Volumetric properties of the formation of double stranded DNA: A nearest-neighbor analysis

The kinetics of the helix-coil transition have been studied by performing UV-monitored melting and reannealing curves of DNA and analyzing the resultant hysteresis between these curves. The analysis assumes a single-step bimolecular transition with duplex formation defined as the forward reaction. Volume parameters of the helix-coil transition were obtained by measuring the pressure dependence of the rate constants from 5-200 MPa. The data were interpreted in terms of several possible nearest-neighbor models, ranging from one to eleven parameters. Twenty-four oligonucleotide duplexes 22 base pairs in length were used to solve for individual nearest-neighbor activation volumes and transition volumes. Statistically, the most valid fit of the volumetric data was obtained with a sixparameter model in which the directionality of the dinucleotide steps is not considered, for example, 5ʹAG/CT is the same as 5ʹGA/TC. The resultant transition volumes at 48°C ranged from -7.1 (plus-minus) 0.8 mL/mol (GC/CG) to +2.9 (plus-minus) 0.3 mL/mol (AA/TT). The success of the six-parameter model suggests that the relative size of the nearest-neighbor dinucleotides is the most important factor determining the magnitude of the volumetric parameters. The finding that the magnitude of the volumetric parameters correlates with the change in the solvent accessible surface area of the bases during the helix-coil transition corroborates this hypothesis.