Interaction of GelRed™ with single-stranded DNA oligonucleotides: Preferential binding to thymine-rich sequencesстатья
Статья опубликована в высокорейтинговом журнале
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Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 27 октября 2021 г.
Аннотация:GelRed (GR) is a widely used nucleic acid-binding dye. It interacts with double-stranded DNA (dsDNA) via intercalation between the base-pairs, which enhances the dye's fluorescence. Binding of GR to single-stranded DNA (ssDNA) is much less efficient, yet the dye is still used for ssDNA staining in such applications as gel electrophoresis. The nature of GR interactions with ssDNA is not well understood. Here, preferential binding of GR to thymine-rich sequences was demonstrated, with ~20-fold increase in the dye's fluorescence in the presence of equimolar T20 concentration. Based on pH and ionic strength dependences, electrostatic interactions with oligonucleotide backbone and hydrogen bonding between thymine and exocyclic amino groups of GR were proposed as likely stabilizing forces in GR-oligothymidylate binding. Lack of the C5-methyl group in dU20 decreased GR affinity to the oligonucleotide ~2-fold. Molecular dynamic simulations were used to propose a possible structure of the GR-oligothymidilate complex.