Conformational Study of the Tandem Repeat Sequence in RNA Polymerase II by Circular Dichroism Spectroscopy.

The largest subunit of RNA polymerase II has an interesting C-terminal domain, which consists of a multiple tandem repeat of a heptapeptide with the consensus sequence Ser-Pro-Thr-Ser-Pro-Ser-Tyr. However, the functional role of this sequence is unclear. One might assume that the conformation of the tandem repeat is very important for its function. The conformation of poly(Ser-Pro-Thr-Ser-Pro-Ser-Tyr) and H-Ser-Pro-Thr-Ser-Pro-Ser-Tyr-OH, corresponding to the repeat and the repeating unit of the C-terminal domain, respectively, were investigated exhaustively by circular dichroism (CD). The CD spectrum of H-Ser-Pro-Thr-Ser-Pro-Ser-Tyr-OH indicated the presence of a turn structure in water, which was further stabilized in 2,2,2-trifluoroethanol (TFE) and in acetonitrile. The CD spectra of the polyheptapeptide poly(Ser-Pro-Thr-Ser-Pro-Ser-Tyr) suggested that the disordered conformation was predominant in water and that the rum structure was stabilized by increasing the content of TFE or acetonitrile in the solvent. We suggest that the polyheptapeptide forms not only a turn structure at the heptapeptide unit Ser-Pro-Thr-Ser-Pro-Ser-Tyr, but also a kind of super conformation induced by the periodicity of the sequence in TFE or acetonitrile.