We have determined a structure of a DNA oligonucleotide containing GGGAGCG repeats found in the regulatory region of the PLEKHG3 gene, which is connected to autism. Even though the oligonucleotide is rich in guanine residues it does not fold into a G-quadruplex. Instead of G-quartets the fold is stabilized by four G-C base pairs in Watson-Crick geometry, four G∙A base pairs in N7-N1 amino carbonyl and six G∙G base pairs in N1-carbonyl symmetric geometry. The G∙A and G-C base pairs form a cavity in the center of the structure. On each side of the structure two edgewise loops are stabilized by three G∙G base pairs in N1-carbonyl symmetric geometry. Additionally, two adenine residues not bound by H-bonds are orientated inside the structure and are tightly packed with three G∙G base pairs and two G∙A base pairs. Because the structure is not stabilized by G-quartets it folds into the final structure in the presence of Li+ cations alone. The fold was retained in the presence of Li+, Na+, K+ and NH4+ ions.
COBISS.SI-ID: 5625626