Table 2.

Destabilizing due to dangling ssDNA sections, as found in simulations

Duplex length	T/°C	m	n	(kcal/mol)
6	25	10	0	1.46 [1.2]
		0	10	1.38 [1.0]
		10	10	2.72 [3.2]
8	55	10	0	0.87 [0.60]
		0	10	0.94 [0.78]
		10	10	1.65 [1.79]

m is the length of the excess ssDNA attached to the hairpin, and n the length attached to the shorter strand. Values for , the free energy of formation of the duplex, are extracted from simulations. The reported value, , is given by . is then the destabilization of the duplex due to the ssDNA overhangs. The values in square brackets correspond to values inferred from our experimental studies for the closest equivalent lengths of dangling ssDNA. Note that and found here are compared to and from experiment – the local nature of the destabilisation makes this reasonable.