Double-ended zipper model of the oligonucleotide duplex. (A) Unzipping of the relatively short duplexes is initiated at the duplex ends only. The end-domain opening, which progresses back and forth (nucleotide by nucleotide) in a stepwise, zipper-like fashion, can be considered a biased random walk. The energy level of the partially denatured hybridization state Sk,l(with respect to the completely hybridized ground state) is determined by summation over the NN free energies of the unzipped NN-pairs (from 1 to k and from l to N). (B) Single base MMs (non-Watson-Crick base pairing affect the stabilities of two adjacent NN-pairs at positions x and x + 1. (C) Base insertions and deletions result in bulged duplexes with an unpaired base. The surplus base (depicted in a looped out conformation), similar as a MM defect, results in a reduced binding affinity.