Helix-random coil transitions in synthetic DNAs of alternating sequence

Abstract

The helix-coil transitions of two synthetic DNA copolymers have been studied as models for the behavior of natural DNAs and in order to learn how to form hybrid molecules by a coil-helix transition. Hybrid formation is made possible by the regularly alternating base sequence which is adenine-thymine in dAT† and adenine-5-bromouracil in dA BU ¯ . The helix-coil transitions of dAT and dA BU ¯ are similar to those of natural DNAs but show three striking differences. First the optical density melting curves are reversible, a fact noted by Marmur & Doty and explained by the alternating sequences. Second, the thermal transition becomes broad in high salt: there is a 20-fold increase in width from the lowest to the highest salt concentration studied. Third, viscosity melting curves measured at the ambient temperature show a pre-transition zone in which the viscosity drops without an observable change in optical density, and in low or moderate salt the viscosity rises as the transition in optical density takes place. In low salt there is a difference of 9°C in the melting temperatures of the two copolymers, dA BU ¯ being the more stable, but this difference disappears in high salt. In the alkaline pH transition dA BU ¯ melts 1·5 pH units below dAT, which is explained by the difference in pK'a between 5-bromouracil (8·0) and thymine (9·8). In both types of transition, conditions can be found where the optical density melting curves for a mixture of dAT and dA BU ¯ show two clearly resolved steps.