. 2016 Apr 4;113(16):E2277–E2285. doi: 10.1073/pnas.1600279113

Table S1.

Calculation of free energy (37 °C) for matched and mismatched duplexes with dangling ends by melting temperature

Entry	Primer/template	T_m, °C^*	$Δ G_{VH}^{°}$ , kcal/mol	$Δ G_{fit}^{°}$ , kcal/mol	$Δ G_{avg}^{°}$ ^†, kcal/mol	ΔΔG°, kcal/mol
	Primer T/DNA_t
1	ATATCACAT	27.1 ± 0.5	−6.8 ± 0.4	−6.9 ± 0.2	−6.9 ± 0.4	—
1	TATAGTGTATGTCT	27.1 ± 0.5	−6.8 ± 0.4	−6.9 ± 0.2	−6.9 ± 0.4	—
2	ATATCACATA	30.3 ± 0.1	−7.8 ± 0.1	−7.5 ± 0.2	−7.7 ± 0.2	−0.8 ± 0.5
2	TATAGTGTATGTCT	30.3 ± 0.1	−7.8 ± 0.1	−7.5 ± 0.2	−7.7 ± 0.2	−0.8 ± 0.5
3	ATATCACATT	27.2 ± 0.4	−7.2 ± 0.2	−6.8 ± 0.2	−7.0 ± 0.3	−0.1 ± 0.5
3	TATAGTGTATGTCT	27.2 ± 0.4	−7.2 ± 0.2	−6.8 ± 0.2	−7.0 ± 0.3	−0.1 ± 0.5
	Primer T/DNA_g
4	ATATCACAT	29.5 ± 0.3	−7.7 ± 0.2	−7.3 ± 0.2	−7.5 ± 0.3	—
4	TATAGTGTAGTTCT	29.5 ± 0.3	−7.7 ± 0.2	−7.3 ± 0.2	−7.5 ± 0.3	—
5	ATATCACATC	35.8 ± 0.2	−8.8 ± 0.0	−8.7 ± 0.2	−8.7 ± 0.2	−1.2 ± 0.3
5	TATAGTGTAGTTCT	35.8 ± 0.2	−8.8 ± 0.0	−8.7 ± 0.2	−8.7 ± 0.2	−1.2 ± 0.3
6	ATATCACATT	28.4 ± 0.1	−7.6 ± 0.1	−7.1 ± 0.2	−7.4 ± 0.2	0.1 ± 0.3
6	TATAGTGTAGTTCT	28.4 ± 0.1	−7.6 ± 0.1	−7.1 ± 0.2	−7.4 ± 0.2	0.1 ± 0.3
	Primer A/DNA_a
7	ATATCACGA	33.8 ± 0.4	−8.6 ± 0.0	−8.1 ± 0.2	−8.4 ± 0.2	—
7	TATAGTGCTAGGCT	33.8 ± 0.4	−8.6 ± 0.0	−8.1 ± 0.2	−8.4 ± 0.2	—
8	ATATCACGAT	37.4 ± 0.6	−9.0 ± 0.1	−9.0 ± 0.2	−9.0 ± 0.2	−0.7 ± 0.3
8	TATAGTGCTAGGCT	37.4 ± 0.6	−9.0 ± 0.1	−9.0 ± 0.2	−9.0 ± 0.2	−0.7 ± 0.3
9	ATATCACGAA	32.2 ± 0.5	−8.3 ± 0.1	−7.9 ± 0.1	−8.1 ± 0.1	0.3 ± 0.3
9	TATAGTGCTAGGCT	32.2 ± 0.5	−8.3 ± 0.1	−7.9 ± 0.1	−8.1 ± 0.1	0.3 ± 0.3
	Primer A/DNA_c
10	ATATCACGA	31.9 ± 0.5	−8.1 ± 0.2	−7.9 ± 0.2	−8.0 ± 0.3	—
10	TATAGTGCTCAACT	31.9 ± 0.5	−8.1 ± 0.2	−7.9 ± 0.2	−8.0 ± 0.3	—
11	ATATCACGAG	41.6 ± 0.2	−9.7 ± 0.0	−9.9 ± 0.1	−9.8 ± 0.1	−1.8 ± 0.4
11	TATAGTGCTCAACT	41.6 ± 0.2	−9.7 ± 0.0	−9.9 ± 0.1	−9.8 ± 0.1	−1.8 ± 0.4
12	ATATCACGAA	31.7 ± 0.4	−8.2 ± 0.1	−7.9 ± 0.1	−8.0 ± 0.2	0.0 ± 0.4
12	TATAGTGCTCAACT	31.7 ± 0.4	−8.2 ± 0.1	−7.9 ± 0.1	−8.0 ± 0.2	0.0 ± 0.4
	Primer G/DNA_t
13	ATATCACCG	36.3 ± 0.9	−8.4 ± 0.0	−8.6 ± 0.4	−8.5 ± 0.4	—
13	TATAGTGGCTATCT	36.3 ± 0.9	−8.4 ± 0.0	−8.6 ± 0.4	−8.5 ± 0.4	—
14	ATATCACCGA	40.2 ± 0.2	−9.1 ± 0.4	−9.4 ± 0.3	−9.3 ± 0.5	−0.8 ± 0.6
14	TATAGTGGCTATCT	40.2 ± 0.2	−9.1 ± 0.4	−9.4 ± 0.3	−9.3 ± 0.5	−0.8 ± 0.6
15	ATATCACCGG	37.0 ± 0.8	−8.7 ± 0.2	−9.1 ± 0.2	−8.9 ± 0.3	−0.4 ± 0.5
15	TATAGTGGCTATCT	37.0 ± 0.8	−8.7 ± 0.2	−9.1 ± 0.2	−8.9 ± 0.3	−0.4 ± 0.5

Conditions: 50 mM Na•Pipes, pH 7.5, 8 mM MgCl₂; 2 μM DNA strand concentration for T_m shown.

^{^†}

Average free energy from van’t Hoff calculations and MeltWin fits; error was propagated from the SDs of the two methods.