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A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA

New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has be...

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Detalles Bibliográficos
Autores principales: Gagnon, Keith T., Ju, Show-Yi, Goshe, Michael B., Maxwell, E. Stuart, Franzen, Stefan
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685102/
https://www.ncbi.nlm.nih.gov/pubmed/19304744
http://dx.doi.org/10.1093/nar/gkp177
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author Gagnon, Keith T.
Ju, Show-Yi
Goshe, Michael B.
Maxwell, E. Stuart
Franzen, Stefan
author_facet Gagnon, Keith T.
Ju, Show-Yi
Goshe, Michael B.
Maxwell, E. Stuart
Franzen, Stefan
author_sort Gagnon, Keith T.
collection PubMed
description New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu(2+), as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification's role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.
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spelling pubmed-26851022009-05-21 A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA Gagnon, Keith T. Ju, Show-Yi Goshe, Michael B. Maxwell, E. Stuart Franzen, Stefan Nucleic Acids Res RNA New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu(2+), as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification's role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism. Oxford University Press 2009-05 2009-03-20 /pmc/articles/PMC2685102/ /pubmed/19304744 http://dx.doi.org/10.1093/nar/gkp177 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Gagnon, Keith T.
Ju, Show-Yi
Goshe, Michael B.
Maxwell, E. Stuart
Franzen, Stefan
A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
title A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
title_full A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
title_fullStr A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
title_full_unstemmed A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
title_short A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA
title_sort role for hydrophobicity in a diels–alder reaction catalyzed by pyridyl-modified rna
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685102/
https://www.ncbi.nlm.nih.gov/pubmed/19304744
http://dx.doi.org/10.1093/nar/gkp177
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