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The research makes use of a structure model, in addition to the various energy transfer distance measurements to study the T7 RNA polymerase, which causes bending of its promoter DNA on binding by various proteins and other complexes. The analysis proves the existence of a bent and an open model for the initiation complex of T7 and also shows that in spite of the massive changes, the DNA of the active site is very much identical in initiation as well as elongation complexes.

A novel mode of interaction between ubiquitin and the cyclin-dependent kinase subunit of Saccharomyces cerevisae, Cks1p, an adaptor protein involved in transcriptional regulation through recruitment of proteasomal subunits to gene promoters is reported. Cks1p interacts specifically with monoubiquitin and tetraubiquitin with an affinity several orders of magnitude greater than that of other ubiquitin-binding domains.

Fluorescence resonance energy transfer (FRET) is used to investigate the conformation of promoter DNA in the closed and open complexes of T7 RNA polymerase (T7 RNA P). It is proposed that promoter opening occurs spontaneously upon DNA bending and/or untwisting as free energy is gained through interactions of the melted promoter with the T7 RNAP active site.

Elucidation of the temporal coupling in DNA binding, bending, and opening processes that occur during initiation is presented. The results provided are consistent with the mechanism in which the initial binding of T7 RNAP to the promoter results in a closed complex, which is then converted into an open complex in which promoter is both sharply bent and melted.