Fig. 4.

DNA sequence context changes the current difference pattern when a modified cytosine replaces a cytosine at a CpG site. Shown are the current difference patterns caused by the sequence XY^mCpG in A or XY^hCpG in B, where X and Y are any of the four nucleotides A, C, G, and T. The rightmost column and bottom row of each figure display the current differences averaged over the nucleotides X or Y, respectively, and the bottom right box displays the average current difference for all studied sequence contexts. Both the amplitude and the shape of current difference change with sequence context. (A) The maximum difference reaches 7 pA for AA^mCpG and is only 1–2 pA when XY contains a thymine. The average maximum difference is ∼2 pA. The number of levels showing a significant current difference varies from 3 to 5. The difference is maximal when the ^mC is immediately above the constriction and the distribution is skewed. (B) Current deviations due to ^hC are more complex. Generally, when the ^hC is centered within MspA’s constriction, the difference is −2 to −1 pA. However, some contexts involve positive differences. The differences associated with sequences containing XT^hCpG, XA^hCpG, AY^hCpG, and CY^hCpG are small, with only ∼1σ differences. As seen for ^mC, difference patterns caused by ^hC involve between 3 and 5 levels and are also skewed. The average difference patterns due to ^mC and ^hC are similar; both difference patterns map out a single tight recognition site within MspA’s constriction (Fig. 5).