DNA variability in five crystal structures of d(CGCAATTGCG)

Abstract

The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures.