Thermal denaturation of DNA molecules: A comparison of theory with experiment

Experimental and theoretical results on the helix-coil transition of DNA are reviewed. The theoretical model of the transition is described, and the influence of heterogeneous base pair stacking, and strand dissociation on the predicted melting transition is examined. New experimental transition data on seven DNAs, 154–587 base pairs (bp) long, are reported and compared with theoretical calculations. We review and evaluate previous studies on long DNAs (≥1000 bp) as well as previous and recent results on short DNAs. The comparison of theory with equilibrium melting curves of short DNAs indicates that base pair sequence has a relatively small influence on the stacking free energy. Excellent agreement is obtained between theory and equilibrium transitions of 14 out of 15 fragments 80–587 pb. The deviation between theory and experiment for a 516 bp DNA can be attributed to the formation of stem-loop structures. This may provide the explanation for inconsistent results observed with long DNAs. The effect of single base pair changes on DNA transitions is discussed. Current views on fluctuational opening of base pairs at temperatures below the transition are described.