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. The plain text files include an extrapolation of the initiation out to 30 unpaired nucleotides.
References
A set of references is available here.
Examples