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Turner 2004

Bulge Loops

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