Additional file 2.
Duplex stability of DNA duplexes with bulged loops of different sequences as a function of loop length. Instead of the discussed poly-T loop sequences, we synthesize probes containing poly-C loop sequences and random loop sequences respectively at three different positions (the number of additional bases vary from one to thirteen; the random loop sequences are listed in table b) of this file). Upon hybridization with the target sequence listed in table 1, we note a monotonic decrease of the fluorescent signal as a function of loop length. After averaging over all loop positions, we compare the experimental signals as a function of loop length with the model predictions. We show that the experimental data is reproduced by our theory.
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Trapp et al. BMC Biophysics 2011 4:20 doi:10.1186/2046-1682-4-20