The Stability of a Model Substrate for Topoisomerase 1-Mediated DNA Religation Depends on the Presence of Mismatched Base Pairs
Figure 6
(a) Overall conformations adopted in the four clusters. The first ten base pairs of the centroids of each of the four clusters are shown in VMD’s NewRibbon format. Cluster 1 (see Table 2 for numbering) is blue, cluster 2 is red, cluster 3 is gray, and cluster 4 is orange. (b) Conformations near the mismatched site in the four clusters. The two base pairs of the centroids of each of the four clusters downstream from the mismatched site are shown in VMD’s New Ribbon format. Cluster 1 (see Table 2 for numbering) is blue, cluster 2 is red, cluster 3 is gray, and cluster 4 is orange. (c) Overall conformations of cluster 2 and cluster 4. The first ten base pairs of the centroids of each of the most common and the rarest clusters for matched DNA are shown in VMD’s NewRibbon format. Cluster 2 (see Table 2 for numbering) is red and cluster 4 is orange.
