We studied the structure of heterogenous DNA in the native state. There are two different regimes in the sample-to-sample fluctuations of the free energy in the native state, which can be interpreted via the concept of local free energy of base pairs. In the first low-temperature frozen regime, local free energies are random and there are large sample-to-sample fluctuations for short DNAs. In the high-temperature molten regime, the weakly bounded base pairs are opened and do not give random contribution to the free energy of native DNA. As a result, sample-to-sample fluctuations are suppressed in the molten regime. (C) 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 2432-2436, 2010