Structures of synthetic polynucleotides in the A-RNA and A′-RNA conformations: X-ray diffraction analyses of the molecular conformations of polyadenylic acid · polyuridylic acid and polyinosinic acid · polycytidylic acid

Abstract

X-ray dinraction patterns snow that syntnetic RNA A aoubie-helices, poly(A) · poly(U) and poly(I) · poly(C), are 11-fold and can exist in fibers in a crystalline form isomorphous with · -A-RNA from reovirus. The data from poly(A) · poly(U) were used to refine molecular parameters (and calculate their estimated standard deviations) for A-RNA; the values of these parameters are very similar to those obtained from independent refinements using data from α- and β- A-RNA (reovirus), but for the more numerous poly (A) · poly(U) data the parameters are defined more precisely. Poly(I) · poly(C) and poly(A) · poly(U) can undergo a salt-induced transition to the 12-fold helices of A′-RNA. Molecular parameters of A′-RNA, with their estimated standard deviations, were obtained from a refinement using X-ray diffraction data from poly(I) · poly(C). The reported structure of the synthetic DNA-RNA hybrid poly(I) · poly(dC) is not significantly different from A′-RNA. A′-RNA and A′-RNA are very similar to each other, and to A-DNA, in having antiparallel polynucleotide chains, C3- endo puckered furanose rings and Watson-Crick base pairs about 4 Å from the helix axis. The most obvious difference between these molecules is in the “tilt” of the base pairs. Structural similarities between poly(A) · poly(U) and poly(I) · poly(C) are consistent with their comparable ability to induce Interferon; the tendency of poly(A) · poly(U) to form a triple helix under conditions when poly(I) · poly(C) merely undergoes the A to A′ transition may explain why it has sometimes been found to be less effective. The homopolymer sequences of poly(A) · poly(U) and poly(I) · poly(C) may help to stabilize A-type conformations. Since homopolymer stretches in DNA appear to act as control sites for RNA transcription, the possible enhanced stability of their A conformations is consistent with a suggestion that DNA might adopt the A conformation during transcription.