Table 2.

Stacking proficiency of base analogues, as measured by thermodynamic data for self-complementary duplexes containing a 5′ dangling modified base. Sequence is 5′-dXCGCGCG.^a

dangling base	Tmb (°C)	ΔG°37c (kcal/mol)	ΔΔG°37d (kcal/mol)
(none)	41.7 ± 0.5	-8.1 ± 0.2	---
yyT	66.3 ± 0.5	-12.5 ± 0.3	-4.4 ± 0.5
yyC	60.8 ± 0.5	-11.1 ± 0.7	-3.0 ± 0.9
yTe	56.6 ± 0.5	-10.9 ± 0.1	-2.8 ± 0.3
yCe	53.4 ± 0.5	-9.7 ± 0.2	-1.6 ± 0.4
Te	50.0 ± 0.5	-9.2 ± 0.5	-1.1 ± 0.7
Ce	47.8 ± 0.5	-9.3 ± 0.2	-1.2 ± 0.4

^aConditions: 1 M NaCI, 10 mM phosphate (pH 7.0) with 0.1 mM EDTA.

^bT_m values are for 5.0 μM oligonucleotide.

^cAverages of values from van't Hoff and curve fitting methods.

^dValues per each dangling base, relative to the core duplex.

^eData from ref. 8b.