Oligomers of PNA:PNA duplexes with different amino acids appended to one strand of each duplex have been synthesized and studied for their chiral optical properties. The terminal amino acid is known to affect both the handedness and amplitude of the CD signal from a given duplex. Here we have investigated an extended set of duplexes with several different amino acids appended, determining the CD, absorbance, and denaturation behavior of these chains in water and glycerol. Thermal unfolding profiles of the duplexes together with NMR data point to conformational heterogeneity as a function of amino acid, oligomer length, and solvent. The results suggest that the PNA:PNA double helix has access in solution to a dynamic ensemble of conformational states rather than a single dominant state. The conformational ensemble varies as a function of oligomer length according to the cooperative properties of the competing conformations of the double helix. A simplified statistical theoretical model allowing only two conformational states with distinct cooperative properties consistent with the denaturation results can account for much of the experimental data. This conformational heterogeneity in PNA duplexes is reflected in significantly greater flexibility of PNA:DNA duplexes relative to either DNA or RNA double helices. The results demonstrate that the principles of chiral cooperativity such as seen in the sergeants and soldiers and majority rule experiments must be altered when the structure of the system becomes a variable depending on the chiral information input.