CONTEXTUAL CONSTRAINTS IN THE CHOICE OF SYNONYMOUS CODONS

From EMBL Nucleotide Sequence Database, protein coding sequences of al l E. coli and its DNA phages, were extracted using our computer progra mme. Same programme has been used to form a database of sequence of ol igonucleotides of length 18 nucleotides on both sides of each of the 6 1 codons. From analysis of this database and study of variations in tw ist parameter (Tw) values, as an indicator of sequence dependent varia tions in B-DNA helix, a method is developed to fix the codon among the set of synonymous codons. The accuracy of the method was checked on e nlarged data set by adding data from more prokaryotes. Our method assi gn the codon 85-90% times correctly if the selection has to be made be tween codons having different sequence in terms of R and Y. The accura cy of the method is somewhat lower when choice of the codon has to be made between codons having same codes in terms of R and Y. This study points out that the major factors which decide the choice of a codon f rom a set of synonymous codons are contextual constraints arising from flanking regions.