Table 3.
Thermodynamic profile obtained for sequences with loop length of 10–14
| Oligo Name | Gene | Total | Quadruplexa |
Duplexb |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Tm (°C) | ΔH (kcal/mol) | ΔS (cal/mol/K) | ΔG37 (kcal/mol) | Tm (°C) | ΔH (kcal/mol) | ΔS (cal/mol/K) | ΔG37 (kcal/mol) | ΔΔG37 (kcal/mol) | |||
| Q21 | c-MYC | 10 | 75.0 | −32.6 ± 0.4 | −95.0 ± 1.0 | −3.2 ± 0.1 | 75.8 | −169.6 | −458.6 | −27.4 | −24.3 |
| Q22 | NFKB 2 | 10 | 75.0 | −42.0 ± 0.3 | −119.0 ± 0.7 | −5.1 ± 0.1 | 87.1 | −194.2 | −511.6 | −35.6 | −30.5 |
| Q23 | GLI 1 | 10 | 73.5 | −44.6 ± 0.3 | −129.0 ± 0.7 | −4.6 ± 0.1 | 81.6 | −178.7 | −476.3 | −31.0 | −26.4 |
| Q24 | HCK | 10 | 52.0 | −39.0 ± 0.8 | −119.5 ± 2.5 | −2.0 ± 0.03 | 76.7 | −174.2 | −470.4 | −28.4 | −26.4 |
| Q25 | HCK | 10 | 62.4 | nd | 76.7 | −174.2 | −470.4 | −28.4 | nd | ||
| Q26 | YES 1 | 11 | 66.0 | nd | 77.3 | −180.6 | −488.0 | −29.4 | nd | ||
| Q27 | AKT 1 | 11 | 57.3 | nd | 85.5 | −197.8 | −524.0 | −35.4 | nd | ||
| Q28 | BCL 2 | 11 | 66.6 | nd | 80.4 | −186.7 | −500.6 | −31.5 | nd | ||
| Q29 | NOTCH 1 | 11 | 70.0 | nd | 79.1 | −191.0 | −514.8 | −31.4 | nd | ||
| Q30 | c − KIT | 11 | 71.6 | −29.0 ± 0.2 | −82.0 ± 0.4 | −3.6 ± 0.1 | 80.4 | −183.2 | −490.75 | −31.1 | −27.5 |
| Q31 | JUNB | 11 | 70.0 | nd | 79.3 | −185.2 | −498.0 | −30.8 | nd | ||
| Q32 | SRC | 11 | 57.2 | nd | 76.5 | −183.0 | −496.0 | −29.3 | nd | ||
| Q33 | VAV 2 | 11 | 80.8 | nd | 78.7 | −187.3 | −504.8 | −30.8 | nd | ||
| Q34 | AKT 2 | 11 | 87.0 | −66.0 ± 1.8 | −182.0 ± 5.1 | −9.6 ± 0.2 | 82.4 | −182.3 | −485.2 | −32.0 | −22.3 |
| Q35 | MYB | 11 | 87.0 | −80.8 ± 2.3 | −227.0 ± 6.2 | −10.0 ± 0.4 | 83.1 | −186.4 | −495.8 | −32.7 | −22.3 |
| Q36 | ROS 1 | 11 | 77.5 | −70.0 ± 1.0 | −198.0 ± 2.6 | −8.6 ± 0.2 | 73.4 | −176.5 | −481.8 | −27.1 | −18.5 |
| Q37 | TAL 1 | 12 | 81.2 | nd | 86.3 | −201.4 | −532.8 | −36.2 | nd | ||
| Q38 | WNT1 | 12 | 75.0 | −36.8 ± 0.3 | −104.7 ± 0.7 | −4.3 ± 0.1 | 84.4 | −195.6 | −519.7 | −34.5 | −30.2 |
| Q39 | CTTN | 12 | 78.7 | nd | 82.8 | −202.7 | −542.0 | −34.7 | nd | ||
| Q40 | AXL | 12 | 74.0 | −45.4 ± 0.4 | −130.0 ± 1.0 | −5.2 ± 0.1 | 81.2 | −201.3 | −540.6 | −33.7 | −28.6 |
| Q41 | FGF 3 | 12 | 65.8 | −38.0 ± 0.8 | −111.0 ± 2.2 | −3.6 ± 0.1 | 74.8 | −195.9 | −535.6 | −30.0 | −26.3 |
| Q42 | MAF | 13 | 70.0 | nd | 78.6 | −196.9 | −532.3 | −32.0 | nd | ||
| Q43 | MPL | 13 | 66.8 | nd | 77.2 | −195.8 | −531.5 | −31.0 | nd | ||
| Q44 | MYB | 13 | 67.0 | nd | 83.3 | −210.3 | −562.6 | −36.0 | nd | ||
| Q45 | ABL 1 | 13 | 75.0 | −74.0 ± 5.0 | −210.5 ± 14 | −8.7 ± 0.7 | 80.2 | −200.3 | −539.4 | −33.1 | −24.4 |
| Q46 | MYEOV | 13 | 63.8 | −109.0 ± 9 | −330.0 ± 20 | −6.7 ± 2.0 | 69.8 | −190.9 | −529.3 | −26.8 | −20.1 |
| Q47 | VEGF | 13 | 64.0 | −34.6 ± 1.1 | −102.6 ± 3.4 | −2.8 ± 0.1 | 73.0 | −199.0 | −547.4 | −29.2 | −26.4 |
| Q48 | FLI 1 | 14 | 71.0 | −27.0 ± 0.2 | −78.0 ± 0.5 | −3.0 ± 0.1 | 77.4 | −201.5 | −547.3 | −31.8 | −28.8 |
| Q49 | FGR | 14 | 58.5 | −33.6 ± 0.2 | −102.4 ± 0.6 | −1.8 ± 0.01 | 77.7 | −208.0 | −565.4 | −32.7 | −31.0 |
| Q50 | WNT 3 | 14 | 70.0 | nd | 84.2 | −215.1 | −574.5 | −37.0 | nd | ||
| Q51 | CSF 1R | 14 | 65.0 | nd | 78.7 | −207.9 | −563.5 | −33.2 | nd | ||
| Q52 | THRA | 14 | 83.0 | −54.1 ± 0.6 | −152.0 ± 1.6 | −6.8 ± 0.1 | 88.6 | −219.5 | −579.3 | −40.0 | −33.2 |
| Q53 | FES | 14 | 68.0 | −34.0 ± 0.3 | −98.2 ± 0.7 | −3.5 ± 0.1 | 86.8 | −217.2 | −576.0 | −38.6 | −35.1 |
| Q54 | REL | 14 | 63.7 | nd | 82.7 | −213.7 | −573.2 | −36.0 | nd | ||
aThermodynamic profiles for quadruplexes (2 µM) obtained from UV melting performed in 10 mM sodium cacodylate buffer, 100 mM KCl, pH 7.4. Tm values differed by ±1.5°C. Thermodynamic parameters were determined by non-linear least square curve fitting (Details in Materials and method section). nd, not determined. Thermodynamic profile of mixed quadruplex conformation was not calculated.
bPredicted thermodynamic parameters for duplex formed by all sequences obtained through HYTHER (ozone2.chem.wayne.edu) using experimental conditions of 2 µM strand concentration and 100 mM monovalent cations.