Evidence for unexpected off-path intermediates to DNA duplex formation is presented.  These off-path intermediates are shown to involve unimolecular and, in one case, bimolecular structure in one of the single strands of complementary DNA.  Three models are developed to account for the observed single-stranded structures that are formed in parallel with duplex formation.  These models are applied to the analysis of stopped-flow data for eight different non self-complementary duplex formation reactions in order to extract the elementary rate constant for formation of the duplex from the complementary random-coil single-stranded DNA.  The free-energy of activation (at 25 <sup>o</sup>C) for the denaturation of each duplex is calculated from these data and is shown to have a linear correlation to the overall standard free-energy for duplex formation (also at 25 <sup>o</sup>C).  Duplexes that contain mismatches obey a parallel linear free energy (LFE) relationship with a larger y-intercept than those without mismatches.  Slopes near unity for the LFE relationships indicate that all duplexes go through an early, unstructured transition state.

Modeling stopped-flow data for nucleic acid duplex formation reactions

249th National Meeting (2015)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.