- DNA denaturation has been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear structural transition. Many aspects of this phenomenon, however, remain poorly understood. Existing models fit quite well with experimental results on the fraction of unbound base pairs versus temperature, but yield incorrect results for other essential quantities such as the base pair fluctuation time scales. Here we demonstrate that nanoscale thermal transport can serve as a sensitive probe of the underlying microscopic physics responsible for the dynamics of DNA denaturation. Specifically, we show that the heat transport properties of DNA are altered significantly as it denatures, and this alteration encodes detailed information on the dynamics of thermal fluctuations and their interaction along the strand. This finding allows for the discrimination between models of DNA denaturation and will help shed new light on the nonlinear vibrational dynamics of this important molecule.