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Chemical synthesis and characterization of duplex DNA containing a new base pair: a nondisruptive, benzofused pyrimidine analog

A new base pair appropriate for incorporation into B-DNA was designed with the goal of allowing fusion of a benzene substituent across the 4 and 5 carbons of a pyrimidine analog. Such a residue may have utility in the preparation of DNA duplexes bearing precisely spatially positioned and conformationally constrained unnatural substituents such as reporter groups. The design called for the incorporation of the β-anomer of a C-linked deoxyriboside of 2-hydroxyquinoline (dQ) opposite the β-N 9 deoxyriboside of 2-aminopurine (dAP). Several duplex DNA were synthesized containing this new base pair as well as the analog in which 2-hydroxypyridine replaces 2-hydroxyquinoline (dP)