We have successfully gained insight into the conformation of DNA single strands by using experimental thermodynamic results describing B-form DNA complexes to predict ?structural? parameters within the context of a primitive cylindrical rod model with which we describe the electrostatic behavior of the single strand polynucleotide chains. For the DNA- NaCl- water system , a three-component thermodynamic analysis shows that the enthalpy of transition, and the melting temperature of the helix-coil transition are related to the difference of the Donnan membrane salt distribution parameters of the coil and helix forms. By combining these experimental parameters with published membrane equilibrium data for B-form DNA, we obtain the salt distribution parameter of the single strand forms at various salt concentrations, which we compare with values predicted from numerical solutions of the Poisson-Boltzmann equation for a uniformly charged cylindrical rod in electrolyte solution. These calculations have now been extended to take into account the variation of the dielectric constant of water with temperature. By adjusting the dimensions of the model cylinder representing the single strand forms to provide agreement with the observed dependence of the melting temperature upon salt concentration, we find at 298 K that the axial charge spacing of the cylindrical rod representing the single strand polynucleotide is somewhat larger for the poly(dA)+poly(dT) system (3.8 A) than for DNA (3.4 A). This result possibly reflects greater intra-strand interaction in the guanine-cytosine containing single-strands of DNA. The methodology that we have developed successfully accounts for the thermodynamic behavior of single-strand nucleic acids and according to this primitive model shows that the axial charge spacing is sequence-dependent.
| Ross, Philip D; Howard, Frank B (2003) The thermodynamic contribution of the 5-methyl group of thymine in the two- and three-stranded complexes formed by poly(dU) and poly(dT) with poly(dA). Biopolymers 68:210-22 |
