Table 2.
Thermodynamic profiles obtained for sequences with loop length of 5–9
| 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) | |||
| Q1 | VEGF | 5 | 80.8 | −50.6 ± 0.5 | −142.1 ± 1.4 | −6.5 ± 0.1 | 66.0 | −129.5 | −353.8 | −19.8 | −13.3 |
| Q2 | WNT 3 | 5 | 86.0 | −101.5 ± 2.5 | −277.0 ± 5.0 | −15.6 ± 0.1 | 75.6 | −136.6 | −364.2 | −23.7 | −8.1 |
| Q3 | WNT5A | 5 | 65.0 | −44.0 ± 0.8 | −130 ± 2.4 | −3.7 ± 0.1 | 66.2 | −129.8 | −355.1 | −19.7 | −16.0 |
| Q4 | PDGFB | 6 | 83.0 | −70.0 ± 1.2 | −195.0 ± 3.4 | −9.6 ± 0.2 | 69.1 | −139.7 | −380.7 | −21.7 | −12.1 |
| Q5 | JUNB | 6 | 77.7 | −26.0 ± 0.1 | −73.5 ± 0.3 | −3.3 ± 0.02 | 78.0 | −145.5 | −386.8 | −25.6 | −22.3 |
| Q6 | TAL1c | 6 | 80.0 | nd | 77.4 | −141.1 | −375.0 | −24.8 | nd | ||
| Q7 | THPOc | 6 | 82.0 | nd | 70.6 | −136.7 | −370.3 | −22.0 | nd | ||
| Q8 | FOS | 7 | 72.4 | −30.7 ± 0.3 | −87.7 ± 0.8 | −3.5 ± 0.1 | 70.1 | −146.0 | −397.6 | −22.6 | −19.1 |
| Q9 | PIM1 | 7 | 82.8 | −71.3 ± 1.2 | −200.0 ± 3.3 | −9.3 ± 0.2 | 82.5 | −157.0 | −414.0 | −28.7 | −19.4 |
| Q10 | FGF 3 | 7 | 62.0 | −23.3 ± 0.3 | −69.2 ± 0.8 | −1.8 ± 0.1 | 72.9 | −147.6 | −399.1 | −24.0 | −22.1 |
| Q11 | FES | 7 | 58.0 | −53.0 ± 0.5 | −160.0 ± 1.1 | −3.4 ± 0.2 | 70.7 | −146.8 | −399.5 | −23.0 | −19.5 |
| Q12 | VAV1 | 7 | 62.8 | −17.7 ± 0.2 | −48.0 ± 0.5 | −2.8 ± 0.1 | 68.5 | −146.7 | −402.0 | −22.1 | −19.3 |
| Q13 | IGF2 | 8 | 59.6 | −30.6 ± 0.3 | −91.0 ± 0.8 | −2.4 ± 0.1 | 74.0 | −159.1 | −431.0 | −25.5 | −23.1 |
| Q14 | FOSL1 | 8 | 73.7 | −36.0 ± 0.2 | −101 ± 0.5 | −4.7 ± 0.1 | 81.9 | −167.1 | −443.2 | −29.7 | −25.0 |
| Q15 | TAL1 | 8 | 81.5 | −43.8 ± 0.4 | −123.7 ± 1.0 | −5.4 ± 0.1 | 84.3 | −169.4 | −446.5 | −31.0 | −25.6 |
| Q16 | AKT2c | 8 | 88.0 | nd | 80.3 | −156.2 | −414.5 | −27.7 | nd | ||
| Q17 | THRAc | 8 | 81.6 | nd | 83.9 | −165.0 | −434.7 | −30.2 | nd | ||
| Q18 | FBXW 7 | 8 | 75.8 | −31.0 ± 0.9 | −89.0 ± 2.3 | −3.4 ± 0.2 | 83.9 | −165.0 | −434.7 | −30.2 | −26.8 |
| Q19 | HRAS | 9 | 53.7 | −28.1 ± 0.3 | −85.2 ± 0.7 | −1.7 ± 0.1 | 77.6 | −167.2 | −449.2 | −28.0 | −26.2 |
| Q20 | WNT1 | 9 | 50.0 | −46.0 ± 1.5 | −141.5 ± 4.7 | −2.1 ± 0.1 | 68.1 | −161.6 | −446.0 | −23.3 | −21.2 |
aThermodynamic profiles for quadruplexes (2 µM) obtained from UV experiment 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).
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.
cnd, not determined. The sequences shown are those which displayed predominantly one conformation in CD and gel studies, and concentration independent Tm.