Table 1.
Symbol | Definition | Typical value | Reference |
---|---|---|---|
D± | Diffusivity of adsorbed enzymes | 5 × 106 bp2/s | (17) |
υ | Electron velocity | 1010 bp/s | (18) |
f | Electron flip rate | 109–1010 s−1 | ∗ |
m | Electron release rate | ∼106 s−1 | (19) |
Ω | Bacterium volume | 3.7 × 108nm3 | (20) |
L | Length of DNA | 5 × 106 bp | |
kon | MutY2+ attachment rate | 2000 s−1 | (16) |
koff | MutY2+ detachment rate | 7 × 10−3 s−1 | † |
n0 | Copy number of MutY in E. coli | 20–30 | (21,22) |
r | Electron reflectivity of lesions | 0–1 | — |
g0 | Number of oxoGs on E. coli DNA | ∼30 | ‡ |
The mean free path of an electron is estimated to be λ ∼ 1–10 basepairs and the flip rate approximated as υ/λ.
Estimated using the time taken for the restriction endonuclease BsoBI to unbind from DNA (23), toff = 150 s and taking koff = 1/toff. This value of toff may not be an accurate value for the unbinding time for MutY.
Assumes that ∼1 in 40,000 guanine bases are oxoGs (24) and the length of E. coli DNA is L = 5 × 106 bp.