THE B-DNA DODECAMER AT HIGH-RESOLUTION REVEALS A SPINE OF WATER ON SODIUM

We describe a very accurate addition (called structure X here) to the B-DNA dodecamer family of X-ray structures. Our results confirm the ob servation of Drew and Dickerson [(1981) J. Mel. Biol, 151, 535-556] th at the spine of hydration in AT tract DNA is two layers deep. However, our results suggest that the primary spine is partially occupied by s odium ions. We suggest that many sequence-dependent features of DNA co nformation are mediated by site specific binding of cations, For examp le, preferential localization of cations, as described here within the minor groove of structure X, is probably the structural origin of AT tract bending and groove narrowing. The secondary spine, which does no t interact directly with the DNA, is as geometrically regular as the p rimary spine, providing a model for transmission of sequence informati on into solvent regions. A fully hydrated magnesium ion located in the major groove of structure X appears to pull cytosine bases partially out from the helical stack, exposing x-systems to partial positive cha rges of the magnesium ion and its outer sphere. A partially ordered sp ermine molecule is located within the major groove of structure X. Dod ecamer structures are derived from crystals of [d(CGCGAATTCGCG)](2) in space group P2(1)2(1)2(1) (a = 25 Angstrom, b = 40 Angstrom, and c = 66 Angstrom). On average, those crystals diffracted to around 2.5 Angs trom resolution with 2500 unique reflections. Structure X, with the sa me space group, DNA sequence, and crystal form as the ''Dickerson dode camer'', is refined against a complete, low-temperature, 1.4 Angstrom resolution data set, with over 11000 reflections. Structure X appears to be conformationally more ordered than previous structures, suggesti ng that at least a portion of the conformational heterogeneity previou sly attributed to DNA sequence in fact arises from experimental error.