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 degrees 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 segments of phased (dA)5 tracks separated by five segments of five randomized 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. The integrated enthalpy change for this helix-to-helix intramolecular event only is about 16% of the global duplex-to-single-strands melting enthalpy and is relatively broad compared to the global melting event (about 30 vs 15 degrees C for the full width at half maxima). Electric birefringence decay measurements show that the phased 45 bp duplex has a rotational time constant of 100 ns at 5 degrees C which increases to 220 ns above 40 degrees C. Simple modeling of the dynamics within the junction model for bending yields that the bend per A-tract is 42 degrees at 5 degrees C, decreasing to 0 degrees above 40 degrees C. We suggest that this sequence-dependent structure which "melts" at physiological temperatures may be relevant to DNA topology and function.