NMR evidence for dynamic secondary structure in helices II and III of the RNA of Escherichia coli.

A new ribonuclease A (RNase A) resistant fragment of the 5S ribonucleic acid (RNA) from Escherichia coli has been isolated and characterized. This fragment comprises helix III and most of helix II of the parent molecule, a part of the 5S RNA molecule for which several energetically equivalent secondary structures have been proposed [De Wachter, R., Chen, M.-W., & Vandenberghe, A. (1984) Eur. J. Biochem. 143, 175-182]. The imino proton spectrum of this fragment has been studied by nuclear magnetic resonance methods at 500 MHz. The data obtained are readily rationalized in terms of one of the structures proposed for this region of 5S RNA. They also suggest that upon heating, this structure is replaced by a second, different one, consistent with the view that the helix II-helix III region of 5S RNA is able to switch between alternative structures. Among the products of the nucleolytic digestion of 5S RNA is a species whose sequence indicates that RNase A can ligate RNA as well as hydrolyze it.