# 38Internal Loops

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

## 38.1 Examples

### 2×2 internal loop

ΔG°37 = ΔG°37(Watson-Crick-Franklin stacks) + ΔG°37 intermolecular initiation + ΔG°37(Internal Loop)

ΔG°37 = ΔG°37(CG followed by MU) + ΔG°37(CG followed by GC) + ΔG°37 intermolecular initiation + ΔG°37(2×2 Internal Loop)

ΔG°37 = -1.3 kcal/mol -2.4 kcal/mol + 4.1 kcal/mol -1.1 kcal/mol

ΔG°37 = -0.7 kcal/mol

Note that the internal loop lookup tables account for terminal MU pairs that are adjacent to internal loops.

### 1×5 internal loop

ΔG°37 = ΔG°37(Watson-Crick-Franklin stacks) + ΔG°37 intermolecular initiation + ΔG°37(Internal Loop)

ΔG°37 = ΔG°37(CG followed by MU) + ΔG°37(CG followed by GC) + ΔG°37 intermolecular initiation + ΔG°37 initiation(6) + ΔG°37 asymmetry×|n1 - n2| + ΔG°37 mismatch(mismatch 1) + ΔG°37 mismatch(mismatch 2)

ΔG°37 = -1.3 kcal/mol – 2.36 kcal/mol + 4.09 kcal/mol + 2.0 kcal/mol + 0.6×|1 - 5| kcal/mol + 0 kcal/mol + 0 kcal/mol

ΔG°37 = +4.8 kcal/mol

Note that the free energy change for first mismatches in 1×(n-1) internal loops is 0 kcal/mol.

### 2×3 internal loop with stabilizing mismatches

ΔG°37 = ΔG°37(Watson-Crick-Franklin stacks) + ΔG°37 intermolecular initiation + ΔG°37(Internal Loop)

ΔG°37 = ΔG°37(CG followed by AU) + ΔG°37(CG followed by GC) + ΔG°37 intermolecular initiation + ΔG°37 initiation(5) + ΔG°37 asymmetry×|n1 - n2| + ΔG°37 mismatch(mismatch 1) + ΔG°37 mismatch(mismatch 2) + ΔG°37 AU closure

ΔG°37 = –2.11 kcal/mol – 2.36 kcal/mol + 4.09 kcal/mol + 2.0 kcal/mol + 0.6×|2 - 3| kcal/mol – 0.8 kcal/mol – 1.2 kcal/mol + 0.7 kcal/mol

ΔG°37 = +0.9 kcal/mol

## 38.2 Parameter Tables

1×1 internal loop free energy change tables are available in text. Note that these tables incorporate the AU closure penalties and therefore no AU helix end penalty should be applied for internal loop closure.

1×2 internal loop free energy change tables are available in text. Note that these tables incorporate the AU closure penalties and therefore no AU helix end penalty should be applied for internal loop closure.

2×2 internal loop free energy change tables are available in text. Note that these tables incorporate the AU closure penalties and therefore no AU helix end penalty should be applied for internal loop closure.