Determining the base sequence of RNA molecules using continuous degradation kinetics

A kinetic approach to sequence analysis is presented. A polymer chain composed of a small number of monomer types is degraded continuously with degradation proceeding in only one direction of the chain. Ordinarily, the direct determination of the sequence from the amount of degraded monomers is hampered by the rapid loss of reaction synchrony. However, it is shown, that if the monomers can be measured reasonably accurately, one can solve a system of linear equations with the unknowns giving the positions of the monomers in the chain, and the syn chrony loss due to the stochastic nature of the degradation process can be accounted for. Model calculations are presented.