Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
Identifieur interne : 000F31 ( Pmc/Curation ); précédent : 000F30; suivant : 000F32Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
Auteurs : Felix Zellmann ; Laura Thomas ; Ute Scheffer ; Roland K. Hartmann ; Michael W. GöbelSource :
- Molecules [ 1420-3049 ] ; 2019.
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
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DOI: 10.3390/molecules24040807
PubMed: 30813393
PubMed Central: 6412833
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Site-Specific Cleavage of RNAs Derived from the <italic>PIM1</italic> 3′-UTR by a Metal-Free Artificial Ribonuclease</title><author><name sortKey="Zellmann, Felix" sort="Zellmann, Felix" uniqKey="Zellmann F" first="Felix" last="Zellmann">Felix Zellmann</name><affiliation><nlm:aff id="af1-molecules-24-00807">Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany;<email>Felix.Zellmann@gmx.net</email> (F.Z.);<email>U.Scheffer@chemie.uni-frankfurt.de</email> (U.S.)</nlm:aff></affiliation></author><author><name sortKey="Thomas, Laura" sort="Thomas, Laura" uniqKey="Thomas L" first="Laura" last="Thomas">Laura Thomas</name><affiliation><nlm:aff id="af2-molecules-24-00807">Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany;<email>laura.thomas@pharmazie.uni-marburg.de</email> (L.T.);<email>roland.hartmann@staff.uni-marburg.de</email> (R.K.H.)</nlm:aff></affiliation></author><author><name sortKey="Scheffer, Ute" sort="Scheffer, Ute" uniqKey="Scheffer U" first="Ute" last="Scheffer">Ute Scheffer</name><affiliation><nlm:aff id="af1-molecules-24-00807">Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany;<email>Felix.Zellmann@gmx.net</email> (F.Z.);<email>U.Scheffer@chemie.uni-frankfurt.de</email> (U.S.)</nlm:aff></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><nlm:aff id="af2-molecules-24-00807">Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany;<email>laura.thomas@pharmazie.uni-marburg.de</email> (L.T.);<email>roland.hartmann@staff.uni-marburg.de</email> (R.K.H.)</nlm:aff></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><nlm:aff id="af1-molecules-24-00807">Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany;<email>Felix.Zellmann@gmx.net</email> (F.Z.);<email>U.Scheffer@chemie.uni-frankfurt.de</email> (U.S.)</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">30813393</idno><idno type="pmc">6412833</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412833</idno><idno type="RBID">PMC:6412833</idno><idno type="doi">10.3390/molecules24040807</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000F31</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F31</idno><idno type="wicri:Area/Pmc/Curation">000F31</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F31</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Site-Specific Cleavage of RNAs Derived from the <italic>PIM1</italic> 3′-UTR by a Metal-Free Artificial Ribonuclease</title><author><name sortKey="Zellmann, Felix" sort="Zellmann, Felix" uniqKey="Zellmann F" first="Felix" last="Zellmann">Felix Zellmann</name><affiliation><nlm:aff id="af1-molecules-24-00807">Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany;<email>Felix.Zellmann@gmx.net</email> (F.Z.);<email>U.Scheffer@chemie.uni-frankfurt.de</email> (U.S.)</nlm:aff></affiliation></author><author><name sortKey="Thomas, Laura" sort="Thomas, Laura" uniqKey="Thomas L" first="Laura" last="Thomas">Laura Thomas</name><affiliation><nlm:aff id="af2-molecules-24-00807">Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany;<email>laura.thomas@pharmazie.uni-marburg.de</email> (L.T.);<email>roland.hartmann@staff.uni-marburg.de</email> (R.K.H.)</nlm:aff></affiliation></author><author><name sortKey="Scheffer, Ute" sort="Scheffer, Ute" uniqKey="Scheffer U" first="Ute" last="Scheffer">Ute Scheffer</name><affiliation><nlm:aff id="af1-molecules-24-00807">Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany;<email>Felix.Zellmann@gmx.net</email> (F.Z.);<email>U.Scheffer@chemie.uni-frankfurt.de</email> (U.S.)</nlm:aff></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><nlm:aff id="af2-molecules-24-00807">Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany;<email>laura.thomas@pharmazie.uni-marburg.de</email> (L.T.);<email>roland.hartmann@staff.uni-marburg.de</email> (R.K.H.)</nlm:aff></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><nlm:aff id="af1-molecules-24-00807">Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany;<email>Felix.Zellmann@gmx.net</email> (F.Z.);<email>U.Scheffer@chemie.uni-frankfurt.de</email> (U.S.)</nlm:aff></affiliation></author></analytic><series><title level="j">Molecules</title><idno type="eISSN">1420-3049</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 <italic>PIM1</italic> 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Trawick, B N" uniqKey="Trawick B">B.N. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Molecules</journal-id><journal-id journal-id-type="iso-abbrev">Molecules</journal-id><journal-id journal-id-type="publisher-id">molecules</journal-id><journal-title-group><journal-title>Molecules</journal-title></journal-title-group><issn pub-type="epub">1420-3049</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">30813393</article-id><article-id pub-id-type="pmc">6412833</article-id><article-id pub-id-type="doi">10.3390/molecules24040807</article-id><article-id pub-id-type="publisher-id">molecules-24-00807</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Site-Specific Cleavage of RNAs Derived from the <italic>PIM1</italic> 3′-UTR by a Metal-Free Artificial Ribonuclease</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zellmann</surname><given-names>Felix</given-names></name><xref ref-type="aff" rid="af1-molecules-24-00807">1</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-9551-3743</contrib-id><name><surname>Thomas</surname><given-names>Laura</given-names></name><xref ref-type="aff" rid="af2-molecules-24-00807">2</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-5921-640X</contrib-id><name><surname>Scheffer</surname><given-names>Ute</given-names></name><xref ref-type="aff" rid="af1-molecules-24-00807">1</xref></contrib><contrib contrib-type="author"><name><surname>Hartmann</surname><given-names>Roland K.</given-names></name><xref ref-type="aff" rid="af2-molecules-24-00807">2</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-5694-4823</contrib-id><name><surname>Göbel</surname><given-names>Michael W.</given-names></name><xref ref-type="aff" rid="af1-molecules-24-00807">1</xref><xref rid="c1-molecules-24-00807" ref-type="corresp">*</xref></contrib></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Strömberg</surname><given-names>Roger</given-names></name><role>Academic Editor</role></contrib></contrib-group><aff id="af1-molecules-24-00807"><label>1</label>Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany;<email>Felix.Zellmann@gmx.net</email> (F.Z.);<email>U.Scheffer@chemie.uni-frankfurt.de</email> (U.S.)</aff><aff id="af2-molecules-24-00807"><label>2</label>Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, D-35032 Marburg, Germany;<email>laura.thomas@pharmazie.uni-marburg.de</email> (L.T.);<email>roland.hartmann@staff.uni-marburg.de</email> (R.K.H.)</aff><author-notes><corresp id="c1-molecules-24-00807"><label>*</label>Correspondence: <email>m.goebel@chemie.uni-frankfurt.de</email>; Tel.: +49-69-798-29222</corresp></author-notes><pub-date pub-type="epub"><day>23</day><month>2</month><year>2019</year></pub-date><pub-date pub-type="collection"><month>2</month><year>2019</year></pub-date><volume>24</volume><issue>4</issue><elocation-id>807</elocation-id><history><date date-type="received"><day>06</day><month>2</month><year>2019</year></date><date date-type="accepted"><day>19</day><month>2</month><year>2019</year></date></history><permissions><copyright-statement>© 2019 by the authors.</copyright-statement><copyright-year>2019</copyright-year><license license-type="open-access"><license-p>Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>).</license-p></license></permissions><abstract><p>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 <italic>PIM1</italic> 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.</p></abstract><kwd-group><kwd>2-aminobenzimidazole</kwd><kwd>cleavage of large RNA molecules</kwd><kwd>cleavage site selection</kwd><kwd>DNA/LNA mixmers</kwd><kwd>dye labeling</kwd><kwd>guanidine analogs</kwd><kwd>oligonucleotides</kwd><kwd>specificity of cleavage</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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