Influence of dA · dT and d(2aminoA) · dT base pairs on the B⇄Z transition of DNA fragments

Abstract

The helical structures of [deoxy] d(C-G-C-A-m5 [5-methyl] C-G-T-G-m5C-G), d(m5C-G-C-A-m5C-G-T-G-C-G) and d(C-2aminoA-C-G-T-G) were studied in aqueous solution at various salt concentrations and temperatures by 1H-NMR spectroscopy. In 0.1 M NaCl solution, only the B form was evidenced for these DNA fragments; in 4 M NaCl, both B and Z forms, in slow exchange on the NMR time scale, were observed. Under these conditions, the Z form accounted for < 60% of the decamer conformation; conversely, d(C-G)3 hexamers containing methylated cytidines were predominantly in the Z form (> 90%) [Trans-Dinnh et al. 1984; Cavailles et al. (1984). d(C-2aminoA-C-G-T-G), in which the d(2aminoA) .cntdot. dT base pair form 3 H bonds, was found to adopt the Z conformation in 4 M NaCl solution; this was not the case for d(C-A-C-G-T-G). The B .dblarw. Z transition in solution is highly sequence-dependent, and a correlation exists between the stability of the duplexes (essentially governed by the number of H bonds between complementary bases) and their ability to adopt the Z conformation.