Turner 1999Folding Free Energy Change
Hairpin loops of 4 or more unpaired nucleotides
The prediction of folding free energy changes for hairpins
of 4 or more unpaired nucleotides is made with the following equation:
ΔG°37 hairpin (>3 nucleotides in loop) = ΔG°37 initiation (n) + ΔG°37 (terminal mismatch) + ΔG°37 (UU or GA first mismatch) + ΔG°37 (special GU closure) + ΔG°37
penalty (all C loops)
In this equation, n is
the number of nucleotides in loop, the terminal mismatch parameter is the
sequence-dependent term for the first mismatch stacking on the terminal base pair,
UU and GA first mismatches receive a bonus (not applied to AG first
mismatches), the special GU closure term
is applied only to hairpins in which a GU closing pair (not UG) is preceded by
two Gs, and finally loops with all C nucleotides receive a penalty.
The
penalty for all C loops of more than three unpaired nucleotides is predicted
using a linear equation:
ΔG°37
penalty (all C loops; > 3 unpaired nucleotides) = An + B
Hairpin loops of 3 unpaired nucleotides
For hairpin loops of 3 nucleotides, the folding
free energy change is estimated using:
ΔG°37
hairpin (3 unpaired nucleotides) = ΔG°37 initiation (3) +
ΔG°37 penalty (all C loops)
As
opposed to longer hairpin loops, hairpin loops of three nucleotides do
not receive a sequence-dependent first mismatch term. All C hairpin loops of three nucleotides
receive a stability penalty.
Frequently Occuring Tetraloops
Tetraloop sequences, i.e. hairpin loops with four nucleotides, that occur frequently in the database of known secondary structures receive an enhanced stability in the form of a free energy bonus. These bonuses are sequence-dependent and appear in a lookup table.
Short hairpin loops
The nearest neighbor rules prohibit hairpin loops with fewer than 3 nucleotides.
Parameter Tables
Length dependent initiation
parameters are available in plain text or html format.
Initiation parameters are based on experiments for sizes up to 9 nucleotides, but can be extrapolated to longer loops. For free energy changes,
the extrapolation is ΔG°37 initiation (n>9)
The terminal mismatch tables are available in plain text. These
parameters are also available in html.
The bonus/penalty
terms (including the all-C loop terms) are available in html format.
The lookup table of for tertraloops with enhanced stability is available as plain text or html.
References
A set of references is available here.
Examples