Bacteriophages therapy is an alternative method to treat secondary infections. Some pathogenic bacteria develop resistance to antibiotics, bacteriophage can be used to treat such bacterial infections due to their ability to attach to the bacteria cell, extract DNA or RNA, carried in the protein capsid, into the host cell, disrupt bacteria metabolism, and destroy it. Sequence dependent mechanical coupling of the DNA to the thermodynamics of packing can change efficiency and possibly inhibit packing of some sequences. Understanding the biophysical basis of the biological process which transfers a viral genome to infect a cell is very important to the cellular machinery and many disease related fields central to the sequence design issue for reprogramming phages for emerging strains. We model the process of DNA extraction from the bacteriophage using all-atoms molecular dynamics combined with experimental data to model the structure and the thermodynamics of DNA confined by surfaces. The inside of the full capsid has a different concentration of species than the surrounding environment creating an osmotic pressure difference. We employ all-atoms molecular dynamics simulations to calculate osmotic pressure of one or multiple single strained DNA(s) in aqueous solution and concentrated polyethylene glycol (PEG) polymers solution, we discuss correlation between DNA conformations and osmotic pressure, we analyzed folded/unfolded DNA structures, hydrogen bonds formations in DNA, the ions distribution around the DNA strand(s) for the different salt and PEG concentrations, and dependence of osmotic pressure of DNA on the osmotic barrier proximity, and DNA molarity.

Osmotic pressure calculations in the systems with the highly concentrated DNA and polyethylen glycol polymers solutions using all-atoms molecular dynamic simulations as a way to understand biophysical processes of DNA extraction from bacteriophages

2019 Spring National Meeting

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