# Possible scenarios of DNA double helix unzipping process

## TL;DR

This paper investigates DNA unzipping mechanisms by analyzing force-distance curves and proposing two scenarios based on base pair opening energies, with implications for understanding biological processes like transcription.

## Contribution

It introduces two distinct models of DNA unzipping based on experimental data and atomistic calculations, highlighting conditions for each scenario's occurrence.

## Key findings

- Two force plateaus observed at 12-14 pN in unzipping curves.
- Estimation of base pair opening energies using atom-atom potential functions.
- Proposed scenarios differ in unzipping speed and pathway, relevant to in vivo processes.

## Abstract

Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as well as peaks appearance in the plateau area, to which it was not paid essential attention earlier. Using atom-atom potential function method the estimations of Watson-Crick base pairs opening energies are made. On the basis of this results two possible scenarios of the DNA double helix unzipping process are proposed. According to the first scenario DNA unzipping takes place slowly and as equilibrium process, with small difference between two plateaus on the unzipping curve. In this case firstly base pairs transit into the 'pre-opened' metastable state along the 'opening' pathway and then open along the 'stretch' pathway. Our estimations show that an important factor for the realization of this scenario is the existence of double-stranded DNA coil in the unopened part of DNA. The second scenario is characterized by higher opening force. In this scenario base pairs open directly along the 'stretch' pathway as non-equilibrium process. The conditions of the first scenario realization show that it can play a key role in the understanding of the DNA unzipping in vivo during transcription and genetic information transfer processes.