Topology Variation and Loop Structural Homology in Crystal and Simulated Structures of a Bimolecular DNA Quadruplex

The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA sequence d(G₄T₃G₄) has been determined at 1.5 Å resolution, together with that of the brominated analogue d(G₄^BrUTTG₄) at 2.4 Å resolution. Both sequences form bimolecular intermolecular G-quadruplexes with lateral loops. d(G₄^BrUTTG₄) crystallized in the monoclinic space group P2₁ with three quadruplex molecules in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and form an eight-G-quartet stack, with a linear array of seven K⁺ ions between the quartets. d(G₄T₃G₄) crystallized in the orthorhombic space group C222 and has a structure very similar to the head-to-tail dimer in the P2₁ unit cell. The sequence studied here is able to form several different folds; however, all four quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the analogous quadruplex with T₄ loops. A total of seven independent T₃ loops were observed in the two structures. These can be classified into two discrete conformational classes, suggesting that these represent preferred loop conformations that are independent of crystal-packing forces.