title: A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides.
abstract: 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.
authors.affiliation: Department of Molecular Genesis, Federal Research and Clinical Center of Physical- Chemical Medicine, Moscow, Russian Federation.
authors.forename: Andrey N
authors.initials: AN
authors.lastname: Chuvilin
authors.affiliation: Department of Molecular Genesis, Federal Research and Clinical Center of Physical- Chemical Medicine, Moscow, Russian Federation.
authors.forename: Igor P
authors.initials: IP
authors.lastname: Smirnov
authors.affiliation: Department of Molecular Genesis, Federal Research and Clinical Center of Physical- Chemical Medicine, Moscow, Russian Federation.
authors.forename: Alena G
authors.initials: AG
authors.lastname: Mosina
authors.affiliation: Department of Molecular Genesis, Federal Research and Clinical Center of Physical- Chemical Medicine, Moscow, Russian Federation.
authors.forename: Anna M
authors.initials: AM
authors.lastname: Varizhuk
authors.affiliation: Department of Molecular Genesis, Federal Research and Clinical Center of Physical- Chemical Medicine, Moscow, Russian Federation.
authors.forename: Galina E
authors.initials: GE
authors.lastname: Pozmogova
mesh_terms: D005456:Fluorescent Dyes / Q000737:chemistry*; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D055668:Photochemical Processes; D013057:Spectrum Analysis; D013194:Staining and Labeling
chemical_list: D005456:Fluorescent Dyes; D009841:Oligonucleotides