# 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}(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