A computational approach to the mechanism of self-cleavage of hammerhead RNA.

Extensive minimization and dynamics computational studies of the hammerhead structural domain of the virusoid of lucerne transient streak virus have been carried out. The following observations at the self-cleavage position are derived from the resulting three-dimensional structure: (i) the cytosine base is at the surface and does not interact with another base (it is free to move), and (ii) the ribose-phosphate backbone is forced to take an abrupt turn since it bridges stems I and III, and this turn points the pro-S and pro-R oxygens of the phosphate to the inward side of the hammerhead. These structural features are independent of the hammerhead being open or closed and allow an unencumbered 3'- to 2'-endo conformational change of the ribose with the resultant creation of an unusual stereochemistry that allows a direct in-line self-cleavage reaction. In the closed hammerhead structure, interactions of stems I and II create a vacancy into which the catalytic hydrated Mg(II) may be docked on labile phosphate. This opening is not present if stems I and II are shortened.