The crowding effect on the melting of short DNA: Comparison with experiments

TL;DR

This study investigates how molecular crowding agents influence the melting behavior of short DNA, comparing computational models with experimental data, and explores the effects of crowder placement and strength on DNA melting temperatures.

Contribution

The paper introduces a computational approach to model crowder effects on DNA melting, matching experimental results and analyzing the impact of crowder location and strength.

Findings

Melting profile matches experimental data when crowder distribution is optimized.

Crowder location at DNA ends affects melting temperature.

Variable crowder strength significantly alters melting behavior.

Abstract

We study the effect of crowders on the melting profile of homogeneous and heterogeneous DNA molecules. We find out the melting profile of short DNA molecules and compare our findings with the experiments. We consider some random distribution of crowders along the chain, and by finding out the best match with the experiments, we attempt to identify the location of crowders in the experimental findings of Ghosh \cite{Ghosh_PNAS_2020}. We also study the melting of homogeneous DNA molecules of different lengths (25, 50, 75) in the presence of only one crowder in the chain. By varying the location of the crowder from one end to the other, we find that the melting temperature is susceptible to the location of the crowder at the ends. At the same time, there is minimal effect on the melting temperature due to the location of the crowder. {\it In vivo}, the strength of a crowders may vary along the chain. We study the melting of long heterogeneous chain in presence of five crowders of different strength. We find that there is a significant variation in the melting process of DNA in presence of crowders of variable strength.