SELECTIVE CONSTRAINTS OVER DNA SEQUENCE G. Cochol, L. Medrano 2 , P. Miramontes 2 , J .L. Rius l 1. Instituto de Fisica, Universidad Nacional Aut6noma de Mexico 2. Facultad de Ciencias, Universidad Nacional Aut6noma de Mexico Apdo. Post 20-364, Mexico 01000 D.F. MEXICO INTRODUCTION 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 ON A is far from being a rigid molecule. Indeed, there do exist several fluctuations in the and the structure is not homogeneous along the polymer. At the evolu- tive 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 synthe- sis 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. NUCLEOTIDE SEQUENCE AND DNA STRUCTURE DNA is a double-stranded nucleotide polymer made up of four kinds of bases attached to a sugar-phosphate backbone. The base sequence carries genetic infor- mation, and the sugar and phosphate groups perform a structural role. The genetic information is encoded in sequences of bases; the four bases are the purines (R), ade- nine (A) and guanine (G), and the pyrimidines (Y) thymine (T) and cytosine (C) (in RNA uracyl (U) replaces thymine but this fact will not be taken into account). The base elements of one strand interact with their counterparts on the other strand in a precise way: A pairs with T, and G pairs with C. This complementarity principle is the basis of replication, t,ramlcription and. repair; if a segment of DNA is known, it 63 L. Peliti (ed.), Biologically Inspired Physics © Springer Science+Business Media New York 1991