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 beta-anomer of a C-linked deoxyriboside of 2-hydroxyquinoline (dQ) opposite the beta-N9 deoxyriboside of 2-aminopurine (dAP). Several duplex DNAs were synthesized containing this new base pair as well as the analog in which 2-hydroxypyridine replaces 2-hydroxyquinoline (dP). Phosphoramidites 17 and 18 were synthesized and incorporated into synthetic oligonucleotides using automated methodology. That dQ and dP had been incorporated without chemical modification was proven by enzymatic digestion of the synthetic oligonucleotides to the component nucleosides and analysis by HPLC. Native polyacrylamide gel electrophoresis revealed that admixture of complementary strands containing dP or dQ opposite dAP gave new substances with mobility comparable to a duplex DNA of the same length containing only Watson-Crick base pairs. Solution circular dichroism measurements were consistent with these substances existing in the B conformation. T(m), DELTAH, and DELTAS were measured for synthetic duplex DNAs containing pairings of dQ and dP with dAP, dA, dC, dG, and dT. Of these, duplexes in which dAP was the partner of dP or dQ were most thermodynamically stable (DELTAG 25-degrees-C) and highest melting, with T(m) values lower by 1 to 5-degrees-C than the corresponding dA.dT-containing duplex. Solution H-1 NMR measurements from delta 11-15 on an 11-mer duplex containing the dAP.dQ pair were diagnostic for the presence of 11 base pairs. The resonance for the dAP-dQ base pair was assigned on the basis of a combination of 1D NOE measurements, temperature-dependent line width, and chemical shift measurements. We conclude that dP and dQ are competent base-pairing partners for dAP in duplex DNA and are reasonable condidates for use in the design of novel base-pairing nucleoside analogs.