Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene

• Published in: Journal of the American Chemical Society 2012-03, Vol.134 (9), p.4132-4141
• Main Authors: Trajkovski, Marko, Webba da Silva, Mateus, Plavec, Janez
• Format: Article
• Language: English
• Subjects: Base Sequence; G-Quadruplexes; Genes, myc - genetics; Introns; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Oligonucleotides - chemical synthesis; Oligonucleotides - chemistry; Potassium - chemistry
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja208483v

A multidimensional heteronuclear NMR study has demonstrated that a guanine-rich DNA oligonucleotide originating from the N-myc gene folds into G-quadruplex structures in the presence of K+, NH4 +, and Na+ ions. A monomeric G-quadruplex formed in K+ ion containing solution exhibits three G-quartets and flexible propeller-type loops. The 3D structure with three single nucleotide loops represents a missing element in structures of parallel G-quadruplexes. The structural features together with the high temperature stability are suggestive of the specific biological role of G-quadruplex formation within the intron of the N-myc gene. An increase in K+ ion and oligonucleotide concentrations resulted in transformation of the monomeric G-quadruplex into a dimeric form. The dimeric G-quadruplex exhibits six stacked G-quartets, parallel strand orientations, and propeller-type loops. A link between the third and the fourth G-quartets consists of two adenine residues that are flipped out to facilitate consecutive stacking of six G-quartets.