Stabilization of the i-motif by intramolecular adenine-adenine-thymine base triple in the structure of d(ACCCT)

The crystal structure of d(ACCCT), solved by molecular replacement, shows a four-stranded i-motif conformation, where two parallel duplexes intercalat e with one another in opposite orientations. Each duplex is stabilized by h emi-protonated C-C+ base pairing between parallel strands, and a string of water molecules bridge the cytosine N4 atoms to phosphate O atoms. This str ucture of d(ACCCT) shows examples of reversed Hoogsteen and Watson-Crick ba se pairing in both intermolecular and intramolecular manners to stabilize t he tetraplex. Noticeably, the four-stranded complex is further stabilized a t one end by a three-base hydrogen-bonding network, in which two adenines a nd a thymine form four hydrogen bonds via a reverse Hoogsteen and an asymme tric adenine-adenine base pairing. The structure of d(ACCCT) shows a simila r local structure to that found in the d(TAA) part of the crystal structure of d(TAACCC) and provides further structural evidence that these base arra ngements are essential for stabilizing these novel DNA supersecondary struc tures.