Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.

ARNA Laboratory Inserm U1212 CNRS UMR 5320 Université de Bordeaux Bordeaux France

Inserm U1024 CNRS UMR 8197 IBENS Paris France

Institute of Biophysics of the CAS v v i Kraálovopolskaá 135 612 65 Brno Czech Republic

Swarthmore College 500 College Ave Swarthmore PA 19081 USA

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Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites

Mapping and characterization of G-quadruplexes in the genome of the social amoeba Dictyostelium discoideum