Structures of two RNA octamers containing tandem G.A base pairs

The crystal structures of two RNA octamers, 5'-GGC(GA)GCC-3' and 5'-GIC(GA)GCC-3', have been determined from X-ray diffraction data to 2.8 and 2.7 A resolution, respectively. The RNA octamers crystallize in isomorphous unit cells containing two mispairs arranged in a self-complementary manner and one single strand in the asymmetric unit. The single strand pairs with another single strand related by crystallographic symmetry to form a third unique double helix. Tandem non-Watson-Crick G.A/A.G base pairs of the sheared type comprise an internal loop in the middle of each duplex. The NMR structure of this octameric RNA sequence is also known, allowing comparison of the variation between the six crystallographic duplexes and the solution structure. In the symmetric duplex of the octamer containing inosine, the sheared G.A pairs incorporate a bound water molecule. This duplex also binds one water molecule per strand in the minor groove adjacent to the G.A pairs.