X-ray structure analysis of oligonucleotides shows that self-fitting of B-DNA molecules by groove-backbone interaction can trigger modification of the secondary structure of the double helix in a sequence-dependent manner, leading to a "pre-melted" transition state. This work reveals that some sequences respond to the DNA-DNA intermolecular interactions by forming rearranged H-bonding schemes which stabilize the transition states. This study suggests that the close and specific approach of DNA segments occurring in genome packaging, DNA looping, synapsis formation or supercoiling can contribute directly to the secondary structure changes needed for DNA processing.