Synthesis of 2′‐Aminoalkyl‐Substituted Fluorinated Nucleobases and Their Influence on the Kinetic Properties of Hammerhead Ribozymes
Identifieur interne : 003150 ( Main/Merge ); précédent : 003149; suivant : 003151Synthesis of 2′‐Aminoalkyl‐Substituted Fluorinated Nucleobases and Their Influence on the Kinetic Properties of Hammerhead Ribozymes
Auteurs : Astrid E. Klöpffer ; Joachim W. Engels [Allemagne]Source :
- ChemBioChem [ 1439-4227 ] ; 2004-05-03.
Descripteurs français
- KwdFr :
- ARN catalytique (), ARN catalytique (métabolisme), Catalyse, Cinétique, Conformation d'acide nucléique, Données de séquences moléculaires, Fluor (), Ribonucléosides (), Ribonucléosides (métabolisme), Ribonucléosides (synthèse chimique), Spécificité du substrat, Séquence nucléotidique, Thermodynamique.
- MESH :
- métabolisme : ARN catalytique, Ribonucléosides.
- synthèse chimique : Ribonucléosides.
- ARN catalytique, Catalyse, Cinétique, Conformation d'acide nucléique, Données de séquences moléculaires, Fluor, Ribonucléosides, Spécificité du substrat, Séquence nucléotidique, Thermodynamique.
English descriptors
- KwdEn :
- Base Sequence, Catalysis, Fluorine (chemistry), Kinetics, Molecular Sequence Data, Nucleic Acid Conformation, RNA, Catalytic (chemistry), RNA, Catalytic (metabolism), Ribonucleosides (chemical synthesis), Ribonucleosides (chemistry), Ribonucleosides (metabolism), Substrate Specificity, Thermodynamics.
- MESH :
- chemical , chemical synthesis : Ribonucleosides.
- chemical , chemistry : Fluorine, RNA, Catalytic, Ribonucleosides.
- chemical , metabolism : RNA, Catalytic, Ribonucleosides.
- Teeft :
- Ach2, Amersham biosciences, Analogue, Anhydrous, Anhydrous pyridine, Aqueous solution, Artificial nucleosides, Base Sequence, Base pair, Bch2, Benzimidazole, Black bars, Carom, Catalysis, Catalytic activity, Cdcl3, Chem, Chembiochem, Cleavage, Cleavage rates, Cleavage reactions, Crude product, Dropwise, Dropwise addition, Duplex, Engels, Equiv, Gene expression, Gmbh, Hammerhead, Hammerhead ribozyme, Hammerhead ribozymes, Harom, Hphth, Hydrogen bonds, Kgaa, Kinetic analysis, Kinetic parameters, Kinetic properties, Kinetics, Methyl bromoacetate, Mgso4, Mismatch, Mismatch complexes, Mismatch variants, Mmol, Molecular Sequence Data, Mutation, Natural nucleosides, Nucleic Acid Conformation, Nucleobase, Nucleobase analogues, Nucleobases, Nucleoside, Nucleoside analogue, Nucleoside analogues, Organic extracts, Phosphoroamidite, Point mutations, Possible substrates, Primary alcohol, Pyridine, Reaction mixture, Reaction rates, Ribozyme, Ribozymes, Rna, Room temperature, Sichch3, Sodium hydride, Substrate Specificity, Sugar moiety, Tetrabutylammonium fluoride, Thermodynamic data, Thermodynamics, Universal nucleobases, Unmodified, Unmodified ribozyme, Verlag, Verlag gmbh, Weinheim, Weinheim chembiochem, White foam.
Abstract
Hammerhead ribozymes are ribonucleic acids that catalyse the hydrolytic cleavage of RNA. They interfere with gene expression in a highly specific manner and recognize the mRNA target through Watson–Crick base pairing. To overcome the problem of point mutations (Watson–Crick “mismatches”) occurring in viral genomes, we developed 2′‐aminoethyl‐substituted fluorinated nucleosides, which are universal nucleobases. The highly efficient synthetic pathway, which features a direct phthaloylamination of a primary alcohol under Mitsunobu conditions, leads to modified phosphoroamidites. The 1′‐deoxy‐1′‐(4,6‐difluoro‐1H‐benzimidazol‐1‐yl)‐2′‐(β‐aminoethyl)‐β‐D‐ribofuranose nucleoside analogue does not differentiate between the four natural nucleosides and leads to a RNA duplex that is as stable as the unmodified parent duplex. Upon incorporation into a ribozyme, the analogue's catalytic activity is equal for all four possible substrates, and the cleavage rates for the modified ribozymes are significantly higher (up to a factor of 13) than for the natural Watson–Crick “mismatch” base pairs. In agreement with the thermodynamic data obtained by measurement of the Tm values of the RNA 12‐mers, the cleavage rates for the 2′‐substituted fluorinated benzimidazole derivative 4 are slightly higher than for the corresponding fluorinated benzene derivative 3.
Fluorinated nucleoside analogues and modified RNAs: The optimised synthesis of 2′‐aminoethyl‐substituted fluorinated benzene and benzimidazole nucleosides (see scheme) and their incorporation into oligoribonucleotides is reported. The influence of these universal bases on the thermodynamic stability of RNA 12‐mer duplexes was investigated by UV/Vis melting studies. The effect of these artificial nucleobases on the reaction rate of ribozyme‐catalysed RNA cleavage was studied by kinetic analyses to evaluate their tolerance against point mutations in biological systems. Owing to their improved properties for RNA recognition and their easy incorporation into hammerhead ribozymes, the nucleosides are applicable to a variety of different mRNA targets.
Url:
DOI: 10.1002/cbic.200300809
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<front><div type="abstract" xml:lang="en">Hammerhead ribozymes are ribonucleic acids that catalyse the hydrolytic cleavage of RNA. They interfere with gene expression in a highly specific manner and recognize the mRNA target through Watson–Crick base pairing. To overcome the problem of point mutations (Watson–Crick “mismatches”) occurring in viral genomes, we developed 2′‐aminoethyl‐substituted fluorinated nucleosides, which are universal nucleobases. The highly efficient synthetic pathway, which features a direct phthaloylamination of a primary alcohol under Mitsunobu conditions, leads to modified phosphoroamidites. The 1′‐deoxy‐1′‐(4,6‐difluoro‐1H‐benzimidazol‐1‐yl)‐2′‐(β‐aminoethyl)‐β‐D‐ribofuranose nucleoside analogue does not differentiate between the four natural nucleosides and leads to a RNA duplex that is as stable as the unmodified parent duplex. Upon incorporation into a ribozyme, the analogue's catalytic activity is equal for all four possible substrates, and the cleavage rates for the modified ribozymes are significantly higher (up to a factor of 13) than for the natural Watson–Crick “mismatch” base pairs. In agreement with the thermodynamic data obtained by measurement of the Tm values of the RNA 12‐mers, the cleavage rates for the 2′‐substituted fluorinated benzimidazole derivative 4 are slightly higher than for the corresponding fluorinated benzene derivative 3.</div>
<div type="abstract" xml:lang="en">Fluorinated nucleoside analogues and modified RNAs: The optimised synthesis of 2′‐aminoethyl‐substituted fluorinated benzene and benzimidazole nucleosides (see scheme) and their incorporation into oligoribonucleotides is reported. The influence of these universal bases on the thermodynamic stability of RNA 12‐mer duplexes was investigated by UV/Vis melting studies. The effect of these artificial nucleobases on the reaction rate of ribozyme‐catalysed RNA cleavage was studied by kinetic analyses to evaluate their tolerance against point mutations in biological systems. Owing to their improved properties for RNA recognition and their easy incorporation into hammerhead ribozymes, the nucleosides are applicable to a variety of different mRNA targets.</div>
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<front><div type="abstract" xml:lang="en">Hammerhead ribozymes are ribonucleic acids that catalyse the hydrolytic cleavage of RNA. They interfere with gene expression in a highly specific manner and recognize the mRNA target through Watson–Crick base pairing. To overcome the problem of point mutations (Watson–Crick “mismatches”) occurring in viral genomes, we developed 2′‐aminoethyl‐substituted fluorinated nucleosides, which are universal nucleobases. The highly efficient synthetic pathway, which features a direct phthaloylamination of a primary alcohol under Mitsunobu conditions, leads to modified phosphoroamidites. The 1′‐deoxy‐1′‐(4,6‐difluoro‐1H‐benzimidazol‐1‐yl)‐2′‐(β‐aminoethyl)‐β‐D‐ribofuranose nucleoside analogue does not differentiate between the four natural nucleosides and leads to a RNA duplex that is as stable as the unmodified parent duplex. Upon incorporation into a ribozyme, the analogue's catalytic activity is equal for all four possible substrates, and the cleavage rates for the modified ribozymes are significantly higher (up to a factor of 13) than for the natural Watson–Crick “mismatch” base pairs. In agreement with the thermodynamic data obtained by measurement of the Tm values of the RNA 12‐mers, the cleavage rates for the 2′‐substituted fluorinated benzimidazole derivative 4 are slightly higher than for the corresponding fluorinated benzene derivative 3.</div>
<div type="abstract" xml:lang="en">Fluorinated nucleoside analogues and modified RNAs: The optimised synthesis of 2′‐aminoethyl‐substituted fluorinated benzene and benzimidazole nucleosides (see scheme) and their incorporation into oligoribonucleotides is reported. The influence of these universal bases on the thermodynamic stability of RNA 12‐mer duplexes was investigated by UV/Vis melting studies. The effect of these artificial nucleobases on the reaction rate of ribozyme‐catalysed RNA cleavage was studied by kinetic analyses to evaluate their tolerance against point mutations in biological systems. Owing to their improved properties for RNA recognition and their easy incorporation into hammerhead ribozymes, the nucleosides are applicable to a variety of different mRNA targets.</div>
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<PubMed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Synthesis of 2'-aminoalkyl-substituted fluorinated nucleobases and their influence on the kinetic properties of hammerhead ribozymes.</title>
<author><name sortKey="Klopffer, Astrid E" sort="Klopffer, Astrid E" uniqKey="Klopffer A" first="Astrid E" last="Klöpffer">Astrid E. Klöpffer</name>
<affiliation wicri:level="3"><nlm:affiliation>Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Marie Curie Strasse 11, 60439 Frankfurt/Main, Germany.</nlm:affiliation>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Marie Curie Strasse 11, 60439 Frankfurt/Main</wicri:regionArea>
<placeName><region type="land" nuts="1">Hesse (Land)</region>
<region type="district" nuts="2">District de Darmstadt</region>
<settlement type="city">Francfort-sur-le-Main</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Engels, Joachim W" sort="Engels, Joachim W" uniqKey="Engels J" first="Joachim W" last="Engels">Joachim W. Engels</name>
</author>
</titleStmt>
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<date when="2004">2004</date>
<idno type="RBID">pubmed:15122643</idno>
<idno type="pmid">15122643</idno>
<idno type="doi">10.1002/cbic.200300809</idno>
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<idno type="wicri:doubleKey">1439-4227:2004:Klopffer A:synthesis:of:aminoalkyl</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Synthesis of 2'-aminoalkyl-substituted fluorinated nucleobases and their influence on the kinetic properties of hammerhead ribozymes.</title>
<author><name sortKey="Klopffer, Astrid E" sort="Klopffer, Astrid E" uniqKey="Klopffer A" first="Astrid E" last="Klöpffer">Astrid E. Klöpffer</name>
<affiliation wicri:level="3"><nlm:affiliation>Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Marie Curie Strasse 11, 60439 Frankfurt/Main, Germany.</nlm:affiliation>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Marie Curie Strasse 11, 60439 Frankfurt/Main</wicri:regionArea>
<placeName><region type="land" nuts="1">Hesse (Land)</region>
<region type="district" nuts="2">District de Darmstadt</region>
<settlement type="city">Francfort-sur-le-Main</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Engels, Joachim W" sort="Engels, Joachim W" uniqKey="Engels J" first="Joachim W" last="Engels">Joachim W. Engels</name>
</author>
</analytic>
<series><title level="j">Chembiochem : a European journal of chemical biology</title>
<idno type="ISSN">1439-4227</idno>
<imprint><date when="2004" type="published">2004</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term>
<term>Catalysis</term>
<term>Fluorine (chemistry)</term>
<term>Kinetics</term>
<term>Molecular Sequence Data</term>
<term>Nucleic Acid Conformation</term>
<term>RNA, Catalytic (chemistry)</term>
<term>RNA, Catalytic (metabolism)</term>
<term>Ribonucleosides (chemical synthesis)</term>
<term>Ribonucleosides (chemistry)</term>
<term>Ribonucleosides (metabolism)</term>
<term>Substrate Specificity</term>
<term>Thermodynamics</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN catalytique ()</term>
<term>ARN catalytique (métabolisme)</term>
<term>Catalyse</term>
<term>Cinétique</term>
<term>Conformation d'acide nucléique</term>
<term>Données de séquences moléculaires</term>
<term>Fluor ()</term>
<term>Ribonucléosides ()</term>
<term>Ribonucléosides (métabolisme)</term>
<term>Ribonucléosides (synthèse chimique)</term>
<term>Spécificité du substrat</term>
<term>Séquence nucléotidique</term>
<term>Thermodynamique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemical synthesis" xml:lang="en"><term>Ribonucleosides</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Fluorine</term>
<term>RNA, Catalytic</term>
<term>Ribonucleosides</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA, Catalytic</term>
<term>Ribonucleosides</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN catalytique</term>
<term>Ribonucléosides</term>
</keywords>
<keywords scheme="MESH" qualifier="synthèse chimique" xml:lang="fr"><term>Ribonucléosides</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Catalysis</term>
<term>Kinetics</term>
<term>Molecular Sequence Data</term>
<term>Nucleic Acid Conformation</term>
<term>Substrate Specificity</term>
<term>Thermodynamics</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ARN catalytique</term>
<term>Catalyse</term>
<term>Cinétique</term>
<term>Conformation d'acide nucléique</term>
<term>Données de séquences moléculaires</term>
<term>Fluor</term>
<term>Ribonucléosides</term>
<term>Spécificité du substrat</term>
<term>Séquence nucléotidique</term>
<term>Thermodynamique</term>
</keywords>
</textClass>
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<front><div type="abstract" xml:lang="en">Hammerhead ribozymes are ribonucleic acids that catalyse the hydrolytic cleavage of RNA. They interfere with gene expression in a highly specific manner and recognize the mRNA target through Watson-Crick base pairing. To overcome the problem of point mutations (Watson-Crick "mismatches") occurring in viral genomes, we developed 2'-aminoethyl-substituted fluorinated nucleosides, which are universal nucleobases. The highly efficient synthetic pathway, which features a direct phthaloylamination of a primary alcohol under Mitsunobu conditions, leads to modified phosphoroamidites. The 1'-deoxy-1'-(4,6-difluoro-1H-benzimidazol-1-yl)-2'-(beta-aminoethyl)-beta-D-ribofuranose nucleoside analogue does not differentiate between the four natural nucleosides and leads to a RNA duplex that is as stable as the unmodified parent duplex. Upon incorporation into a ribozyme, the analogue's catalytic activity is equal for all four possible substrates, and the cleavage rates for the modified ribozymes are significantly higher (up to a factor of 13) than for the natural Watson-Crick "mismatch" base pairs. In agreement with the thermodynamic data obtained by measurement of the T(m) values of the RNA 12-mers, the cleavage rates for the 2'-substituted fluorinated benzimidazole derivative 4 are slightly higher than for the corresponding fluorinated benzene derivative 3.</div>
</front>
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