Table 2.

Calculated contour length (including 0.25 nm extra length owing to dye labeling), experimentally measured mean end-to-end separation, $\overline{r}$, of FRET dye pair and the associated variance σ

Melted bubble size (bp)	rcontour(nm)	$\overline{r}$(nm)	σ(nm)
0	5.69	5.69 ± 0.02	0.50 ± 0.01
1	6.05	5.72 ± 0.03	0.46 ± 0.02
2	6.41	5.80 ± 0.02	0.49 ± 0.02
4	7.13	5.58 ± 0.02	0.48 ± 0.03

Results are for DNA containing one centrally located melting bubble with variable size.