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/Curation ); 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></record>Pour manipuler ce document sous Unix (Dilib)
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