Fishing for G-Quadruplexes in Solution with a Perylene Diimide Derivative Labeled with Biotins

Abstract

A new fluorescent, non-cytotoxic perylene diimide derivative with two biotins at the peri position, PDI2B, has been synthesized. This molecule is able to interact selectively with G-quadruplexes with scarce or no affinity towards single- or double-stranded DNA. These features have made it possible to design a simple, effective, safe, cheap, and selective method for fishing G-quadruplex structures in solution by use of PDI2B and streptavidin coated magnetic beads. The new cyclic method reported leads to the recovery of more than 80 % of G-quadruplex structures from solution, even in the presence of an excess of single-stranded or duplex DNA as competitors. Moreover, PDI2B is a G4 ligand that can display higher thermal stabilization and greater affinity for 2- over 3-tetrad quadruplexes, which constitutes a novel type of behavior.

Keywords: DNA; G-quadruplexes; biophysics; nucleic acids; perilene.