Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases.
Identifieur interne : 000031 ( Ncbi/Merge ); précédent : 000030; suivant : 000032Sequence-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
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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><wicri:noRegion>California 94720</wicri:noRegion></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><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Hang, B" sort="Hang, B" uniqKey="Hang B" first="B" last="Hang">B. Hang</name><name sortKey="Singer, B" sort="Singer, B" uniqKey="Singer B" first="B" last="Singer">B. Singer</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Sagi, J" sort="Sagi, J" uniqKey="Sagi J" first="J" last="Sági">J. Sági</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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