Molecular structure of cyclic diguanylic acid at 1 Å resolution of iwo crystal forms: Self-association, interactions with metal ion/planar dyes and modeling studies

Cyclic ribodiguanylic acid, c-(GpGp), is the endogenous effector regulator of cellulose synthase. Its three dimensional structure from two different crystal forms (tetragonal and trigonal) has been determined by x-ray diffraction analysis at 1 A resolution. Both structures were solved by direct methods and refined by block-matrix least squares refinement to R-factors of 0.112 (tetragonal) and 0.119 (trigonal). In both crystal forms, two independent c-(GpGp) molecules associate with each other to form a self-intercalated dimer. All four c-(GpGp) molecules have very similar backbone conformation. The riboses are in the C3’-endo pucker with pseudorotation angles ranging from -7.2° to 16.5° and the bases have an ft glycosyl x angles (-175.5° to 179.7°). In the tetragonal form, a hydra ted cobalt ion is found to coordinateto two N7atomsofadjacentguanines, forcingthese two guanines to destackwitha large dihedral angle (33°). This metal coordination mechanism has been noted previously in other Pt-or Co-GMP complexes and may be relevant to the binding of the anticancer drug cisplatin to a GpG sequence in DNA. A model of the adduct between cisplatin and a d(CAATGG ATTG) duplex has been constructed in which the induced bending of the DNA helix at the Pt crosslinking site is 33°, consistent with earlier electrophoretic analyses. Moreover, c-(GpGp) exhibits unusual spectral properties not seen in other cyclic dinucieotides. It interacts with planar organic intercalator molecules in ways similar to double helical DNA. We propose a cage-like model consisting of a tetrameric c-(GpGp) aggregate in which a large cavity (host molecule) is generated to afford a binding site for certain planar inter-calators (guests molecules). The aggregate likely uses a hydrogen bonding scheme the same as that found in the G-quartet molecules, e.g., telomere DNA. The conformationofc-(GpGp) also suggests that certain nearest-neighbor intercalators may be synthesized on the basis of its unique molecular framework. Modeling studies have been carried out to test this hypothesis.