Notation of. Zextended,right. Here, each line represents one base, a loop of length L = 9 (nine additional thymine bases) is inserted after base number 12 of the PM probe motif (loop position P = 12). The red lines represent hybridized duplex parts (Watson-Crick base pairing) and black lines denatured parts (the black lines in the middle of the probe include the additional loop bases). To the right of the loop position P, probe and target strand can bind in every possible conformation to each other resulting in Watson-Crick and non-Watson-Crick base pairing (green lines). The free energy of this part of the duplex is accounted for by ΔG7,28,23. In this way, bulged loops form in probe and target strand of different lengths. Here, a loop of length M1 = 16 bases and M2 = 11 bases is formed in probe and target respectively. Both loops reunite after base number i = 28 of the probe and base number j = 23 of the target strand. The black, rightmost part of the duplex is denatured and not considered in the computation. To reduce computing time, the duplex part left of the loop position is considered hybridized all the time. The free energy ΔGleft of this part is calculated with the help of the zipper model (6).
Trapp et al. BMC Biophysics 2011 4:20 doi:10.1186/2046-1682-4-20