A spectroscopic and calorimetric study of the melting behaviors of a "bent" and a "normal" DNA duplex: [d(GA₄T₄C)]₂ versus [d(GT₄A₄C)]₂

We have calorimetrically detected and energetically characterized a premelting event in the "bent" duplex [d(GA₄T₄C)]₂ that is absent in the "normal" duplex [d(GT₄A₄C)]₂. This premelting may correspond to the thermally induced "unbending" of the duplex. Specifically, we have used a combination of spectroscopic and calorimetric techniques to evaluate whether differences in the electrophoretic and hydrogen exchange properties of the bent duplex, [d(GA₄T₄C)]₂, and the normal duplex, [d(GT₄A₄C)]₂, are paralleled by differences in the equilibrium melting properties of these duplexes. Our results reveal that the bimolecular global meltings of both duplexes exhibit two-state behavior and are characterized by the expected thermodynamic changes, as well as the expected salt-dependencies. Significantly, however, at temperatures below duplex melting and over a similar temperature range in which the aberrant electrophoretic mobility is observed (≈<35°C), the bent duplex exhibits calorimetric premelting behavior absent in the normal duplex. Analysis of the calorimetric data in this preglobal melting domain (≈<35°C) allows us to estimate a lower-limit value of 1.6 kcal/(mol-base pair) for the thermally induced unbending of the decameric duplex.