Signal dependence on loop position. a) A loop at a duplex end may result in dangling ends owing to the low probability of duplex closing. The large green region may provide high duplex stability and a strong fluorescent signal. b) If the loop is located towards the center of the duplex, it is likely that the duplex is closed at both sides of the loop due to the large number of possible binding partners on both sides of the loop. c) At a position located between end and center of the strand, the duplex is less stable than in a) and b).
Trapp et al. BMC Biophysics 2011 4:20 doi:10.1186/2046-1682-4-20