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. Author manuscript; available in PMC: 2011 Jan 25.
Published in final edited form as: J Mol Biol. 2009 Jul 22;392(5):1145–1157. doi: 10.1016/j.jmb.2009.07.048

Figure 5.

Figure 5

Influence of base stacking on nucleophilic attack and exciplex formation in duplex DNA. A) View down helix axis from 3'-end, and B) a side view of a AT=TA cyclobutane dimer (PDB File 1NE4)36 showing that the 5'-A can stack on top of the 5'-T of the dimer and block attack of water, whereas the 3'-A does not stack on the 3'-T and cannot block attack of water. C) View from 3'-end of a ATTA site in duplex DNA (PDB File 1D49) 49 showing significantly more base stacking between the 5'-A and the 5'-T than for the 3'-A with the 3'-T.

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