Figure 11.
Given here are time plots of the PCA first- and second eigenvalues and distribution of the projections of the conformations onto the first principal component axis for the backbone corresponding to internal mismatches in DNA. Considered here are the residues 4–9 on one strand and the complementary residues 16–21 on the other. (Left column) DNA-(CAG)4; (right column) DNA-(GAC)4. (Black) First eigenvalue; (red) second eigenvalue. Initial conformations for the MD runs are as follows: (a) anti-anti, (b) anti-syn, and (c) syn-syn. To see this figure in color, go online.