Sequence-dependent collective properties of DNA and their role in biological systems.

Inside the cell, DNA continuously interacts with the proteins involved in replication, transcription, repair, and regulation processes. During these processes, the DNA transforms between packed and unpacked architectures, like that of chromatin or of other higher-order structures morphing into shapes with structural spikes alternative to the canonical B-form in connection with biological events. The base sequence encodes the dynamics of these transformations from the atomic to the nanometer scale length, and over higher spatial scales. Therefore, an important part of the DNA information content is not localized on the codon regions but is related to collective features of relatively large tracts of sequence. We proposed a model able to model the effects of the sequence on the superstructural properties of DNA by integrating over nano-scale the theoretically evaluated slight structural and electronic features of the different nucleotide steps along the sequence. This model allows the prediction of the thermodynamic constants of the sequence dependent circularization reactions of DNA tracts and their writhing transitions from relaxed to super-coiled circular forms as well as the stability constants and positioning of nucleosomes along eukaryotic genomes in excellent agreement with the experiments.