Incorporation of two anthraquinonylmethyl groups into the 2'-O-positions of oligonucleotides: increased affinity and sequence specificity of anthraquinone-modified oligonucleotides in hybrid formation with DNA and RNA.
Identifieur interne : 005492 ( Main/Merge ); précédent : 005491; suivant : 005493Incorporation of two anthraquinonylmethyl groups into the 2'-O-positions of oligonucleotides: increased affinity and sequence specificity of anthraquinone-modified oligonucleotides in hybrid formation with DNA and RNA.
Auteurs : K. Yamana [Japon] ; T. Mitsui ; J. Yoshioka ; T. Isuno ; H. NakanoSource :
- Bioconjugate chemistry [ 1043-1802 ]
Descripteurs français
- KwdFr :
- MESH :
- métabolisme : ADN, ARN, Oligonucléotides.
- synthèse chimique : Oligonucléotides.
- Anthraquinones, Dichroïsme circulaire, Oligonucléotides, Relation structure-activité.
English descriptors
- KwdEn :
- MESH :
- chemical , chemical synthesis : Oligonucleotides.
- chemical , chemistry : Oligonucleotides.
- chemical , metabolism : DNA, Oligonucleotides, RNA.
- chemical : Anthraquinones.
- Circular Dichroism, Structure-Activity Relationship.
Abstract
Oligonucleotide 15-mers containing one or two anthraquinonylmethyl groups at specified sugar residues have been prepared on an automated DNA/RNA synthesizer by using 5'-O-dimethoxytrityl 2'-O-(2-anthraquinonylmethyl)uridine 3'-O-(2-cyanoethyl)-N, N-diisopropylphosphoramidite. The purification of the modified oligonucleotides was done with denaturing polyacrylamide gel electrophoresis. The base compositions and the presence of anthraquinone group(s) in the oligonucleotides were verified with enzymatic digestion (snake venom phosphodiesterase and alkaline phosphatase) analysis and UV-vis spectral measurements. The UV melting behaviors indicate that all the oligonucleotides with anthraquinone group(s) can bind to both their complementary DNA and RNA in a manner similar to that of the unmodified oligonucleotide. All the oligonucleotides possessing anthraquinone group(s) have higher affinity for both DNA and RNA segments when compared with the unmodified oligonucleotide. The oligomer containing two anthraquinone substituents at sites separated by four nucleotides instead of six exhibits the highest affinity for both the complementary DNA and RNA. The stabilizing effect can be translated into a free energy cost of 7.1 kcal/mol for the DNA hybrid and 3.6 kcal/mol for RNA. It has been shown through mismatch/Tm studies that modification of the oligonucleotide by anthraquinone groups does not alter the sequence specificity in binding to a RNA segment.
DOI: 10.1021/bc960064s
PubMed: 8950490
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Incorporation of two anthraquinonylmethyl groups into the 2'-O-positions of oligonucleotides: increased affinity and sequence specificity of anthraquinone-modified oligonucleotides in hybrid formation with DNA and RNA.</title><author><name sortKey="Yamana, K" sort="Yamana, K" uniqKey="Yamana K" first="K" last="Yamana">K. Yamana</name><affiliation wicri:level="1"><nlm:affiliation>Department of Applied Chemistry, Himeji Institute of Technology, Hyogo, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Applied Chemistry, Himeji Institute of Technology, Hyogo</wicri:regionArea><wicri:noRegion>Hyogo</wicri:noRegion></affiliation></author><author><name sortKey="Mitsui, T" sort="Mitsui, T" uniqKey="Mitsui T" first="T" last="Mitsui">T. Mitsui</name></author><author><name sortKey="Yoshioka, J" sort="Yoshioka, J" uniqKey="Yoshioka J" first="J" last="Yoshioka">J. Yoshioka</name></author><author><name sortKey="Isuno, T" sort="Isuno, T" uniqKey="Isuno T" first="T" last="Isuno">T. Isuno</name></author><author><name sortKey="Nakano, H" sort="Nakano, H" uniqKey="Nakano H" first="H" last="Nakano">H. Nakano</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="????"><PubDate><MedlineDate>1996 Nov-Dec</MedlineDate></PubDate></date><idno type="RBID">pubmed:8950490</idno><idno type="pmid">8950490</idno><idno type="doi">10.1021/bc960064s</idno><idno type="wicri:Area/PubMed/Corpus">002752</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002752</idno><idno type="wicri:Area/PubMed/Curation">002752</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002752</idno><idno type="wicri:Area/PubMed/Checkpoint">002B08</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002B08</idno><idno type="wicri:Area/Ncbi/Merge">002A51</idno><idno type="wicri:Area/Ncbi/Curation">002A51</idno><idno type="wicri:Area/Ncbi/Checkpoint">002A51</idno><idno type="wicri:doubleKey">1043-1802::Yamana K:incorporation:of:two</idno><idno type="wicri:Area/Main/Merge">005492</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Incorporation of two anthraquinonylmethyl groups into the 2'-O-positions of oligonucleotides: increased affinity and sequence specificity of anthraquinone-modified oligonucleotides in hybrid formation with DNA and RNA.</title><author><name sortKey="Yamana, K" sort="Yamana, K" uniqKey="Yamana K" first="K" last="Yamana">K. Yamana</name><affiliation wicri:level="1"><nlm:affiliation>Department of Applied Chemistry, Himeji Institute of Technology, Hyogo, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Applied Chemistry, Himeji Institute of Technology, Hyogo</wicri:regionArea><wicri:noRegion>Hyogo</wicri:noRegion></affiliation></author><author><name sortKey="Mitsui, T" sort="Mitsui, T" uniqKey="Mitsui T" first="T" last="Mitsui">T. Mitsui</name></author><author><name sortKey="Yoshioka, J" sort="Yoshioka, J" uniqKey="Yoshioka J" first="J" last="Yoshioka">J. Yoshioka</name></author><author><name sortKey="Isuno, T" sort="Isuno, T" uniqKey="Isuno T" first="T" last="Isuno">T. Isuno</name></author><author><name sortKey="Nakano, H" sort="Nakano, H" uniqKey="Nakano H" first="H" last="Nakano">H. Nakano</name></author></analytic><series><title level="j">Bioconjugate chemistry</title><idno type="ISSN">1043-1802</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Anthraquinones</term><term>Circular Dichroism</term><term>DNA (metabolism)</term><term>Oligonucleotides (chemical synthesis)</term><term>Oligonucleotides (chemistry)</term><term>Oligonucleotides (metabolism)</term><term>RNA (metabolism)</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (métabolisme)</term><term>ARN (métabolisme)</term><term>Anthraquinones</term><term>Dichroïsme circulaire</term><term>Oligonucléotides ()</term><term>Oligonucléotides (métabolisme)</term><term>Oligonucléotides (synthèse chimique)</term><term>Relation structure-activité</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemical synthesis" xml:lang="en"><term>Oligonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Oligonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>Oligonucleotides</term><term>RNA</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Anthraquinones</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>ARN</term><term>Oligonucléotides</term></keywords><keywords scheme="MESH" qualifier="synthèse chimique" xml:lang="fr"><term>Oligonucléotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Circular Dichroism</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Anthraquinones</term><term>Dichroïsme circulaire</term><term>Oligonucléotides</term><term>Relation structure-activité</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Oligonucleotide 15-mers containing one or two anthraquinonylmethyl groups at specified sugar residues have been prepared on an automated DNA/RNA synthesizer by using 5'-O-dimethoxytrityl 2'-O-(2-anthraquinonylmethyl)uridine 3'-O-(2-cyanoethyl)-N, N-diisopropylphosphoramidite. The purification of the modified oligonucleotides was done with denaturing polyacrylamide gel electrophoresis. The base compositions and the presence of anthraquinone group(s) in the oligonucleotides were verified with enzymatic digestion (snake venom phosphodiesterase and alkaline phosphatase) analysis and UV-vis spectral measurements. The UV melting behaviors indicate that all the oligonucleotides with anthraquinone group(s) can bind to both their complementary DNA and RNA in a manner similar to that of the unmodified oligonucleotide. All the oligonucleotides possessing anthraquinone group(s) have higher affinity for both DNA and RNA segments when compared with the unmodified oligonucleotide. The oligomer containing two anthraquinone substituents at sites separated by four nucleotides instead of six exhibits the highest affinity for both the complementary DNA and RNA. The stabilizing effect can be translated into a free energy cost of 7.1 kcal/mol for the DNA hybrid and 3.6 kcal/mol for RNA. It has been shown through mismatch/Tm studies that modification of the oligonucleotide by anthraquinone groups does not alter the sequence specificity in binding to a RNA segment.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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