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 °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 °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 °C which increases to 220 ns above 40 °C. Simple modeling of the dynamics within the junction model for bending yields that the bend per A-tract is 42° at 5 °C, decreasing to 0° above 40 °C. We suggest that this sequence-dependent structure which “melts” at physiological temperatures may be relevant to DNA topology and function.
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