High-resolution A-DNA crystal structures of d(AGGGGCCCCT) an A-DNA model of poly(dG) · poly(dC)

A-DNA conformation is favored by guanine-rich sequences, such as (dG)(n) · (dC)(n), or under low-humidity conditions. Earlier A-DNA crystal structures revealed some conformational variations which may be the result of sequence-dependent effects and/or crystal packing forces. Here we report the high-resolution crystal structure of d(AGGGGCCCCT) in two crystal forms (either in the P2₁2₁2₁ or the P6₁22 space group) to gain insights into the conformation and dynamics of the (dG)(n) · (dC)(n) sequence. The P2₁2₁2₁ form has been analyzed using data to 1.1 Å resolution by the anisotropic temperature factor refinement procedure of the SHELX97 program. Such analysis affords us with the detailed geometric, conformational and motional property of an A-DNA structure. The backbone torsional angles fall in a narrow range, except for the α/γ angles which have two distinct combinations (gauche_-/gauche⁺ or trans/trans). An A-DNA model of poly(dG) · poly(dC) has been constructed using the conformational parameters derived from the crystal structure of the P2₁2₁2₁ form. In the crystal structure of the P6₁22 space group, the central eight base pairs of the decamer adopt A-DNA conformation with the two terminal nucleotides flipped out to form base pairs with the neighboring nucleotides. Comparison of the A-DNA structure of the same sequence from two different crystal forms, reinforced the conclusion that molecules crystallized in the same space group have a more similar conformation, whereas the same molecule crystallized in different space groups has different (local) conformations.