Identification of a class of lysines within the non-specific DNA-binding site of RNA polymerase core enzyme from Escherichia coli.

The imido ester, methyl acetimidate, which specifically amidinates lysine residues, modifies RNA polymerase core enzyme, leading to rapid loss of activity. Calf thymus DNA partially protects the enzyme against this inactivation, an effect which disappears at high salt concentration. DNA protects 17 +/- 6 lysines from amidination at low salt concentration. The dependence of amidination on methyl acetimidate concentration is examined in the presence of DNA at high and low salt concentration. Analysis of the data suggests a class of approximately 12 lysines which are protected by DNA, consistent with the above estimate. These lysines are approximately 5--10-fold more reactive than most other available lysine residues.