Table 1.
Effect of nearest-neighbor sequence context on hMSH2-hMSH6 and mismatch binding kinetics and oligonucleotide melting
| Mismatch | Sequence context | kon (M−1s−1 × 105) | koff (s−1 × 10−3) | KD (M × 10−9) |
Tm,°C |
ΔH, kcal/mol | ΔG, kcal/mol | |
|---|---|---|---|---|---|---|---|---|
| Predicted | Observed | |||||||
| G/T | 2 × 3′ purines | 7.5 (+/−1.6) | 1.4 (+/−0.1) | 1.9 (+/−0.4) | 35.1 | 31.3 (+/−0.5) | 59.6 | 8.9 |
| 2 × 3′ pyrimidines | 9.4 (+/−1.9) | 4.1 (+/−1.2) | 4.6 (+/−2.2) | 35.4 | 31.7 (+/−0.6) | 56.5 | 8.9 | |
| G/T* | 2 × 3′ purines | 37.4 | 34.0 (+/−0.3) | 53.7 | 9.2 | |||
| 2 × 3′ pyrimidines | 45.6 | 42.6 (+/−0.1) | 69.7 | 11.5 | ||||
| C/A | 2 × 3′ purines | 8.7 (+/−1.9) | 5.5 (+/−1.7) | 6.7 (+/−3.5) | 11.9 | 11.7 (+/−2.8) | 34.4 | 5.4 |
| 2 × 3′ pyrimidines | 6.8 (+/−0.1) | 4.6 (+/−0.3) | 6.8 (+/−0.4) | 29.3 | 24.4 (+/−0.5) | 50.0 | 7.7 | |
| G/G | 2 × 3′ purines | 5.1 (+/−0.2) | 4.9 (+/−1.5) | 9.5 (+/−3.2) | 29.4 | 24.9 (+/−0.3) | 55.1 | 7.8 |
| 2 × 3′ pyrimidines | 5.3 (+/−0.6) | 23.1 (+/−0.7) | 43.0 (+/−8.0) | 40.8 | 36.2 (+/−0.4) | 64.1 | 10.2 | |
| G/A | 2 × 3′ purines | 10.7 (+/−1.1) | 7.5 (+/−2.6) | 7.1 (+/−3.2) | 31.5 | 27.5 (+/−0.5) | 57.1 | 8.3 |
| 2 ×3′ pyrimidines | 11.3 (+/−0.1) | 23.6 (+/−0.1) | 20.9 (+/−3.1) | 39.6 | 35.8 (+/−0.2) | 68.4 | 10.3 | |
| A/A | 2 × 3′ purines | 8.6 (+/−0.4) | 12.8 (+/−0.2) | 14.9 (+/−3.6) | 26.5 | 21.0 (+/−0.8) | 45.7 | 7.2 |
| 2 × 3′ pyrimidines | 4.4 (+/−0.5) | 10.1 (+/−0.2) | 23.5 (+/−6.6) | 31.5 | 25.6 (+/−0.2) | 43.6 | 7.9 | |
| C/T | 2 × 3′ purines | 3.9 (+/−0.6) | 28.5 (+/−0.9) | 72.3 (+/−13.0) | 23.3 | 18.6 (+/−1.5) | 42.3 | 6.9 |
| 2 × 3′ pyrimidines | 4.5 (+/−0.2) | 29.1 (+/−0.9) | 65.6 (+/−22) | 24.5 | 19.5 (+/−0.1) | 38.4 | 6.9 | |
| T/A | 2 × 3′ purines | 41.5 | 38.3 (+/−0.5) | 65.8 | 10.5 | |||
| 2 × 3′ pyrimidines | 45.7 | 42.7 (+/−0.4) | 73.7 | 11.7 | ||||
| G/C | 2 × 3′ purines | 4.1 (+/−0.5) | 63.0 (+/−5.8) | 146.6 (+/−6.8) | 50.3 | 47.4 (+/−0.2) | 72.1 | 12.6 |
| 2 × 3′ pyrimidines | 49.1 | 46.4 (+/−0.1) | 78.1 | 12.9 | ||||
*The 2 × 3′ purine context is CxG, and the 2 × 3′ pyrimidine context is GxC.