Structural polymorphism and raman conformation markers of cyclic deoxytriadenylic acid

X-ray analysis of two different trigonal crystal forms (space groups R32 and P3 ) of cyclic deoxytriadenylic acid [c(dAp)3] indicates for each an asymmetric unit consisting of two conformationally similar c(dAp)3molecules. Raman spectroscopy supports the X-ray interpretation for the R32 crystal, but identifies another c(dAp)3conformation not revealed in the P3 X-ray structure. The results for the P3 crystal can be explained if an additional c(dAp)3conformer is present but not sufficiently ordered within the lattice to contribute to X-ray diffraction. The Raman signature of aqueous c(dAp)3, which differs from signatures of both the R32 and P3 crystals, exhibits backbone markers similar to those of thermally denatured DNA and indicates that c(dAp)3molecules in solution populate a wider range of phosphoester ring conformations than in R32 and P3 crystals. Thus, polymorphism is observed for both crystal and solution structures of c(dAp)3. The results imply a highly flexible phosphoester ring that may be relevant to the function of cyclic oligonucleotides as biological effectors. A novel Raman marker at 821 cm-1is demonstrated as diagnostic of phosphoester torsions alpha and zeta in the gauche+ range. Specific Raman markers are also identified for the S -type (C2'- endo) deoxyadenosine conformations that occur in R32 and P3 crystal structures of c(dAp)3.