Transcription initiation

The initial stage of transcription, including RNA polymerase association with a promoter, local DNA opening, and the first RNA synthesis events before productive elongation. Open-complex formation, abortive synthesis and promoter escape are distinct transitions; an unwound bubble need not disappear when escape occurs.

An open promoter complex is a promoter-bound RNA polymerase assembly in which a short region of DNA is unwound and the template strand is accessible to the active site. This distinguishes it from the initially bound closed complex; it need not yet have escaped into productive elongation.

Consider unbound U, bound closed C and open O in a continuous-time Markov chain, with rates $U\to C=a$, $C\to U=b$, $C\to O=c$, and O absorbing over the observation interval. The mean first-opening times satisfy $T_U=1/a+T_C$ and $T_C=1/(b+c)+b{T}_U/(b+c)$, hence $T_U=(a+b+c)/(ac)$. Repeated unsuccessful binding attempts make this different from $1/c$. A FRET trace that cannot distinguish U from C does not by itself identify the individual binding and opening rates.