Superstructural informations in the base sequences of nucleic-acids

Proteins and nucleic acids are the most important basic elements of biological systems. Proteins are involved in a wide spectrum of biological functions as a result of their structural polymorphism and conformational versatility. This is due to the large chemical dispersion of the 20 different amino-acid side groups, which strongly modulate the conformational features of the polypeptide chain. Many attempts have been made to predict the tertiary structures of proteins from their aminoacid sequence. In spite of the large progress in the study on the nature of intermolecular forces and the present power of computational systems and techniques, the full solution to this problem is still far from being found. On the contrary, the substantial homogeneity and the consequent conformational degeneracy of the nucleotide residues along DNA double helix, have recently allowed good progress in the knowledge of the molecular mechanisms that control the functional organization of the genome as well as the prediction of some biologically relevant structural properties in terms of the sequence. In fact, the perfect base pairing of the DNA double helix restricts the structural variance in the biological conditions to relatively slow modulations of the B-DNA structure. These modulations can produce superstructures when phased with theDNA helical periodicity. They are relevant for their physical–chemical properties and biological functions. In fact, many DNAs were found to be curved in biologically important tracts, such as protein-binding regions, transcription loops or nucleosomes. In addition, it is reasonable that the differential flexibility of the DNA chain could favor the structural deformations involved in these processes. This suggests that sequence-dependent curvature and flexibility play a relevant role in the management of the complex physical–chemical transformations in the living matter.