Mapping of DNA base-pair sequence from breathing dynamics of hetero-polymeric DNA: A genetic algorithm-based study

Abstract

A strategy to obtain the DNA base-pair sequence is proposed from the information of the time series data of the size fluctuations (breathing) of local denaturation zones (bubbles). In one of the previous publication of the author,¹ it was shown how the DNA stability parameters were evaluated from an equilibrium distribution profile of bubble opening for a known sequence of heteropolymeric DNA. This paper attempts to know whether the reverse could be done, i.e., by knowing the stability parameters and the distribution profile for an unknown DNA sequence, whether the proper base-pair sequence can be evaluated or not. To get the DNA sequence, a non-trivial search process has been used. The problem has been cast as one of optimization problem and stochastic optimizer Genetic Algorithm has been used to optimize the DNA sequence in order to reach the correct or objective equilibrium distribution profile. We have tested the strategy for three DNA sequences, L33B9, L42B18 and the promoter sequence of the T7 bacteriophage.

Graphical abstract

The DNA base pair sequence could be obtained from the information of the time series data of the size fluctuations (breathing) of local denaturation zones (bubbles). The problem has been cast as one of optimization problem and stochastic optimizer Genetic Algorithm.