G-Tract Length Shapes the Fate of G-Quadruplexes

Abstract

Guanine (G)-rich DNA sequences can form unusual secondary structures known as G-quadruplexes (or G4s). The stability of these structures, whose folding is mainly driven by the formation and stacking of G-quartets, is influenced by several factors, foremost among them the nature of the sequence itself, particularly the nucleobases flanking the G-tracts, and the loops connecting them. A considerable effort has been devoted to understanding how the size, position, and composition of each loop and flanking sequences affect the stability of the resulting G4 fold. However, most of these studies have been restricted to sequences forming a three G-quartet G4 core. To better understand how the length of the G-tracts (from three to five Gs) and loops (from one to seven nucleotides) act in concert, we studied a set of 261 different sequences covering different possible combinations. A systematic biophysical analysis suggests that sequences with longer G-tracts tend to form more stable G4s, but also a mixture of species; it further shows that loop composition and position also influence the topology and stability of the resulting G4s. Collectively, this work provides an unprecedented view on how G4-forming sequences fold upon themselves and of the structural features that govern the stability of the resulting G4s.