The along-groove packing motif (AGPM). (Left) Schematic representation of AGPM. Trapezoids stand for base pairs opened toward the minor grooves. Arrows represent backbones directed 5′→3′. The external (P, R) and internal (Q, S) strands are labeled. The internal strand of each helix is packed along the minor groove of the opposite helix. Rotation of one helix for 180° around the symmetry axis (dash-dotted line) superposes it with the other helix. (Right) Juxtaposition of the base pairs at the 0-level (for the definition of layers, see Fig. 2). Dashed lines stand for hydrogen bonds. In most known cases of AGPM, one base pair is WC, while the other one is GU. The characteristic geometry of the GU base pair makes the shapes of the minor grooves of the two helices complementary to each other (Gagnon and Steinberg 2002).
