn>
</Pagination>
<Abstract><AbstractText>We previously reported that 15-mer oligonucleotides with a central 1, N(6)-epsilonA were cleaved by alkylpurine-DNA N-glycosylase as a function of T(m), modulated by neighbor bases [Hang, B., Sági, J., and Singer, B. (1998) J. Biol. Chem. 273, 33406-33413]. This type of investigation has now been extended to cleavage by Escherichia coli endonuclease IV of a centrally placed synthetic AP site using both 15-mer and 35-mer duplexes. In 15-mers, the triplet sequences adjunct to the central AP site greatly affected the thermodynamic stability. The repair rate paralleled the thermal stability since endonuclease IV requires a double-stranded substrate. When the AP site-containing duplexes were 35-mers, there was also a general correlation between the thermostability and cleavage efficiency. However, the difference in the cleavage rates between different sequences was much less than with the 15-mers. Since the 35-mers were more than 96% annealed, this difference presumably results from local stability and structure adjacent to the AP site. These results suggest that under enzyme limiting conditions or overproduction of AP sites, sequence-dependent differential repair could occur in vivo.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sági</LastName>
<ForeName>J</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Donner Laboratory, University of California, Berkeley, California 94720, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hang</LastName>
<ForeName>B</ForeName>
<Initials>B</Initials>
</Author>
<Author ValidYN="Y"><LastName>Singer</LastName>
<ForeName>B</ForeName>
<Initials>B</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>CA47723</GrantID>
<Acronym>CA</Acronym>
<Agency>NCI NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant><GrantID>CA72079</GrantID>
<Acronym>CA</Acronym>
<Agency>NCI NIH HHS</Agency>
<Country>United States</Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
<PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>Chem Res Toxicol</MedlineTA>
<NlmUniqueID>8807448</NlmUniqueID>
<ISSNLinking>0893-228X</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D055598" MajorTopicYN="N">Chemical Phenomena</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002627" MajorTopicYN="N">Chemistry, Physical</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D004260" MajorTopicYN="Y">DNA Repair</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020287" MajorTopicYN="N">In Situ Nick-End Labeling</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009841" MajorTopicYN="N">Oligonucleotides</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013816" MajorTopicYN="N">Thermodynamics</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1999</Year>
<Month>10</Month>
<Day>20</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>1999</Year>
<Month>10</Month>
<Day>20</Day>
<Hour>0</Hour>
<Minute>1</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>1999</Year>
<Month>10</Month>
<Day>20</Day>
<Hour>0</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">10525266</ArticleId>
<ArticleId IdType="pii">tx990088y</ArticleId>
<ArticleId IdType="doi">10.1021/tx990088y</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002617 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 002617 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Curation |type= RBID |clé= pubmed:10525266 |texte= Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:10525266" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |