Table 1.
Effects of synthetic peptides and depsipeptides on RNA duplex thermal stability.
| Entry | Sequence | # Cationic residues | RNA duplex 1 ΔTm (°C) | RNA duplex 2 ΔTm (°C) | RNA duplex 3 ΔTm (°C) | H26a RNA ΔTm (°C) |
|---|---|---|---|---|---|---|
| 1 | Ac-Lys-NH2 (1 mM) | +1 | 0.0 | |||
| 2 | Ac-Tyr-Gly-Ala-Dab-Lys-NH2 (400 μM) | +2 | −0.1 | −0.2 | −1.1 | 1.3 |
| 3 | Ac-Tyr-Gly-Ala-Dab-Lys-Ala-Dab-Lys-NH2 (200 μM) | +4 | 0.7 | |||
| 4 | Ac-Tyr-Gly-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-NH2 (133 μM) | +6 | 3.4 | |||
| 5 | Ac-Tyr-Gly-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-NH2 (100 μM) | +8 | 8.1 | 9.5 | ||
| 6 | Ac-Tyr-Gly-Ala-Dab-Lys-lac-Dab-Lys-lac-Dab-Lys-lac-Dab-Lys-NH2 (14) | +8 | 8.6 | 9.1 | 10.0 | 10.4 |
| 7 | Ac-Tyr-Gly-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys NH2 (80 μM) | +10 | 9.6 | |||
| 8 | Aba-Gly-Ala-Dab-Lys-Ala-Dab-Arg-lac-Dab-Lys-Ala-Dab-Lys-NH2 (7) | +8 | 8.7 | 8.1 | 12.0 | 11.4 |
| 9 | Aba-Gly-Ala-Dab-Lys-Ala-Dab-His-lac-Dab-Lys-Ala-Dab-Lys-NH2 (8) (pH 5.0) | +8 | 11.1 | |||
| 10 | Aba-Gly-Ala-Dab-Lys-Ala-Dab-His-lac-Dab-Lys-Ala-Dab-Lys-NH2 (8) (pH 7.0) | +8 | 5.1 | |||
| 11 | Aba-Gly-Ala-Dab-Lys-Ala-Dab-Lys-lac-Dab-Lys-Ala-Dab-Lys-NH2 (9) | +8 | 10.4 | 8.2 | 9.9 | 11.5 |
| 12 | Aba-Gly-Ala-Dab-Lys-Ala-Dab-Orn-lac-Dab-Lys-Ala-Dab-Lys-NH2 (10) | +8 | 4.9 | 8.2 | 2.5 | 3.5 |
| 13 | Aba-Gly-Ala-Dab-Lys-Ala-Dab-Dab-lac-Dab-Lys-Ala-Dab-Lys-NH2 (11) | +8 | 4.9 | |||
| 14 | Aba-Gly-Ala-Asp-Glu-Ala-Asp-Lys-lac-Asp-Glu-Ala-Asp-Glu-NH2 | −6 | 0.3 | 0.7 | −1.5 | 1.1 |
| 15 | Aba-Arg-Ala-Arg-Ala-Arg-Ala-Arg-Ala-Arg-Ala-Arg-Ala-Arg-Ala-Arg-Ala-NH2 | +8 | 5.9 | |||
| 16 | Aba-Arg-lac-Arg-lac-Arg-lac-Arg-lac-Arg-lac-Arg-lac-Arg-lac-Arg-lac-NH2 (2) | +8 | 5.3 | |||
| 17 | Aba-His-Ala-His-Ala-His-Ala-His-Ala-His-Ala-His-Ala-His-Ala-His-Ala-NH2 (pH 5.0) | +8 | 4.2 | |||
| 18 | Aba-His-lac-His-lac-His-lac-His-lac-His-lac-His-lac-His-lac-His-lac-NH2 (3) (pH 5.0) | +8 | 4.6 | |||
| 19 | Aba-His-lac-His-lac-His-lac-His-lac-His-lac-His-lac-His-lac-His-lac-NH2 (3) (pH 7.0) | +8 | 0.5 | |||
| 20 | Ac-Tyr-Gly-Lys-Ala-Lys-Ala-Lys-Ala-Lys-Ala-Lys-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH2 | +8 | 3.1 | 3.0 | 4.5 | 4.1 |
| 21 | Aba-Lys-lac-Lys-lac-Lys-lac-Lys-lac-Lys-lac-Lys-lac-Lys-lac-Lys-lac-NH2 (4) | +8 | 2.6 | 1.5 | 3.9 | 6.3 |
| 22 | Ac-Tyr-Gly-Orn-Ala-Orn-Ala-Orn-Ala-Orn-Ala-Orn-Ala-Orn-Ala-Orn-Ala-Orn-Ala-NH2 | +8 | 4.5 | 7.6 | 8.3 | 9.0 |
| 23 | Aba-Orn-lac-Orn-lac-Orn-lac-Orn-lac-Orn-lac-Orn-lac-Orn-lac-Orn-lac-NH2 (5) | +8 | 0.0 | 1.0 | 0.5 | −1.1 |
| 24 | Ac-Tyr-Gly-Dab-Ala-Dab-Ala-Dab-Ala-Dab-Ala-Dab-Ala-Dab-Ala-Dab-Ala-Dab-Ala-NH2 | +8 | 6.9 | 8.0 | 11.0 | 10.3 |
| 25 | Aba-Dab-lac-Dab-lac-Dab-lac-Dab-lac-Dab-lac-Dab-lac-Dab-lac-Dab-lac-NH2 (6) | +8 | 0.4 | 2.6 | −0.4 | 0.5 |
| 26 | Ac-Tyr-Gly-Dpr-Ala-Dpr-Ala-Dpr-Ala-Dpr-Ala-Dpr-Ala-Dpr-Ala-Dpr-Ala-Dpr-Ala-NH2 | +8 | 0.9 | |||
| 27 | 5-FAM-Gly-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys NH2 (12) (80 μM) | +10 | 10.6 | |||
| 28 | 5-FAM-Gly-Ala-Dab-Lys-Ala-Dab-Lys-Ala-Dab-Lys-lac-Dab-Lys-Ala-Dab-Lys NH2 (13) (80 μM) | +10 | 12.2 | |||
| 29 | Ac-Tyr-Gly-Ala-Lys-Lys-Ala-Ala-Lys-Lys-Ala-Ala-Lys-Lys-Ala-Ala-Lys-Lys-Ala-NH2 | +8 | 3.4 | |||
| 30 | Ac-Tyr-Gly-Ala-Dab-Dab-Ala-Ala-Dab-Dab-Ala-Ala-Dab-Dab-Ala-Ala-Dab-Dab-Ala-NH2 | +8 | 6.8 | 8.9 | 9.9 | 8.4 |
| 31 | Ac-Tyr-Gly-Ala-Dab-Dab-Ala-lac-Dab-Dab-Ala-Ala-Dab-Dab-Ala-lac-Dab-Dab-Ala-NH2 | +8 | 7.1 | 7.2 | 10.6 | 10.9 |
| 32 | Ac-Tyr-Gly-Gly-Lys-Lys-Gly-Lys-Lys-Gly-Lys-Lys-Gly-Lys-Lys-NH2 | +8 | 5.8 | |||
| 33 | Ac-Tyr-Gly-Gly-Lys-Lys-Gly-Lys-Lys-Gly-Lys-Lys-Gly-Lys-Lys-NH2 | +8 | 5.8 | |||
| 34 | Ac-Tyr-Gly-Gly-Lys-Lys-Gly-Lys-Lys-Gly-Lys-Lys-Gly-Lys-Lys-NH2 | +8 | 6.3 |
RNA duplex 1 = 5′-rCrGrCrUrArArArUrCrG-3’ & 5’-rCrGrArUrUrUrArGrCrG-3′; RNA duplex 2 = 5′-rArArArArUrUrUrArUrArUrUrArUrUrA-3′ and 5′-rUrArArUrArArUrArUrArArArUrUrUrU-3′; RNA duplex 3 = 5′-rArArCrGrUrArUrArCrGrUrU-3′ (palindromic); H26a RNA = 5′-rArUrGrArGrUrArArCrCrGrUrArArGrGrUrGrArArArUrU-3′. RNA was present in each assay at a final concentration of 2.5 μM of the folded structure (2.5 μM each strand for duplex 1 and duplex 2, 5.0 μM palindromic strand for duplex 3, 2.5 μM strand for H26a RNA). The observed Tm values of the RNA structures alone at pH 7.0 were 43.8 ± 0.4 °C for duplex 1, 33.7 ± 0.7 °C for duplex 2, 48.6 ± 0.7 °C for duplex 3, and 53.4 ± 0.5 °C for H26a RNA. The observed Tm values of RNA duplex 1 alone at pH 5.0 was 41.5 ± 0.3 °C. Unless otherwise noted, the concentration of peptide/depsipeptide was 100 μM and the pH of the measurement was 7.0. Data represent the mean ± SD of 2–4 replicate experiments. The buffers contained 10 mM phosphate, 100 mM NaCl at pH 7.0; or 10 mM acetate, 100 mM NaCl at pH 5.0. Aba = acetamidobenzoic acid, which was appended to the N-terminus of some sequences for improved UV absorbance. Underlined residues denote d-chirality. Lactic acid residues are shown in bold. ΔTm values are the difference in Tm for a given entry compared to the RNA alone at the matched pH value.