Analysis of high-resolution thermal dispersion profiles of DNA: Treatment as a collection of discrete subtransitions

High Sensitivity Differential Scanning Calorimetry Study of DNA-Cationic Liposome Complexes

PURPOSE

To investigate plasmid DNA interactions with liposomes prepared from dimyristoylglyceroethylphosphocholine (EDMPC) and DOPE using high sensitivity differential scanning calorimetry (HSDSC).

MATERIALS AND METHODS

Large unilamellar liposomes of EDMPC with DOPE (mol ratio 0-50%) were prepared. Plasmid DNA was added to give a final DNA/lipid (-/+) charge ratio of 0.5. Samples were placed into an HSDSC and cooled to 3 degrees C, held isothermally for 30 min and then the temperature was ramped to 120 degrees C at a rate of 1 degree C/min.

RESULTS

On heating EDMPC liposomes, the main phase transition occurred at 21.2 degrees C, with a low temperature shoulder on the endothermic peak. At low DOPE concentrations the main phase transition temperatures and enthalpies of transition were lower than for pure EDMPC, with a peak corresponding to a pure EDMPC phase occurring at DOPE concentrations of 12-17 mol%. At 50 mol%, no main transition endotherm was observed. DNA solution produced two endothermic peaks with numerous 'satellite' peaks indicating thermal denaturation. DNA binding to EDMPC changed the shape of the thermogram, indicating alteration in lipid packing within the bilayer. DNA induced demixing in the bilayers of DOPE-containing liposomes.

CONCLUSION

HSDSC provided information for characterizing liposome formulations and DNA interactions with such vesicles.

Thermal stability of DNA

Tij and Delta Hij for stacking of pair i upon j in DNA have been obtained over the range 0.034-0.114 M Na+from high-resolution melting curves of well-behaved synthetic tandemly repeating inserts in recombinant pN/MCS plasmids. Results are consistent with neighbor-pair thermodynamic additivity, where the stability constant, sij , for different domains of length N depend quantitatively on the product of stability constants for each individual pair in domains, sijN . Unit transition enthalpies with average errors less than +/-5%, were determined by analysis of two-state equilibria associated with the melting of internal domains and verified from variations of Tij with [Na+]. Enthalpies increase with Tij , in close agreement with the empirical function: Delta Hij = 52.78@ Tij - 9489, and in parallel with a smaller increase in Delta Sij . Delta Hij and Delta Sij are in good agreement with the results of an extensive compilation of published Delta Hcal and Delta Scal for synthetic and natural DNAs. Neighbor-pair additivity was also observed for (dA@dT)-tracts at melting temperatures; no evidence could be detected of the familiar and unusual structural features that characterize tracts at lower temperatures. The energetic effects of loops were determined from the melting behavior of repeating inserts installed between (G+C)-rich barrier domains in the pN/MCS plasmids. A unique set of values for the cooperativity, loop exponent and stiffness parameters were found applicable to internal domains of all sizes and sequences. Statistical mechanical curves calculated with values of Tij([Na+]) , Delta Hij and these loop parameters are in good agreement with observation.

Electrostatic forces at helix-coil boundaries in DNA

The Tm of internal loop-forming (dA.dT)N domains in pBR322 DNA has been measured over a tenfold range of [Na+]. The slopes SN = dTm/d log [Na+] are linear and decrease in magnitude with decreasing loop size N, signaling a reduction in Na+ released during the transition of these domains to the coil state. Values of SN decrease linearly with increasing N-1 in accordance with the expectation of a simple model for the occurrence of a gradient of long-range electrostatic forces at helix-coil boundaries, and extrapolate almost precisely to the value of S infinity observed for (dA.dT) infinity. These results indicate (1) less counterion is released per phosphate residue from the finite loop than from the infinite-sized loop, and (2) the difference in binding is constant for each boundary formed and independent of the size of the loop within the range examined: approximately 350 base pair (bp) greater than N greater than 71 bp. The slope of the dependence of SN on N-1 indicates the region of higher charge density at the boundary extends at least 18 A into the coil and probably 40-50 A before dropping to a value characteristic of the unperturbed coil. The free energy for excess counterion binding at boundaries can be expressed by -delta G/RT = 10.47 log[Na+] + 5.234 When the loop entropy function in a statistical mechanical algorithm for the dissociation of DNA is weighted by this quantity, calculated Tm are seen to vary by only +/- 0.09 degrees C from observed.