Table 4.

Newly Derived RNA Correction Factors

Eq no.	Name	Equation	Accuracyc
RNA Tm Correction Factors
18	Modified SantaLucia Tm equationa, b	$\frac{1}{T_m(2)}=\frac{1}{T_m(1)}+\frac{0.3153N}{\mathrm{\Delta }H°}\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}$	1.0 °C
19	Modified Owczarzy Tm linear equation	$T_m(2)=T_m(1)+(-1.842fGC+4.314)\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}$	0.9 °C
20	Modified Owczarzy 1/Tm linear equationb	$\frac{1}{T_m(2)}=\frac{1}{T_m(1)}+(2.297fGC-4.575)\times {10}^{-5}\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}$	0.9 °C
21	Modified Owczarzy Tm quadratic equation	$T_m(2)=T_m(1)+(-1.842fGC+2.675)\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}-0.7348({\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_2-{\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_1)$	0.7 °C
22	Modified Owczarzy 1/Tm quadratic equationb	$\frac{1}{T_m(2)}=\frac{1}{T_m(1)}+(2.297fGC-2.886)\times {10}^{-5}\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}+7.575\times {10}^{-6}({\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_2-{\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_1)$	0.7 °C
RNA ΔG°37 Correction Factors
23	ΔG°37 derived equation	$\mathrm{\Delta }{G°}_{37}(2)=\mathrm{\Delta }{G°}_{37}(1)-310.15\times \mathrm{\Delta }H°\times [(2.297fGC-2.886)\times {10}^{-5}\times \text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}+7.575\times {10}^{-6}\times ({\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_2-{\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_1)]$	0.14 kcal/mol
24	ΔG°37 linear equation	$\mathrm{\Delta }{G°}_{37}(2)=\mathrm{\Delta }{G°}_{37}(1)+(0.324fGC-0.765)\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}$	0.17 kcal/mol
25	1/ΔG°37 linear equation	$\frac{1}{\mathrm{\Delta }{G°}_{37}(2)}=\frac{1}{\mathrm{\Delta }{G°}_{37}(1)}+(-0.0213fGC+0.0261)\times {10}^{-5}\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}$	0.19 kcal/mol
26	ΔG°37 quadratic equation	$\mathrm{\Delta }{G°}_{37}(2)=\mathrm{\Delta }{G°}_{37}(1)+(0.324fGC-0.468)\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}+0.133({\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_2-{\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_1)$	0.14 kcal/mol
27	1/ΔG°37 quadratic equation	$\frac{1}{\mathrm{\Delta }{G°}_{37}(2)}=\frac{1}{\mathrm{\Delta }{G°}_{37}(1)}+(-0.0213fGC+0.016)\times {10}^{-5}\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}-0.0045({\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_2-{\text{ln}}^2{\left[{\mathit{\text{Na}}}^{+}\right]}_1)$	0.17 kcal/mol
28	Modified SantaLucia ΔG°37 equationa	$\mathrm{\Delta }{G°}_{37}(2)=\mathrm{\Delta }{G°}_{37}(1)-0.1016\times N\text{ln}\frac{{\left[{\mathit{\text{Na}}}^{+}\right]}_2}{{\left[{\mathit{\text{Na}}}^{+}\right]}_1}$	0.18 kcal/mol

^aN is the total number of phosphates in the duplex divided by 2.

^bIn this equation, T_m should be in units of K.

^cAs mentioned in Materials and Methods, |ΔT_m|_ave is used here for evaluating the accuracy of the RNA T_m correction factors, and |ΔΔG°₃₇|_ave is used here for evaluating the accuracy of the RNA ΔG°₃₇ correction factors.