Polymorphism of G-quadruplexes formed by short oligonucleotides containing a 3-3 inversion of polarity: From G:C:G:C tetrads to - stacked G-wires

G-wires are supramolecular DNA structures based on the G-quadruplex (G4) structural motif obtained by the self-assembly of interlocked slipped G-rich oligonucleotide (ON) strands, or by end-to-end stacking of G4 units. Despite the increasing interest towards G-wires due to their potential applications in DNA nanotechnologies, the self-assembly process to obtain G-wires having a predefined length and stability is still neither completely understood nor controlled. In our previous studies, we demonstrated that the d(5 ' CG(2)-3 '-3 '-G(2)C5 ') ON, characterized by the presence of a 3 '-3 '-inversion of polarity site self-assembles into a G-wire structure when annealed in the presence of K+ ions. Herein, by using CD, PAGE, HPLC size exclusion chromatography, and NMR investigations we studied the propensity of shorter analogues having sequences 5 ' CG(n)-3 '-3 '-G(m)C5 ' (with n = 1 and 1 <= m <= 3) to form the corresponding G-quadruplexes and stacked G-wires. The results revealed that the formation of G-wires starting from d(5 ' CG(n)-3 '-3 '-G(m)C5 ') ONs is possible only for the sequences having n and m > 1 in which both guanosines flanking the 5 '-ending cytosines are not involved into the 3 '-3 ' phosphodiester bond.