Selective Constraints over DNA Sequence

Abstract

After the progress derived from Watson and Crick’s DNA structural model [1953], DNA has frequently been thought as a static and rigid polymer rarely disturbed by random mutations. However, the discovery of processes as transposition, hyper-mutability, genetic drive and gene conversion, shows that DNA is genetically more active than our first notion as being only the heredity keeping guard. From a physical point of view, studies of molecular dynamics and molecular structure have shown that DNA is far from being a rigid molecule. Indeed, there do exist several fluctuations in the molecule and the structure is not homogeneous along the polymer. At the evolutive level, the analysis of nucleotide sequence data has shown regularities that make evident selective constraints other than the protein function derived from amino acid sequence. Other selective constraints acting over the genome include protein synthesis kinetics, tRNA availability, mRNA secondary structure and DNA stability. Thus, genome evolution can be conceived as a dynamical and complex system which might be understood by the search of regularities in genomic nucleotide sequences.