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

TL;DR

A model in which one can define the energy of a base pair between any two neighboring base pairs is constructed, which allows 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.

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'.

Figures (5)

• Figure 1: Energy distribution from Monte Carlo simulation.
• Figure 2: Intergenic region between genes PGBP1 and OVGP1 in chromosome 1
• Figure 3: Intergenic region between genes CDY1 and VAMP7 in chromosome Y
• Figure 4: Introns from gene NLGN4Y-e from chromosome Y
• Figure 5: Intergenic Exons from gene DMD-a from chromosome X