Verification of a new model of the time course of RNA synthesis. Measurement of the rates of initiation and elongation

Abstract

The time course of RNA synthesis in vitro commonly starts with a lag followed by a linear phase. Differing from the earlier interpretation we have previously proposed that, under conditions where the initiation rate is low, the lag represents the time taken for the first RNA polymerase molecule to reach a termination site. During the linear phase, initiation is balanced by termination (Mahon, G.A.T., McWilliam, P., Gordon, R.L. and McConnell, D.J. (1980) J. Theor. Biol. 87, 483-515). We report the use of rifampicin as a further test of this new model. We show that it does apply under conditions of high ionic strength (0.3 M KCl), and under these conditions time courses may be analyzed to yield unbiased estimates of the initiation (Vi) and chain elongation (Vp) rates. We illustrate the application of the method of time course analysis and confirm some of its features by examining the effect of variation in the concentrations of RNA polymerase and nucleoside triphosphate on the estimates of Vi and Vp. The alternative interpretation of the time course applies under conditions of low ionic strength, where the initiation rate is high. (Chamberlin, M.J., Nierman, W.C., Wiggs, J. and Neff, N. (1979) J. Biol. Chem. 254, 10061-10069.) The advantages of each model in measuring Vi and Vp (the major parameters of the transcription reaction) are discussed. © 1985.