Assembly of supramolecular DNA complexes containing both G-quadruplexes and i-motifs by enhancing the G-repeat-bearing capacity of i-motifs

The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3′ or 5′ ends of the cytosine-repeats. Here, a series of oligomers d(XG(i)XC(5)X) and d(XC(5)XG(i)X) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs. Our data demonstrate that tetramolecular i-motif structure can tolerate specific flanking G-repeats. Assemblies of these oligonucleotides are polymorphic, but may be controlled by solution pH and counter ion species. Importantly, we find that the sequences d(TG(i)AC(5)) can form the tetrameric i-motif in large quantities. This leads to the design of two oligonucleotides d(TG(4)AC(7)) and d(TG(Br)GG(Br)GAC(7)) that self-assemble to form quadruplex supramolecules under certain conditions. d(TG(4)AC(7)) forms supramolecules under acidic conditions in the presence of K(+) that are mainly V-shaped or ring-like containing parallel G4s and antiparallel i-motifs. d(TG(Br)GG(Br)GAC(7)) forms long linear quadruplex wires under acidic conditions in the presence of Na(+) that consist of both antiparallel G4s and i-motifs.