Effect of glycerol on free DNA: A molecular dynamics simulation study

Osmolytes are a class of organic solutes that are produced in a variety of organisms in response to stress. They exert diverse effects on macromolecules and their functions. In this work, we investigate the effect of glycerol, one such osmolyte, on the hydration and conformation of four DNA sequence...

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Bibliographic Details
Published in:Journal of molecular graphics & modelling 2022-07, Vol.114, p.108169-108169, Article 108169
Main Authors: Diaz, Aathithya, Jothiraman, Hari Balaji, Ramakrishnan, Vigneshwar
Format: Article
Language:English
Subjects:
DNA - chemistry
Glycerol - chemistry
Molecular Dynamics Simulation
Nucleic Acid Conformation
Thermodynamics
Water - chemistry
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Summary:Osmolytes are a class of organic solutes that are produced in a variety of organisms in response to stress. They exert diverse effects on macromolecules and their functions. In this work, we investigate the effect of glycerol, one such osmolyte, on the hydration and conformation of four DNA sequences that differ by a single base pair and a random DNA sequence. Molecular dynamics simulations reveal DNA sequence-dependent and glycerol concentration-dependent hydration and DNA conformation. Interestingly, we find that the sequence-dependent changes in the hydration reflects the order of preference of these sequences for star activity of the EcoRI enzyme. However, the changes in DNA conformation do not reflect this order of preference. Interaction energy analyses reveal that the per-glycerol interaction energy with DNA is stronger than the per-water interaction energy with DNA. However, the total interaction energy of glycerol with DNA is lower than that of total water-DNA interaction energy indicating that it might be easier for an approaching DNA-binding protein to displace glycerol than water and thus contributing positively to protein-DNA binding. In a larger context, our study brings attention to the need to investigate the effect of osmolytes on free DNA in order to delineate the role of osmolyte in protein-DNA interactions. [Display omitted] •Glycerol causes DNA sequence-dependent hydration of the free DNA reflecting the order of star activity.•Glycerol causes changes in the hydration of free DNA and maybe easily displaced from free DNA interface.•Conformational changes in DNA in the presence of glycerol may not be the cause for star activity of restriction enzymes.
ISSN:1093-3263
1873-4243
DOI:10.1016/j.jmgm.2022.108169