Circular dichroism of quadruplex structures

Abstract

Circular dichroism (CD) is a widespread technique for studying the polymorphism of G-quadruplexes. In this chapter the CD spectral features characteristic of different folding topologies of G4-DNA are analyzed in terms of the sequence of the syn or anti glycosidic bond angle (GBA) within a quadruplex stem. Depending on the GBA sequence, the chiral disposition of two stacked guanines, adjacent along a strand, is different and this leads to a predictable contribution to the overall CD spectrum. The CD spectra of a series of G-quadruplexes, chosen as prototypal of the most common strand folding, are illustrated. The validity and the prediction power of the approach is corroborated by the analysis of CD spectra of structurally modified G4-DNA either with chemically modified guanines or polarity inversion site (5'-5' or 3'-3') along the strands or additional nucleobases contributing to the stacking.