Controlling the G-Quadruplex Topology: Toward the Formation of a Lipid Thrombin Binding Aptamer Prodrug.

Abstract

Important efforts have been devoted toward the development of modified oligonucleotides capable of controlling the secondary structures of the G-quadruplex (G4). Herein, we introduce a photocleavable, lipidated construct of the well-known Thrombin Binding Aptamer (TBA) whose conformation can be dual-controlled by light and/or the ionic strength of the aqueous solution. This novel lipid-modified TBA oligonucleotide spontaneously self-assembles and switches from the conventional antiparallel aptameric fold at low ionic strength to the parallel, inactive conformation of the TBA oligonucleotide strands under physiologically relevant conditions. The latter parallel conformation can be readily and chemoselectively switched back to the antiparallel native aptamer conformation upon light irradiation. Our lipidated construct constitutes an original prodrug of the original TBA with properties that are prone to improving the pharmacodynamic profile of the unmodified TBA.