Computer simulation in template-directed oligonucleotide synthesis

Abstract

It is commonly assumed that template-directed polymerizations have played a key role in prebiotic evolution. A computer simulation that models up to 33 competing reactions was used to investigate the product distribution in a template-directed oligonucleotide synthesis as a function of time and concentration of the reactants. The study focuses on the poly(C)-directed elongation reaction of oligoguanylates, and how it is affected by the competing processes of hydrolysis and dimerization of the activated monomer, which have the potential of severely curtailing the elongation and reducing the size and yield of the synthesized polymers. The simulations show that realistic and probably prebiotically plausible conditions can be found where hydrolysis and dimerization are either negligible or where a high degree of polymerization can be attained even in the face of substantial hydrolysis and/or dimerization.