Bridging the

From our initial studies we had learned that recognition of peptides and their discrimination with single amino acid resolution does not require complex macro-molecular structures but can be achieved with molecules that have two short pep-tide chains on a scaffold and can be selected from combinatorial libraries [5-7]. Although our initial experiments on molecular forceps were performed in organic solvents, we expected similar interactions should occur in aqueous surroundings and that molecular forceps should be able to recognize epitopes on physiologically important proteins and interfere with their biological functions. As it was not obvious whether a flexible or rigid structure would be advantageous for interactions with a particular target, we used both the rigid chenodeoxycholic acid scaffold with a glycine spacer L1 or a flexible lysine L2 as cores to generate an encoded combinatorial library of molecular forceps (MF) on Tentagel beads [22-24]. We also used a trilysine core L3 to study the impact of increased molecular surface on the strength of the interactions. This library contained approximately 150 000 members.

We used this library to find receptors for the CaaX-box of the H-RAS protein. Because selecting molecular forceps from libraries for H-RAS binding does not ensure these forceps will recognize the carboxy terminus of H-RAS, however, we decided to take a two-pronged screening approach - in addition to screening the library with the protein, we sought to screen with the isolated carboxy-terminal peptide from H-RAS to select molecular forceps that bind this epitope specifically.

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