Synthesis of 1H-pyrrolo[3,2-h]quinoline-8-amine derivatives that target CTG trinucleotide repeats

Abstract We describe a new molecular design, synthesis, and investigation of small molecules that bind to CTG trinucleotide repeats in DNA. 1 H -Pyrrolo[3,2- h ]quinoline-8-amine ( PQA ) has a tricyclic aromatic system with unique non-linear hydrogen-bonding surface complementary to thymine. We have synthesized a series of PQA derivatives with different alkylamino linkers. These PQA s showed binding to pyrimidine bulge DNAs and CNG (N = T and C) repeats depending on the linker structure, while quinoline derivatives lacking the pyrrole ring showed much lower binding affinity. PQA is a useful molecular unit for both CTG and CCG repeat binding.