Turner 1999Folding Free Energy Change
Singe Nucleotide Bulge Loops
The prediction of folding free energy changes is made with the following equation:
ΔG°37 bulge (n=1) = ΔG°37 bulge initiation(1) + ΔG°37 (base pair stack)
In this equation, n is the number of unpaired nucleotides and the base pair stack is the stack of the closing pairs as though there is no bulge (using Watson-Crick or GU rules as needed).
Because the helical stack continues across a single nucleotide bulge, the terminal AU/GU penalty is not applied adjacent to single bulges.
Bulges of 2 or More Nucleotides
For bulges of 2 or more nucleotides, the following equation is used:
ΔG°37 bulge (n>1) = ΔG°37 bulge initiation(n)
Experimentally-derived parameters are available for initiation up to n = 3 and a linear extrapolation is used up to n = 6. Beyond 6, the initiation is approximated using a logarithmic function:
ΔG°37 bulge (n>6) = ΔG°37 bulge initiation(6) + 1.75 RT ln(n/6)
where R is the gas constant and T is the absolute temperature, 310.15 K.
Parameter Tables
Bulge loop parameters are available in html or as plain text.
References
A set of references is available here.
Examples