Title
Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques
Author
S. Benito, A. Ferrer, S. Benabou, A. Aviñó, R. Eritja, R. Gargallo
Year
2018
Journal
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
Abstract
Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 105 M−1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.
Instrument
J-810
Keywords
Circular dichroism, DNA structure, Thermal stability, Thermodynamics, DNA folding, Ligand binding, Biochemistry