Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based on the thermodynamic stability of the sequence. The GC-rich stable hairpin together with the destabilizing U-repeat supposedly destabilize the binding of the polymerase enough to cause it to disassociate from the template.
What I'm looking for are specific requirements on the termination sequences that are not based on thermodynamics.
- Are there any specific requirements on the hairpin sequence beyond a certain thermodynamic stability.
- Are there any loop variants that are known to reduce the termination efficiency?
- Does the shape of the hairpin, e.g. any kinks or bulges in it, have an influence on termination efficiency?
The typical requirements I read are 5-14bp and GC-rich, and I'd like to know if there are any more specific requirements, especially ones related to the structure and not the stability of the hairpin.