Some DNA oligonucleotides can fold back and self-associate forming dimeric structures stabilized by intermolecular base pairs. The resulting antiparallel dimer is a tightly packed four-stranded structure formed by a core of minor groove tetrads connected by short loops of unpaired nucleotides. We have explored the sequential requirements for the loop residues and have found that this family of structures is only stable with one- and two-residue loops, with the stability of the former ones being only marginal. Two-residue loops with purines in the first position give rise to the most stable structures due to their enhanced stacking interaction with the adjacent minor groove tetrad. On the other hand, pyrimidines confer more stability than purines in the second position of the loop.

Minor groove aligned tetrads resulting from the association of Watson–Crick base pairs stabilize a distinct class of four-stranded DNA structures, different from G-quadruplexes or i-motifs. These tetrads can be formed by several arrangements of G–C or A–T base pairs. Here we prove that minor groove tetrads can be also formed by G–T mismatches. In this manuscript we describe the dimeric solution structures of two cyclic oligonucleotides stabilized by intermolecular G–T non-canonical base pairs. In the dimeric structure of d, these mismatches interact to each other giving rise to minor groove aligned G:T:G:T or mixed G:T:G:C tetrads. Interestingly, the stability conferred by mismatched G–T containing tetrads is similar to that of minor groove tetrads solely formed by G–C Watson–Crick base pairs.G–T mismatches can form minor groove aligned tetrads (G:C:G:T or G:T:G:T) of similar structure and stability to those formed by G–C Watson–Crick base pairs.

Some DNA oligonucleotides can fold back and self-associate forming dimeric structures stabilized by intermolecular base pairs. The resulting antiparallel dimer is a tightly packed four-stranded structure formed by a core of minor groove tetrads connected by short loops of unpaired nucleotides. We have explored the sequential requirements for the loop residues and have found that this family of structures is only stable with one- and two-residue loops, with the stability of the former ones being only marginal. Two-residue loops with purines in the first position give rise to the most stable structures due to their enhanced stacking interaction with the adjacent minor groove tetrad. On the other hand, pyrimidines confer more stability than purines in the second position of the loop.