Stacking interactions between nucleic acid bases help stabilize nucleic acid structure.  Also, stacking interactions between DNA bases and intercalators are important because intercalators have been shown to be valuable anti-cancer agents.  In order to help understand substituent-substituent interactions in DNA/RNA-intercalator binding, multiple duplexes were melted in the presence of naphthalimides with various substituents at the 3-position.  A traditional QSAR analysis was performed using an electronic parameter and a dispersion/polarizability parameter to generate a theoretical ?TM value.  This was then compared to a QSAR analysis utilizing a novel arene-arene parameter.  The results show that the novel arene-arene parameter correlates equally well or better than the traditional two parameter QSAR analysis.

Predicting DNA-intercalator binding: An application of a new arene-arene stacking parameter

243rd National Meeting (2012)

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