Modeling of possible quadruplexes and i-motifs formed during DNA contacts: strategy, classification, most probable shapes, origami based on quadruplexes.

A strategy for creating 3D models of non-canonical forms of DNA and RNA is proposed in this research. Through this strategy, models of all possible forms of non-canonical structures created by contacts of single-stranded DNA with sequence (G3T)nG3 and/or duplexes with (G3T)nG3 and (C3A)nC3 fragments were built and tested by MD. In particular, models of stacks formed from right and left twisted quadruplexes; the structure resembling the Holliday structure, with the hole, on the border of which the quadruplex (G4) and the i-motif (IM) were located opposite each other; layers formed from G4s grids were constructed. The most probable of these non-canonical forms arising from contacts of duplexes with (G3T)nG3 for n=1,3,5 were determined by estimating the contributions to the free energy.