HAIRPIN FORMATION IN THE SELF-COMPLEMENTARY DODECAMER D-GGTACGCGTACC AND DERIVATIVES CONTAINING GA-MISPAIRS AND IA-MISPAIRS

The dodecamer d-GGTACGCGTACC and four derivatives with GA and IA mispairs in the 6,7 and 5,8 positions have been examined in dilute solution and 0.01-0.1 M sodium chloride. Concentration dependence of T(m), gel electrophoresis, and equilibrium centrifugation indicate that these self-complementary oligomers can forms hairpins under the present conditions. Thermal transitions measured in the ultraviolet primarily represent melting of hairpin to coil [cf. Scheffler et al. (1968, 1970)]. The T(m) values show little or no depression for 6,7 substitution but rather large depression for 5,8 replacement. We interpret the results to indicate that the 6,7 sequences have two-base loops and five base pair stems and that the 5,8 sequences have four-base loops and four base pair stems. A concurrent theoretical modeling study [Raghunathan et al. (1991) Biochemistry (following paper in this tissue)] provides support for this interpretation.