Table 1.
Oligonucleotide sequences and binding free energies to the phylogenetic structure, lowest free energy structure and two suboptimal structures
| Oligonucleotide sequence | Binding site | ΔG°binding to phylogenetic structure (kcal/mol) | ΔG°binding to lowest fee energy structure (kcal/mol) | ΔG°binding to suboptimal structure #1 (kcal/mol) | ΔG°binding to suboptimal structure #2 (kcal/mol) | ΔG°binding to suboptimal structure #3 (kcal/mol) | ΔG°binding to suboptimal structure #4 (kcal/mol) | RNase H cleavage observed using a single sequence? | RNase H cleavage observed in this region using randomized oligonucleotides? |
|---|---|---|---|---|---|---|---|---|---|
| 5-mers | |||||||||
| GTTTC | 56–60 | 4.1 | 3.2 | 1.7 | –0.4 | –1.9 | 3.9 | No | No |
| ATCGG | 70–74 | 1.0 | –0.5 | 3.2 | 1.1 | –0.5 | 3.4 | No | No |
| 6-mers | |||||||||
| GGGACC | 23–28 | –0.2 | –3.5 | –3.5 | 2.1 | 2.1 | 2.1 | No | Yes |
| ACTTCT | 50–54 | 5.5 | –2.3 | 3.1 | –3.5 | –3.5 | –3.5 | No | No |
| CTACCA | 74–79 | 2.1 | 10.0 | 2.5 | 2.1 | 9.7 | 0.2 | No | No |
| CTCTCG | 97–102 | 2.2 | –0.3 | –0.3 | 2.2 | 9.2 | –0.3 | No | No |
| 7-mers | |||||||||
| GCCAGGC | 2–8 | 15.6 | 15.6 | 15.6 | 15.6 | 15.6 | 15.6 | No | No |
| AGGTGGG | 26–32 | –0.3 | 1.7 | 1.7 | –4.0 | –2.3 | –4.0 | No | No |
| CGGCATG | 38–44 | –6.4 | 4.9 | 4.0 | 2.6 | 3.3 | 2.6 | Yes | Yes |
| AGTTCGG | 42–48 | –4.7 | 1.0 | 0.3 | –0.1 | 5.4 | 0.2 | Yes | Yes |
| 8-mers | |||||||||
| CATGGGGT | 34–41 | –7.4 | 14.5 | 14.5 | 10.0 | 4.8 | 10.0 | Yes | Yes |
‘Binding site’ indicates the nucleotides in the E. coli 5S rRNA to which the oligonucleotide probe is complementary. All ΔG°binding values were generated using the OligoWalk program in ‘break local’ structure mode. Observation of RNase H cleavage is indicated for each oligonucleotide.