The kinetic parameters for the renaturation of two DNA decamers, 5’-GAGAGCCTTC/5’-GAAGGCTCTC and 5’-GCATGTACGC/5’-GCGTACATGC have been measured under second order conditions at several salt concentrations and pseudo-first order conditions in 1 M NaCl buffer  using stopped flow UV spectroscopy.  The sequences are identical in base pair composition but differ in sequence, with one strand consisting of five consecutive purines, and the other containing alternating purines and pyrimidines.  Trends in entropic and enthalpic activation parameters with different conditions suggest the presence of a rate-limiting secondary structure in one of the alternating strands.  This idea could be corroborated by thermodynamic optical melting experiments that demonstrate the existence of a secondary structure in the 5’-GCGTACATGC alternating strand.  The presence of such an off-path intermediate in this strand highlights a possibly fundamental difference in the mechanism of DNA duplex formation in the presence of stacked versus alternating purines and pyrimidines. <br/>

Probing the mechanism of DNA duplex formation in sequences with consecutive versus alternating purines and pyrimidines using stopped flow kinetics experiments

249th National Meeting (2015)

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