Circular Dichroism of G-Quadruplex: a Laboratory Experiment for the Study of Topology and Ligand Binding

Abstract

Circular dichroism (CD) has emerged as one of the standard biophysical techniques for the study of guanine-quadruplex (G4) folding, cation effect, and ligand binding. The utility of this technique is based on its robustness, ease of use, and requirement of only small quantities of nucleic acid. This experiment is also extendable to the classroom and adaptable to students from graduate school in a multidisciplinary area, bridging chemistry, biochemistry, and medicinal chemistry. Specifically, students employ a solution of a nucleic acid that can adopt a G4 conformation, anneal it in the presence of a metal cation, and assess the folding and topology by the characteristic CD signatures. During the class experiment, it was also possible to interconvert the G4 topology by changing the cation type, and to determine the melting temperature of the G4 structure in the absence and presence of molecules called G4 ligands. The current experiment used the commercially available porphyrin TMPyP4 as a G4 ligand and hum...