Kinetic Modeling of Transcription Elongation

Transcription elongation is the process by which RNA polymerase (RNAP) moves along template DNA and synthesizes a complementary RNA. During elongation, RNAP carries out a highly processive and directional net motion, even in the presence of a large external load. From an energetics point of view, RNAP is a molecular motor capable of converting chemical energy derived from NTP hydrolysis into mechanical work. Unlike other molecular motors such as kinesin or myosin that move along a uniform track, RNAP transcribes on a DNA substrate with varying sequence content. This variability of sequences significantly affects the kinetics of RNAP motion and results in non-uniform elongation rates. Theoretical modeling of transcription has so far focused on two main aspects of elongation: (1) how RNAP couples chemical catalysis energy to its translocation and mechanical work and (2) how its motion is regulated by the DNA sequence.