Thermodynamics and premelting conformational changes of phased (dA)5 tracts.

Using synthetic 45 bp long DNAs of known sequences, we have studied (i) the unusual structure that the phased a-tracts have at temperatures below 37 o C, (ii) the thermodynamics of the loss of that aberrant structure well below the duplex melting temperature, and (iii) the conformational changes that occur with temperature. Using temperature-dependent circular dichroism, we detect a low-temperature structural transition in a 45-mer duplex with four segment of phased (dA) 5 tracks separated by five segments of five randomised G-C pairs, but none in the corresponding isomeric random sequence 45-mer duplex. Differential scanning calorimetry measurements reveal the enthalpy of this preglobal melting transition to be 3.5 kcal/mol.AT pair or 4.4 kcal/mol-AA step