Interaction of GelRed™ with single-stranded DNA oligonucleotides: Preferential binding to thymine-rich sequences

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 similar to 20-fold increase in the dye's fluorescence in the presence of equimolar T-20 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 dU(20) decreased GR affinity to the oligonucleotide similar to 2-fold. Molecular dynamic simulations were used to propose a possible structure of the GR-oligothymidilate complex.

Automated summary

GelRed is a widely used nucleic acid-binding dye that preferentially binds to thymine-rich sequences in DNA. The interactions between GelRed and oligothymidylate are likely stabilized by electrostatic interactions and hydrogen bonding. The molecular dynamic simulations propose a possible structure of the GelRed-oligothymidilate complex.