Site-Specific Cleavage of RNAs Derived from the PIM1 3'-UTR by a Metal-Free Artificial Ribonuclease.
Identifieur interne : 000628 ( PubMed/Curation ); précédent : 000627; suivant : 000629Site-Specific Cleavage of RNAs Derived from the PIM1 3'-UTR by a Metal-Free Artificial Ribonuclease.
Auteurs : Felix Zellmann [Allemagne] ; Laura Thomas [Allemagne] ; Ute Scheffer [Allemagne] ; Roland K. Hartmann [Allemagne] ; Michael W. Göbel [Allemagne]Source :
- Molecules (Basel, Switzerland) [ 1420-3049 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- métabolisme : Ribonucléases.
- ADN, ARN, Benzimidazoles, Cinétique, Clivage de l'ARN, Guanidine, Oligonucléotides, Sites de fixation, Spécificité du substrat.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Benzimidazoles, DNA, Guanidine, Oligonucleotides, RNA.
- chemical , metabolism : Ribonucleases.
- Binding Sites, Kinetics, RNA Cleavage, Substrate Specificity.
Abstract
Oligonucleotide conjugates of tris(2-aminobenzimidazole) have been reported previously to cleave complementary RNA strands with high levels of sequence and site specificity. The RNA substrates used in these studies were oligonucleotides not longer than 29-mers. Here we show that ~150⁻400-mer model transcripts derived from the 3'-untranslated region of the PIM1 mRNA reacted with rates and specificities comparable to those of short oligonucleotide substrates. The replacement of DNA by DNA/LNA mixmers further increased the cleavage rate. Tris(2-aminobenzimidazoles) were designed to interact with phosphates and phosphate esters. A cell, however, contains large amounts of phosphorylated species that may cause competitive inhibition of RNA cleavage. It is thus important to note that no loss in reaction rates was observed in phosphate buffer. This opens the way to in-cell applications for this type of artificial nuclease. Furthermore, we disclose a new synthetic method giving access to tris(2-aminobenzimidazoles) in multigram amounts.
DOI: 10.3390/molecules24040807
PubMed: 30813393
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Felix.Zellmann@gmx.net.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main</wicri:regionArea></affiliation></author><author><name sortKey="Thomas, Laura" sort="Thomas, Laura" uniqKey="Thomas L" first="Laura" last="Thomas">Laura Thomas</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany. laura.thomas@pharmazie.uni-marburg.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg</wicri:regionArea></affiliation></author><author><name sortKey="Scheffer, Ute" sort="Scheffer, Ute" uniqKey="Scheffer U" first="Ute" last="Scheffer">Ute Scheffer</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany. U.Scheffer@chemie.uni-frankfurt.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main</wicri:regionArea></affiliation></author><author><name sortKey="Hartmann, Roland K" sort="Hartmann, Roland K" uniqKey="Hartmann R" first="Roland K" last="Hartmann">Roland K. Hartmann</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany. roland.hartmann@staff.uni-marburg.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg</wicri:regionArea></affiliation></author><author><name sortKey="Gobel, Michael W" sort="Gobel, Michael W" uniqKey="Gobel M" first="Michael W" last="Göbel">Michael W. Göbel</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany. m.goebel@chemie.uni-frankfurt.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main</wicri:regionArea></affiliation></author></analytic><series><title level="j">Molecules (Basel, Switzerland)</title><idno type="eISSN">1420-3049</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Benzimidazoles (chemistry)</term><term>Binding Sites</term><term>DNA (chemistry)</term><term>Guanidine (chemistry)</term><term>Kinetics</term><term>Oligonucleotides (chemistry)</term><term>RNA (chemistry)</term><term>RNA Cleavage</term><term>Ribonucleases (metabolism)</term><term>Substrate Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ARN ()</term><term>Benzimidazoles ()</term><term>Cinétique</term><term>Clivage de l'ARN</term><term>Guanidine ()</term><term>Oligonucléotides ()</term><term>Ribonucléases (métabolisme)</term><term>Sites de fixation</term><term>Spécificité du substrat</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Benzimidazoles</term><term>DNA</term><term>Guanidine</term><term>Oligonucleotides</term><term>RNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Ribonucleases</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Ribonucléases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Kinetics</term><term>RNA Cleavage</term><term>Substrate Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>ARN</term><term>Benzimidazoles</term><term>Cinétique</term><term>Clivage de l'ARN</term><term>Guanidine</term><term>Oligonucléotides</term><term>Sites de fixation</term><term>Spécificité du substrat</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Oligonucleotide conjugates of tris(2-aminobenzimidazole) have been reported previously to cleave complementary RNA strands with high levels of sequence and site specificity. The RNA substrates used in these studies were oligonucleotides not longer than 29-mers. Here we show that ~150⁻400-mer model transcripts derived from the 3'-untranslated region of the <i>PIM1</i> mRNA reacted with rates and specificities comparable to those of short oligonucleotide substrates. The replacement of DNA by DNA/LNA mixmers further increased the cleavage rate. Tris(2-aminobenzimidazoles) were designed to interact with phosphates and phosphate esters. A cell, however, contains large amounts of phosphorylated species that may cause competitive inhibition of RNA cleavage. It is thus important to note that no loss in reaction rates was observed in phosphate buffer. This opens the way to in-cell applications for this type of artificial nuclease. Furthermore, we disclose a new synthetic method giving access to tris(2-aminobenzimidazoles) in multigram amounts.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30813393</PMID><DateCompleted><Year>2019</Year><Month>10</Month><Day>31</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1420-3049</ISSN><JournalIssue CitedMedium="Internet"><Volume>24</Volume><Issue>4</Issue><PubDate><Year>2019</Year><Month>Feb</Month><Day>23</Day></PubDate></JournalIssue><Title>Molecules (Basel, Switzerland)</Title><ISOAbbreviation>Molecules</ISOAbbreviation></Journal><ArticleTitle>Site-Specific Cleavage of RNAs Derived from the <i>PIM1</i> 3'-UTR by a Metal-Free Artificial Ribonuclease.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E807</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/molecules24040807</ELocationID><Abstract><AbstractText>Oligonucleotide conjugates of tris(2-aminobenzimidazole) have been reported previously to cleave complementary RNA strands with high levels of sequence and site specificity. The RNA substrates used in these studies were oligonucleotides not longer than 29-mers. Here we show that ~150⁻400-mer model transcripts derived from the 3'-untranslated region of the <i>PIM1</i> mRNA reacted with rates and specificities comparable to those of short oligonucleotide substrates. The replacement of DNA by DNA/LNA mixmers further increased the cleavage rate. Tris(2-aminobenzimidazoles) were designed to interact with phosphates and phosphate esters. A cell, however, contains large amounts of phosphorylated species that may cause competitive inhibition of RNA cleavage. It is thus important to note that no loss in reaction rates was observed in phosphate buffer. This opens the way to in-cell applications for this type of artificial nuclease. Furthermore, we disclose a new synthetic method giving access to tris(2-aminobenzimidazoles) in multigram amounts.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zellmann</LastName><ForeName>Felix</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany. Felix.Zellmann@gmx.net.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Thomas</LastName><ForeName>Laura</ForeName><Initials>L</Initials><Identifier Source="ORCID">0000-0002-9551-3743</Identifier><AffiliationInfo><Affiliation>Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany. laura.thomas@pharmazie.uni-marburg.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scheffer</LastName><ForeName>Ute</ForeName><Initials>U</Initials><Identifier Source="ORCID">0000-0002-5921-640X</Identifier><AffiliationInfo><Affiliation>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany. U.Scheffer@chemie.uni-frankfurt.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hartmann</LastName><ForeName>Roland K</ForeName><Initials>RK</Initials><AffiliationInfo><Affiliation>Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany. roland.hartmann@staff.uni-marburg.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Göbel</LastName><ForeName>Michael W</ForeName><Initials>MW</Initials><Identifier Source="ORCID">0000-0002-5694-4823</Identifier><AffiliationInfo><Affiliation>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany. m.goebel@chemie.uni-frankfurt.de.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>LOEWE project SynChemBio</GrantID><Agency>State of Hesse</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>02</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Molecules</MedlineTA><NlmUniqueID>100964009</NlmUniqueID><ISSNLinking>1420-3049</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D001562">Benzimidazoles</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>63231-63-0</RegistryNumber><NameOfSubstance UI="D012313">RNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>E65DE7521V</RegistryNumber><NameOfSubstance 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MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007700" MajorTopicYN="N">Kinetics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009841" MajorTopicYN="N">Oligonucleotides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012313" MajorTopicYN="N">RNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059367" MajorTopicYN="Y">RNA Cleavage</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012260" MajorTopicYN="N">Ribonucleases</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">2-aminobenzimidazole</Keyword><Keyword MajorTopicYN="N">DNA/LNA mixmers</Keyword><Keyword MajorTopicYN="N">cleavage of large RNA molecules</Keyword><Keyword MajorTopicYN="N">cleavage site selection</Keyword><Keyword MajorTopicYN="N">dye labeling</Keyword><Keyword MajorTopicYN="N">guanidine analogs</Keyword><Keyword MajorTopicYN="N">oligonucleotides</Keyword><Keyword MajorTopicYN="N">specificity of cleavage</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>02</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>02</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>3</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>3</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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