Leading edge length

Wayne K. Dawson

Summary

The leading edge length refers to the distance ahead of the current visible structure that is being scanned for pseudoknots. By visible we mean what you currently see as the RNA is folding. The leading edge is at the $3'$ end of the sequence in a sequential folding process ($5'$ to $3'$). This concept is shown schematically in Fig 1. The leading edge is free to bind anywhere $5'$ of the $3'$ end.

The red region on the left of Fig 1 indicates a hot lead. When a stem is potentially 5 or more base pairs (bp) long, and particularly when that pairing involves lots of complimentary Gs and Cs, there is a good chance that it wants to attach somewhere. When this is the case, this edge can drastically melt other parts of the structure $5'$ of itself. Over the entire ``dwell region'', the structure is allowed to combine and local melting is also tested. In essence, most of the structure $5'$ of the leading edge tends to already be built up so the most strongly active part of the sequence is the $3'$ most part of the currently folding sequence.

The red structure on the right indicates that the leading edge has bound to form a linkage stem.

Figure 1: A schematic of the leading edge region showing the leading edge, the dwell region and the secondary structure to which this leading edge region can scan and attach in advance of the secondary structure formation.