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. Author manuscript; available in PMC: 2011 Nov 23.
Published in final edited form as: Biochemistry. 2010 Oct 28;49(46):9943–9945. doi: 10.1021/bi101560y

Figure 2.

Figure 2

(a) the DB[a,l]P aromatic ring system acts as a “bridge” between the two DNA strands through stacking interactions with base T88 of the partner strand (See also Movie S2, Supporting Information). (b) van der Waals stacking interactions involving the DB[a,l]P aromatic ring system and all bases (A203, T88, A204 and G87) comprising the intercalation pocket, and interactions of the same bases in the unmodified NCP (see also Table S1, Supporting Information). Ensemble average values and standard deviations are given. (c) Hydrogen bond quality index (IH) (See Supporting Information) at designated base pairs in the modified and unmodified NCP showing the better hydrogen bond quality at the lesion site in the modified NCP. The larger IH corresponds to more disturbed hydrogen bonding.