Synthesis of dimeric 2-amino-1,8-naphthyridine and related DNA-binding molecules.

The synthetic protocols for dimeric 2-amino-1,8-naphthyridine and related compounds are described in this unit. These compounds represent a novel class of compounds that bind selectively to mismatched base pairs. The compounds consist of two main components: the heterocycles and a linker. Connecting two heterocycles by a linker was found to modulate the binding selectivity. This unit describes the synthesis of dimeric 2-amino-1,8-naphthyridine (which binds to the G-G mismatch), naphthyridine-azaquinolone (for the G-A mismatch), N-alkyl naphthyridine dimer (for the C-C mismatch), and naphthyridine carbamate dimer (for G-G mismatches in the (CGG)(n) trinucleotide repeat). Protocols for connecting the short linker to these molecules providing the compounds suitable for immobilization on solid surface are also described. (c) 2008 by John Wiley & Sons, Inc.