Additional file 3.
Influence of the number of MMs on the fluorescent signal. In order to reproduce our experimental data, it is sufficient to consider up to 3 synthesis-related defects in the zipper model. We confirm this by measuring the fluorescent signals of probes with 1 to 4 MMs. MMs are incorporated into the PM probe motif at 8 given positions resulting in 162 different probe sequences. To generate the MMs, we replace the bases at these specific positions with a thymine base (or with an adenine base, if a thymine base is already present at the specific position). After categorizing the probes into groups according to their number of MMs, we calculate the average signal of each group and plot it against the number of MMs (PM signal is set to 1, background signal is set to 0). Based on this data, we can estimate the error caused by neglecting probes with more than 3 synthesis defects: the error ≪ 4%, smaller than the experimental error.
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Trapp et al. BMC Biophysics 2011 4:20 doi:10.1186/2046-1682-4-20