Table 1 Measured thermodynamic and kinetic parameters of DNA-intercalating cyanine dyes.
Dye | [NaCl] (M) | Equilibrium | Dissociation* | Association* | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
|  |  | K0 (M−1) | n (bp) | Δ x eq (nm) | Φ eq (pN) | k off,0 −1 (s) | Δ x off (nm) | Φ off (pN) | kon,0 (M−1s−1) | Δ x on (nm) | Φ on (pN) |
YO | 0.1 | (2.9±0.9) × 105 | 3.8±1.0 | 0.31±0.03 | 13.1 | 0.009±0.004 | 0.28±0.04 | 14.6 | (3.2±1.7) × 107 | 0.03±0.05 | 151 |
|  | 1.0 | (3.4±0.9) × 103 | 2.1±0.6 | 0.35±0.03 | 11.7 | †| †| †| †| †| †|
SxO | 0.1 | (2.4±0.5) × 106 | 3.0±0.4 | 0.30±0.02 | 13.5 | 0.31±0.08 | 0.24±0.04 | 17.4 | (7.9±2.6) × 106 | 0.07±0.04 | 63 |
|  | 1.0 | (4.4±0.7) × 104 | 2.4±0.6 | 0.32±0.01 | 13.0 | 0.23±0.02 | 0.14±0.02 | 28.4 | (2.0±0.3) × 105 | 0.18±0.02 | 23 |
SbG | 0.1 | (7.8±3.3) × 106 | 3.2±0.5 | 0.30±0.01 | 13.9 | 0.61±0.17 | 0.28±0.03 | 14.5 | (1.2±0.6) × 107 | 0.02±0.03 | 173 |
|  | 1.0 | (4.5±1.2) × 105 | 2.1±0.5 | 0.35±0.03 | 11.9 | 0.21±0.05 | 0.23±0.04 | 17.9 | (2.1±0.8) × 106 | 0.12±0.05 | 33 |
SxG | 0.1 | (1.4±0.3) × 107 | 2.6±0.6 | 0.27±0.02 | 15.5 | 0.51±0.24 | 0.31±0.05 | 13.2 | (2.6±1.1) × 107 | −0.04±0.05 | −118 |
|  | 1.0 | ‡ | ‡ | ‡ | ‡ | ‡ | ‡ | ‡ | ‡ | ‡ | ‡ |
YOYO | 0.1 | § | § | § |  | 48±17 | 0.61±0.10 | 6.8 | § | § | § |
|  | 1.0 | (2.8±1.4) × 104 | 4.7±0.7 | 0.71±0.04 | 5.8 | 0.09±0.06 | 0.58±0.07 | 7.1 | (3.3±2.8) × 105 | 0.13±0.08 | 31 |
POPO | 0.1 | (8.5±6.0) × 104 | 6.5±2.3 | 0.55±0.07 | 7.5 | 0.10±0.06 | 0.56±0.11 | 7.3 | (6.1±5.7) × 105 | 0.02±0.16 | 230 |
|  | 1.0 | (9.5±6.6) × 102 | 4.8±0.7 | 0.67±0.06 | 6.1 | 0.05±0.02 | 0.46±0.26|| | 8.8|| | (1.2±1.0) × 104 | 0.29±0.27|| | 14.1|| |
- *Δxoff/on=kBT/
off/on. - †koff,0 is too fast to be measured (koff,0−1<<0.01 s).
- ‡K0 is too low to be measured.
- §Equilibration is too slow to measure K0.
- ||Because koff exhibited a nonexponential force dependence at high force, data fitting was restricted to 0<F≤24 pN (Fig. 5h).
off/on.