  In the demanding biosensing environment, improving selection efficiency
strategies has become an issue of great significance. DNA minicircles
containing between 200 and 400 base-pairs, also named microDNA, are
representative of the supercoiled DNA loops found in nature. Their short size
makes them extremely susceptible to writhe and twist, which is known to play a
central role in DNA denaturation. We investigate minicircle lengths and
superhelical densities that induce DNA denaturation bubbles of nanometer size
and control well-defined long-life. Mesoscopic modeling and accelerated
dynamics simulations allow us to study accurately the thermodynamic and
dynamical properties associated with the nucleation and closure mechanisms of
long-lived denaturation bubbles. Our results pave the way for new types of DNA
biosensors with enhanced selectivity for specific DNA binding proteins.
