5S RNA. An Analysis of Possible Base Pairing Schemes

Possible ways of arranging base paris which are compatible with the primary structure of 5 S RNA from Escherichia coli and KB cells are discussed. If only A·U and G·C base pairs are allowed, the maximum helical content of clover leaf models with up to four leaves is 68%. In multihelical models with helical regions consisting of a minimum of four base pairs the maximum belical content is 60%. With helical regions consisting of three base pairs, at least some of which are A·U base pairs, the helical content can be raised to 73%. It is unlikely that higher helical contgents are possible unless shorter helices are included. The structures with a given helical content are never unique so that if the secondary structure of 5 S RNA is unique there must be other factors in operation.