Turner 19991×1, 1×2, 2×2 Internal Loops
Small symmetric internal loops have tabulated free energy 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(n1 + n2) + ΔG°37 asymmetry×| n1 – n2| + ΔG°37 mismatch(per UU, GA, or AG first mismatch) + ΔG°37 AU/GU closure(per AU or GU closure)
where the initiation is a length dependent term for the sum of unpaired nucleotides on each side, 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 when they are UU, GA, or AG. The first mismatch bonuses are only applied for loops that have at least 2 unpaired nucleotides on each side of the loop. 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)
Parameter Tables
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1×1 internal loop free energy change tables are available in text and html format. Note that these tables incorporate the AU/GU closure penalties and therefore no AU/GU helix end penalty should be applied for internal loop closure.
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1×2 internal loop free energy change tables are available in text and html format. Note that these tables incorporate the AU/GU closure penalties and therefore no AU/GU helix end penalty should be applied for internal loop closure.
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2×2 internal loop free energy change tables are available in text and html format. Note that these tables incorporate the AU/GU closure penalties and therefore no AU/GU helix end penalty should be applied for internal loop closure.
References
A set of references is available here.
Examples