Energy per base pair model from NN parameters and its applications in genomic research

TL;DR

This paper introduces a model based on nearest-neighbor DNA free energy parameters to estimate the energy per base pair in genomic sequences, revealing insights into the persistence and evolution of ancient DNA sequences in the human genome.

Contribution

The paper develops a novel energy model using NN parameters and applies it to human genome data to study the evolution of DNA energy profiles over time.

Findings

Ancient random sequences still exist in the human genome.

Average energy per base pair has changed by about 22.5% from ancient values.

The model offers a new perspective on the 'age of life' using mutation rates.

Abstract

Nearest-neighbor(NN) free energy parameters for DNA are well studied and reliable values of these parameters exist in the literature. They have been found to be very useful in studying DNA melting and DNA stabilization studies. In this paper, using these parameters, we have constructed a model in which one can define the energy of a base pair between any two neighboring base pairs. This model allows us to use the Boltzmann weighting factor to perform Monte Carlo sampling to probe the average energy per base pair in random sequences that must have existed at the very beginning before life existed. We then employed our model to the publicly available human Genome data. We calculated the average energy per base pair in inter-gene regions where there is no overlap of genes and also for exons and introns separately. We found that (1) these 'ancient' random sequences still persist in human genome although very scarce (2) the average energy per base pair has drifted about $22.5 \%$ of the ancient value. (3) Our model together with known mutation rates provide us with a new way to look at the 'age of life'.