Turner 2004

Internal Loops

1×1, 1×2, 2×2 Internal Loops

Small symmetric internal loops have tabulated free energy and enthalpy changes, where experimentally determined values are used if available.

Other Internal Loops

The stabilities of other internal loops are predicted using the equation:

ΔG°37 internal = ΔG°37 initiation(n) + ΔG°37 asymmetry×| n1 – n2| + ΔG°37 mismatch(mismatch 1) + ΔG°37 mismatch(mismatch 2) + ΔG°37 AU/GU closure(per AU or GU closure)

where the initiation is a length dependent term for n unpaired nucleotides, an asymmetry term is multiplied by the absolute value of the difference in the number of unpaired nucleotides on each side of the loop, and sequence-dependent mismatch terms are applied for first mismatches of specific sequences. The AU/GU closure is applied per AU or GU closing pair and is used instead of the AU or GU penalty at the end of the helix (see Watson-Crick or GU pairs).

Experimental data for ΔG°37 initiation(n) is available for loops up to n = 6. For larger internal loops, an extrapolation is made:

ΔG°37 initiation(n>6) = ΔG°37 initiation(6) + 1.08×ln(n/6)

Similarly, the enthalpy change is predicted with the equation:

ΔH°internal = ΔH°initiation(n) + ΔH°asymmetry×| n1 – n2| + ΔH°mismatch(mismatch 1) + ΔH°mismatch(mismatch 2) + ΔH°AU/GU closure(per AU or GU closure)

where terms are analagous to those for predicting folding free energy changes.

The mismatch parameters are sequence-dependent and are different for 1×(n-1) loop, 2×3 loop, and other internal loops. In the case of 1×(n–1) loops, the mismatches are set to 0 kcal/mol for free energy and enthalpy changes.

In the absence of data for loops larger than n=6, ΔH°initiation(n>6) = ΔH°initiation(6)

Parameter Tables


A set of references is available here.