Interaction of substrate analogues with Escherichia coli DNA-dependent RNA polymerase

The inhibition of RNA polymerase with ATP and UTP analogues modified in the phosphate and ribose moieties has been investigated. 1. Modification of the terminal phosphate with a loss of the negative charge [adenosine 5'-(3-O-methyl)triphosphate, Ki = 1.75 mM] substantially weakens the binding ability of these analogues to the enzyme whereas modification with retention of the charge is not so detrimental [adenosine tetraphosphate, Ki = 0.17 mM]. 2. 2'-Modified analogues are only weak competitive inhibitors [2'-amino-2'-deoxyadenosine 5'-triphosphate, Ki = 2.3 mM] of their corresponding substrates [ATP, Km = 0.07 mM] whereas 3'-modified analogues are extremely potent in their inhibition [3'-amino-3'-deoxyadenosine 5'-triphosphate, Ki = 2.3 muM]. 3. A difference was observed in the inhibition of the elongation step of RNA polymerase by ATP and UTP analogues. Thus ATP analogues showed a strong binding to the CT form of the poly[d(A-T)] ternary complex and only a weak binding to the CA form. UTP analogues, on the other hand, showed a similar binding to both forms of the complex.