32  Watson-Crick-Franklin Helices

32.1 Free Energy Change at 37 °C

Folding free energy changes for Watson-Crick-Franklin helices are predicted using the equation:

ΔG°_{37 Watson-Crick-Franklin} = ΔG°_{37 intermolecular initiation} + ΔG°_{37 AU end penalty} (per AU end) + ΔG°_{37 symmetry (self-complementary duplexes)} + Σ[ΔG°_{37 stacking}]

where intermolecular initiation is applied for bimolecular structure formation, the AU end penalty is applied once per each AU pair at the end of a helix, the symmetry correction is applied to self-complementary duplexes, and the stacking term is a sum of sequence-dependent parameters over all base pair stacks. For helices of P uninterrupted basepairs, there are P-1 stacks of pairs.

32.2 Examples

Self complementary duplex

ΔG°₃₇ = ΔG°_{37 intermolecular initiation} + ΔG°_{37 symmetry} + ΔG°₃₇(MU followed by GC) + ΔG°₃₇(GC followed by CG) + ΔG°₃₇(CG followed by GC) + ΔG°₃₇(GC followed by CG) + ΔG°₃₇(CG followed by UM)

ΔG°₃₇ = 4.1 kcal/mol + 0.43 kcal/mol - 1.6 kcal/mol - 3.4 kcal/mol - 2.4 kcal - 3.4 kcal/mol - 1.6 kcal/mol

ΔG°₃₇ = -7.87 kcal/mol

Note that, for example, the parameters for (MU followed by GC) are the same as (CG followed by UM) because the correct directionality of the strands is preserved.

Non-self complementary duplex

ΔG°₃₇ = ΔG°_{37 intermolecular initiation} + ΔG°₃₇(GC followed by CG) + ΔG°₃₇(CG followed by MU) + ΔG°₃₇(MU followed by CG) + ΔG°₃₇(CG followed by GC)

ΔG°₃₇ = 4.1 kcal/mol - 3.4 kcal/mol - 1.3 kcal/mol - 1.9 kcal/mol - 2.4 kcal/mol

ΔG°₃₇ = -4.9 kcal/mol

32.3 Parameter Tables

The table of parameters is available as plain text for free energy change.