A new pathway of DNA G-quadruplex formation

Abstract

A new folding intermediate of Oxytricha nova telomeric Oxy-1.5 G-quadruplex was characterized in aqueous solution using NMR spectroscopy, native gel electrophoresis, thermal differential spectra (TDS), CD spectroscopy, and differential scanning calorimetry (DSC). NMR experiments have revealed that this intermediate (i-Oxy-1.5) exists in two symmetric bimolecular forms in which all guanine bases are involved in GG N1-carbonyl symmetric base pairs. Kinetic analysis of K(+) -induced structural transitions shows that folding of Oxy-1.5 G-quadruplex from i-Oxy-1.5 is much faster and proceeds through less intermediates than folding from single strands. Therefore, a new folding pathway of Oxy-1.5 G-quadruplex is proposed. This study provides evidence that G-rich DNA sequences can self-assemble into specific pre-organized DNA structures that are predisposed to fold into G-quadruplex when interacting with cations such as potassium ions.

Keywords: cations; hydrogen bonds; intermediates; oligonucleotides; quadruplexes.