Foldamers provide a great opportunity for biomolecules' surface recognition. There are many experimental studies on binding of synthetic oligomers to the DNA minor groove. We are currently working on optimizing an oligoamide mimic of naturally occurring distamycin, which is capable of non-covalently binding to specific sequences in DNA.A number of human cancers are caused by the overexpression of transcription factors leading to an anomalous gene expression. Therefore ligands that are capable of binding DNA in a sequence specific manner and interrupting transcription factor-DNA interactions are of a great interest. We apply computational methods to optimize the design of oligoamides experimentally shown to bind to DNA, by evaluating the influence of the shape of the oligoamide on binding affinity and selectivity as well as the dynamics of DNA upon oligoamide binding. Our aim is to design an oligoamide with appropriate affinity and selectivity for further experimental studies.

Computational design and evaluation of DNA-binding foldamers

243rd National Meeting (2012)

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