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A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides

A common problem of the preparation of hexachlorofluorescein labeled oligonucleotides is the transformation of the fluorophore to an arylacridine derivative under standard ammonolysis conditions. We show here that the arylacridine byproduct with distinct optical characteristics cannot be efficiently...

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Autores principales: Chuvilin, Andrey N., Smirnov, Igor P., Mosina, Alena G., Varizhuk, Anna M., Pozmogova, Galina E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5115841/
https://www.ncbi.nlm.nih.gov/pubmed/27861573
http://dx.doi.org/10.1371/journal.pone.0166911
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author Chuvilin, Andrey N.
Smirnov, Igor P.
Mosina, Alena G.
Varizhuk, Anna M.
Pozmogova, Galina E.
author_facet Chuvilin, Andrey N.
Smirnov, Igor P.
Mosina, Alena G.
Varizhuk, Anna M.
Pozmogova, Galina E.
author_sort Chuvilin, Andrey N.
collection PubMed
description A common problem of the preparation of hexachlorofluorescein labeled oligonucleotides is the transformation of the fluorophore to an arylacridine derivative under standard ammonolysis conditions. We show here that the arylacridine byproduct with distinct optical characteristics cannot be efficiently separated from the major product by HPLC or electrophoretic methods, which hampers precise physicochemical experiments with the labeled oligonucleotides. Studies of the transformation mechanism allowed us to select optimal conditions for avoiding the side reaction. The novel method for the post-synthetic deblocking of hexachlorofluorescein-labeled oligodeoxyribonucleotides described in this paper prevents the formation of the arylacridine derivative, enhances the yield of target oligomers, and allows them to be proper real-time PCR probes.
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spelling pubmed-51158412016-12-08 A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides Chuvilin, Andrey N. Smirnov, Igor P. Mosina, Alena G. Varizhuk, Anna M. Pozmogova, Galina E. PLoS One Research Article A common problem of the preparation of hexachlorofluorescein labeled oligonucleotides is the transformation of the fluorophore to an arylacridine derivative under standard ammonolysis conditions. We show here that the arylacridine byproduct with distinct optical characteristics cannot be efficiently separated from the major product by HPLC or electrophoretic methods, which hampers precise physicochemical experiments with the labeled oligonucleotides. Studies of the transformation mechanism allowed us to select optimal conditions for avoiding the side reaction. The novel method for the post-synthetic deblocking of hexachlorofluorescein-labeled oligodeoxyribonucleotides described in this paper prevents the formation of the arylacridine derivative, enhances the yield of target oligomers, and allows them to be proper real-time PCR probes. Public Library of Science 2016-11-18 /pmc/articles/PMC5115841/ /pubmed/27861573 http://dx.doi.org/10.1371/journal.pone.0166911 Text en © 2016 Chuvilin et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chuvilin, Andrey N.
Smirnov, Igor P.
Mosina, Alena G.
Varizhuk, Anna M.
Pozmogova, Galina E.
A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides
title A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides
title_full A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides
title_fullStr A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides
title_full_unstemmed A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides
title_short A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides
title_sort solution to the common problem of the synthesis and applications of hexachlorofluorescein labeled oligonucleotides
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5115841/
https://www.ncbi.nlm.nih.gov/pubmed/27861573
http://dx.doi.org/10.1371/journal.pone.0166911
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