Many biological recognition events involve extensive interactions between macromolecules. Strategies to design compounds that mimic large peptides or other elements of secondary structure could be useful for blocking interactions between large surfaces. In this paper, the use of oligosaccharides as scaffolds for the design of peptidomimetics is addressed. A functionalized oligosaccharide modeled after a basic region peptide helix has been designed and synthesized. This oligosaccharide binds to duplex DNA with micromolar affinity. The mode of binding has been established by 2D NMR, and shows that the oligosaccharide binds DNA in the minor groove with one surface of the oligosaccharide contacting the floor of the DNA.

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