Validate hairpin-sensor strand displacement by tile A

Determine whether DNA tile A, after release from its nanocarrier, can open the hairpin sensor stem through toehold-mediated strand displacement with sufficient affinity to permit subsequent activation of the fluorescence signal by tile C.

Background

The proposed proof-of-concept relies on DNA tile A initiating strand displacement at the hairpin sensor. If this interaction is thermodynamically or kinetically inadequate, tile C will not obtain an accessible toehold and the sensor will not produce fluorescence. The authors identify this as the most critical unresolved design issue and suggest evaluating it computationally with NUPACK or similar tools before laboratory experimentation.