Folding 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(n) + ΔG°37 (special C bulge) + ΔG°37 (base pair stack) – RT ln(number of states)
In this equation, n is the number of unpaired nucleotides, a special C bulge is a bulged C adjacent to at least one paired C, 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), and the number of states counts the number of possible loops of identical sequence.
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.
Folding Enthalpy Change
Singe Nucleotide Bulge Loops
The prediction of folding free energy changes is made with the following equation:
ΔH°bulge (n=1) = ΔH°bulge initiation(n) + ΔH°(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:
ΔH°bulge (n>1) = ΔH°bulge initiation(n)
Experimentally-derived parameters are available for bulge loop initiations up to n=3. For n>3, the initiation is approximated as that for n=3.
Parameter Tables
Bulge loop parameters are available in html or as plain text for initiation free energy parameters or initiation enthalpy parameters.
References
A set of references is available here.
Examples