Table 1.

Thermal denaturation temperatures (T_m) and dsDNA-targeting potential ($\mathrm{\Delta }{G}_{\mathit{\text{rec}}}^{293}$) of Y-modified probes.^[a]

				Tm [ΔTm] (°C)
Entry	Zipper	ON	Sequence	upper strand vs ssDNA	lower strand vs ssDNA	probe duplex	$\mathrm{\Delta }{G}_{\mathit{\text{rec}}}^{293}(\mathrm{k}\mathrm{J}/\text{mol})$
1	+1	Y1	5'-GGYATATATAGGC	44.5	47.5	36.5	−25
		Y4	3'-CCAYATATATCCG	[+7.0]	[+10.0]	[−1.0]
2	+1	Y2	5'-GGTAYATATAGGC	47.5	48.5	36.5	−28
		Y5	3'-CCATAYATATCCG	[+10.0]	[+11.0]	[−1.0]
3	+1	Y3	5'-GGTATATAYAGGC	47.5	46.5	35.5	−28
		Y6	3'-CCATATATAYCCG	[+10.0]	[+9.0]	[−2.0]
4	2 seq. +1	Y7	5'-GGYAYATATAGGC	51.5	55.5	42.0	−32
		Y9	3'-CCAYAYATATCCG	[+14.0]	[+18.0]	[+4.5]
5	2 sep. +1	Y8	5'-GGYATATAYAGGC	52.5	55.5	49.0	−33
		Y10	3'-CCAYATATAYCCG	[+15.0]	[+18.0]	[+11.5]
6	+5	Y2	5'-GGTAYATATAGGC	47.5	46.5	56.0	−4
		Y6	3'-CCATATATAYCCG	[+10.0]	[+9.0]	[+18.5]
7	−3	Y3	5'-GGTATATAYAGGC	47.5	48.5	57.0	−8
		Y5	3'-CCATAYATATCCG	[+10.0]	[+11.0]	[+19.5]

^[a]ΔT_m = change in T_m relative to corresponding reference duplex D1D2 (T_m = 37.5 °C); thermal denaturation curves recorded in medium salt buffer ([Na⁺] = 110 mM, [Cl⁻] = 100 mM, pH 7.0 (NaH₂PO₄/Na₂HPO₄)), using 1.0 µM of each strand; see main text for definition of $\mathrm{\Delta }{G}_{\mathit{\text{rec}}}^{293}$; see Table S2 for ΔG²⁹³ values; “seq” and “sep” denotes sequential and separated zippers, respectively.