A study of the interaction between promotor DNA and T. thermophilus DNA-dependent RNA polymerase 1,2

As the first step in the process of RNA synthesis, RNA polymerase binds to a specific site (promoter) and forms an open complex. In this process, it is considered that the structure of DNA is changed to an unidentified form. We investigated the structure of this DNA, which consists of an open complex, by means of CD. For this purpose, we used very stable RNA polymerase (of T. thermophilus HB8) and the fd-RF-DNA fragment (Hap-Hga V), which has only one promoter. We have confirmed that the complex of the holo enzyme with Hap-Hga V fragment at 50 degrees C is an open complex. We obtained the CD spectral difference between the open complex and its constituents for the first time. The observed CD difference spectra in the UV region (250-300 nm) were compared with the theoretical difference CD. It was deduced that the DNA of the open complex may be melted around the initiation point over a rather longer range than expected.