Cargando…

Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease

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 t...

Descripción completa

Detalles Bibliográficos
Autores principales: Zellmann, Felix, Thomas, Laura, Scheffer, Ute, Hartmann, Roland K., Göbel, Michael W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412833/
https://www.ncbi.nlm.nih.gov/pubmed/30813393
http://dx.doi.org/10.3390/molecules24040807
_version_ 1783402697290940416
author Zellmann, Felix
Thomas, Laura
Scheffer, Ute
Hartmann, Roland K.
Göbel, Michael W.
author_facet Zellmann, Felix
Thomas, Laura
Scheffer, Ute
Hartmann, Roland K.
Göbel, Michael W.
author_sort Zellmann, Felix
collection PubMed
description 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.
format Online
Article
Text
id pubmed-6412833
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-64128332019-04-09 Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease Zellmann, Felix Thomas, Laura Scheffer, Ute Hartmann, Roland K. Göbel, Michael W. Molecules Article 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. MDPI 2019-02-23 /pmc/articles/PMC6412833/ /pubmed/30813393 http://dx.doi.org/10.3390/molecules24040807 Text en © 2019 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zellmann, Felix
Thomas, Laura
Scheffer, Ute
Hartmann, Roland K.
Göbel, Michael W.
Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
title Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
title_full Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
title_fullStr Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
title_full_unstemmed Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
title_short Site-Specific Cleavage of RNAs Derived from the PIM1 3′-UTR by a Metal-Free Artificial Ribonuclease
title_sort site-specific cleavage of rnas derived from the pim1 3′-utr by a metal-free artificial ribonuclease
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412833/
https://www.ncbi.nlm.nih.gov/pubmed/30813393
http://dx.doi.org/10.3390/molecules24040807
work_keys_str_mv AT zellmannfelix sitespecificcleavageofrnasderivedfromthepim13utrbyametalfreeartificialribonuclease
AT thomaslaura sitespecificcleavageofrnasderivedfromthepim13utrbyametalfreeartificialribonuclease
AT schefferute sitespecificcleavageofrnasderivedfromthepim13utrbyametalfreeartificialribonuclease
AT hartmannrolandk sitespecificcleavageofrnasderivedfromthepim13utrbyametalfreeartificialribonuclease
AT gobelmichaelw sitespecificcleavageofrnasderivedfromthepim13utrbyametalfreeartificialribonuclease