Long range and symmetry considerations in the DNA

Abstract

The common description of DNA is that of a polymer composed of overlapping dinucleotide base pairs. Conformational, thermodynamic and flexibility calculations of the DNA are frequently based on that description. As demonstrated by the good fit with experimental data, such as the free energy of opening the double stranded DNA and the correspondence between the DNA crystal and computed structures, this approach is to a large extent a faithful reproduction of the DNA. Here I show that longer range effects should be considered as well. Statistically strong longer-range sequence patterns are described. Such sequence preferences are clearly translated in the DNA into long range structural propagation. Long range effects have also been observed in some experimental studies, like gel mobility and patterns of DNA cleavage. Long range structural effects are the likely explanation of the effect of mutations at a distance from a protein binding site. They might also aid in understanding DNA looping.