Systematic, computer-simulated elongation of A- and B-DNA double helices beyond the range of normal room temperature fluctuations provides new insights into recent physical manipulations of single DNA molecules. The calculations include unusual states that are energetically disfavored under equilibrium conditions but that become favored as the DNA is highly stretched or compressed. The variation of potential energy vs. stretching provides a detailed picture of cooperative conformational change that points to the possible role played by the non-canonical states. Dramatic structural changes take place as the energies of different conformers approach one another. In particular, large-scale, concerted changes in base pair inclination, brought about by changes in backbone and glycosyl torsions, offer a model of the observed sharp increase in force required to stretch single DNA molecules more than 1.6 times their canonical extension. Small degrees of over- and under-twisting have limited effects on the over-stretching transition, but influence local “melting” of the double helix. The energy landscapes of the systems evaluated here reveal the energetically economical pathways for molecular deformations operative in DNA processing, such as recombination and transcription. ©1999 American Institute of Physics.