Table 2.

Positions of RNase H cleavage of yeast tRNA^Phe with randomized 5-mer oligonucleotides after a 1 or 2 h incubation and the corresponding ΔG°_binding values for the phylogenetic and suboptimal structures

Cleavage position	Phylogenetic structure ΔG°binding (kcal/mol)	Suboptimal structure #2 ΔG°binding (kcal/mol)	Suboptimal structure #3 ΔG°binding (kcal/mol)	Suboptimal structure #4 ΔG°binding (kcal/mol)
18	−4.1	2.9	−4.1	1.7
19	−5.2	0.4	−5.2	0.6
20	−1.1	−2.0	−1.1	6.9
21	2.0	−0.4	2.0	6.3
34	−1.9	10.1	−1.3	3.7
35	−2.2	8.6	−2.2	−0.4
36	−1.9	9.2	−1.9	−1.9
45	−0.1	1.7	5.8	2.6
48	2.1	8.8	3.8	9.6
56	−1.2	−1.2	4.4	6.4
58	−1.9	−1.9	3.1	7.4
59	0.5	0.5	2.7	5.7

The ΔG°_binding values are for the oligonucleotides in which the nucleotide where cleavage occurs is the middle nucleotide of the resulting duplex.