TABLE 1.
Summary of ODMiR inhibition of pre-tRNA processing by E. coli RNase P and predicted ΔG°37’s of oligonucleotides binding to E. coli RNase P RNA by the OligoWalk program when RNA refolding is allowed
| Oligonucleotide | Region of complementarity | 10 μM DNA OligoWalk ΔG°37 | Pre-tRNA processing as percentage of control (10 μM DNA) | 1 μM RNA OligoWalk ΔG°37 | Pre-tRNA processing as percentage of control (1 μM 2′-O-Me RNA) | IC50 (μM) of 2′-O-Me oligo |
|---|---|---|---|---|---|---|
| Oligonucleotides that inhibita | ||||||
| CGGACTTTCCTC | 61–72 | −5.8 | 55 | −11.4 | 49 | ~1 |
| TCACCCTTACCT | 196–180 | −10.5 | 53 | −15.7 | 44 | ~1 |
| TACCGCACCCTT | 181–192 | −8.6 | 40 | −13.8 | 54 | ~1 |
| GTTACCAGCCGC | 205–216 | −6.4 | 33 | −11.8 | 71 | ~3 |
| GTGCCACGGACT | 217–228 | −4.7 | 54 | −11.4 | 86 | ~10 |
| AACCCCTATTTG | 253–264 | −4.8 | 32 | −9 | 66 | ~10 |
| CCGTACCTTATG | 265–276 | −4.2 | 41 | −8.9 | 44 | ~1 |
| ACCCGGGTTCAG | 283–294 | −11.7 | 49 | ~1 | ||
| CAGCCTACCCGG | 289–300 | −9.5 | 51 | −16.1 | 15 | ~0.2 |
| CAGCCTACCC | 291–302 | −14.4 | 67 | ~2 | ||
| CTCAAGCAGCCT | 295–306 | −19.9 | 48 | ~1 | ||
| TCAAGCAGCCT | 296–305 | −18.8 | 96 | ~10 | ||
| Oligonucleotides that do not inhibit | ||||||
| CTGGTCAGCTTC | 1–12 | −1.3 | 81 | −7.1 | N.D.b | N.D. |
| AGCGGCGACTGT | 13–24 | −5.8 | 95 | −13.4 | N.D.b | N.D. |
| GGACGACGACGA | 25–36 | 5.2 | 92 | −5.2 | N.D.b | N.D. |
| CTCCCCCGAAGA | 37–48 | −3.2 | 93 | −9.6 | N.D.b | N.D. |
| CCCTCCGCCCGT | 49–60 | −8.9 | 89 | −13.5 | N.D.b | N.D. |
| CCCTATGGAGCC | 73–84 | −9.1 | 85 | −15.7 | N.D.b | N.D. |
| CCTGGCACCCTG | 85–96 | −5.7 | 85 | −12.4 | N.D.b | N.D. |
| CCCCAGGCGTTA | 97–108 | −4.9 | 104 | −10.1 | N.D.b | N.D. |
| CGTGGGTTTCCC | 109–120 | −7.2 | 100 | −12.4 | N.D.b | N.D. |
| TGTTGCACTGGT | 121–132 | −7.8 | 104 | −14.3 | N.D.b | N.D. |
| CGGTTTGCTCTC | 133–144 | −12.1 | 87 | −17.6 | N.D.b | N.D. |
| GCGGGCCATCGG | 145–156 | −5.7 | 80 | −13.2 | N.D.b | N.D. |
| GATCCCGCTTGC | 157–168 | −6.2 | 87 | −11.7 | N.D.b | N.D. |
| GCGGTGCGCTCT | 193–204 | −5.9 | 99 | −12.5 | N.D.b | N.D. |
| GTGGAGTTTACC | 229–240 | −5.5 | 68 | −10.7 | N.D.b | N.D. |
| GCCTTGCTCCGG | 241–252 | −7.7 | 100 | −13.6 | N.D.b | N.D. |
| GTTCAGTACGGG | 277–288 | −4.7 | 98 | −11.5 | N.D.b | N.D. |
| CACTGGCTCAAG | 301–312 | −6.0 | 68 | −13.8 | N.D.b | N.D. |
| CCAGCAATCGCT | 313–324 | −7.0 | 94 | −13.0 | N.D.b | N.D. |
| CATTCATCTAGG | 325–336 | −9.3 | 81 | −15.2 | N.D.b | N.D. |
| GTCGTGGACAGT | 337–348 | −8.9 | 87 | −16.0 | N.D.b | N.D. |
| AAGCCGGGTTCT | 349–360 | −7.4 | 63 | −13.4 | N.D.b | N.D. |
| AAACTGACCGAT | 361–372 | −1.9 | 90 | −9.1 | N.D.b | N.D. |
| AGGTGAAACTGA | 366–377 | 1.2 | 99 | −8.1 | N.D.b | N.D. |
| GCACTGTCT | 11–19 | −11.4 | 101 | N.D. | ||
| TCCTCCC | 59–65 | −5.6 | 99 | N.D. | ||
| TATGGAGCCCG | 71–81 | −13.4 | 102 | N.D. | ||
| TATGGAG | 75–81 | −4.9 | 89 | N.D. | ||
| CCTGCCCTAT | 79–88 | −8.9 | 63 | N.D. | ||
| CCATCGGC | 144–151 | −10.5 | 101 | N.D. | ||
| CTTACCTGAT | 166–175 | −9.7 | 101 | N.D. | ||
| CTATTTGGCC | 250–259 | −13.6 | 98 | N.D. | ||
aT is replaced by U for 2′-O-Me sequences.
b(N.D.) not determined.