Crystal structure of an RNA 16-mer duplex r(GCAGAGUUAAAUCUGC)(2) with nonadjacent G(syn)center dot A(+)(anti) mispairs

G . A mispairs are one of the most common noncanonical structural motifs of RNA. The 1.9 Angstrom resolution crystal structure of the RNA 16-mer r(GCA GAGUUAAAUCUGC)(2) has been determined with two isolated or nonadjacent G . A mispairs. The molecule crystallizes with one duplex in the asymmetric uni t in space group R3 and unit cell dimensions a = b = c = 49.24 Angstrom and alpha = beta = gamma = 51.2 degrees. It is the longest known oligonucleoti de duplex at this resolution and isomorphous to the 16-mer duplex with the C . A(+) mispairs [Pan, et al., (1998) J. Mel. Biol. 283, 977-984]. The C . A(+) mispair behaves like a wobble pair while the G . A(+) does not. The G . A mispairs are protonated at N1 of the adenines as in the C . A(+) mispa irs, and two hydrogen bonds in the G(syn). A(+)(anti) conformation are form ed. The syn guanine is stabilized by an intranucleotide hydrogen bond betwe en the 2-amino and the 5'-phosphate groups. The G(syn). A(+)(anti) conforma tion can provide a different surface for recognition in the grooves compare d to other G . A hydrogen bonding schemes. The major groove is widened betw een the two mispairs allowing access to ligands. One of the 3-fold axes is occupied by a sodium ion and a water molecule, while a second is occupied b y another water molecule.