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. 2005 Sep 30;89(6):3846–3855. doi: 10.1529/biophysj.105.068866

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DNA free-energy model. The free energy E(S) of a basepairing pattern S contains three separate contributions: first, a negative binding energy for basepairing. For simplicity, we assign the same binding energy for every basepair of type k, regardless of the neighboring bases. Second, a positive free energy cost for internal and bulge loops. We assign the same cost ɛ_ℓ for every loop, regardless of its length and base sequence, since the detailed choice of the loop cost function does not affect our main findings. Third, a stretching energy. For a given pattern S, the stretching energy can be written in the form −f L(S), with an effective length L(S), which is obtained from force-dependent base-to-base distances and for double and single strands, respectively. Note that L(S) does not correspond to the physical length of the DNA molecule (see main text).

Inline graphic — DNA free-energy model. The free energy E(S) of a basepairing pattern S contains three separate contributions: first, a negative binding energy for basepairing. For simplicity, we assign the same binding energy for every basepair of type k, regardless of the neighboring bases. Second, a positive free energy cost for internal and bulge loops. We assign the same cost ɛ_ℓ for every loop, regardless of its length and base sequence, since the detailed choice of the loop cost function does not affect our main findings. Third, a stretching energy. For a given pattern S, the stretching energy can be written in the form −f L(S), with an effective length L(S), which is obtained from force-dependent base-to-base distances and for double and single strands, respectively. Note that L(S) does not correspond to the physical length of the DNA molecule (see main text).