Unique quadruplex structures of d(GGA)4 (12-mer) and d(GGA)8 (24-mer)--direct evidence of the formation of non-canonical base pairs and structural comparison.

Abstract

We have reported that d(GGA)4 (12-mer) folds into an intramolecular parallel quadruplex with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad and that two quadruplexes form a dimer. Here we present the unique structure of d(GGA)8 (24-mer) under physiological conditions. G1-A12 and G13-A24 segments of d(GGA)8 fold into an intramolecular parallel quadruplex with the tetrad and heptad, respectively, and two quadruplexes stack each other in a head-to-head manner. The formation of non-canonical G:G and G:A base pairs was directly certified by observing spin-spin couplings across hydrogen bonds with the aid of 13C-, 15N-labelling of DNA. It was noted that the monomeric architecture of d(GGA)8 resembles the dimeric architecture of d(GGA)4. Interestingly, the recent X-ray study shows that the telomere DNA also folds into the similar intramolecular parallel quadruplex as we have reported for GGA-repeat DNAs.