There are essentially two alternative mechanisms for the binding of telomerase to telomeres, assuming that a protective component is initially bound to the telomerase binding region on the telomeres. Either the protective (or blocking) agent first dissociates and telomerase binds thereafter, or telomerase binds first and the protective agent then dissociates from the ternary complex. In the limit, this second possibility permits the ternary complex to become a transition complex (creating another possible mechanism). Numerical simulation of both rapid mixing and chemical relaxation is used to study these alternatives. We aim to determine how the mechanisms may be distinguished experimentally and identify an appropriate experimental design. We show that rapid mixing experiments are better than chemical relaxation experiments, since the latter are more affected by the statistics of single molecule kinetics. However, hidden fast steps can only be revealed by chemical relaxation. The detection of mechanistic changes hinges on linking fluorescence reporters to the reaction components, either directly (chemically) or indirectly (via an indicator reaction). Fluorescence is excited by two-photon absorption in a small reaction volume. Various detection strategies and design issues are examined, including limitations imposed by diffusion. Constant rather than stopped flow is shown to be preferable.
Available at: http://works.bepress.com/tjalling_ypma/23/