Molecular Simulation of DNA Packaging into the Phi29 Bacteriophage

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Live Poster Session: Zoom Link
Thursday, July 30th 1:15-2:30pm EDT

Nour-Saïda Harzallah
Nour-Saïda Harzallah

Nour-Saïda is a rising senior (’21) from a beautiful coastal city in Tunisia called Monastir. Nour-Saïda is a molecular biology & biochemistry, college of integrative sciences and very recently a Physics major! She is a champion of binge-watching tv shows. In a parallel universe, she is a studio art and music major. She is passionate about graphic design and drawing. You can often hear her sing in Exley’s hallways, her room and sometimes at cultural showcases at Wesleyan. She is on the Wesleyan Women in Science steering committee and is the NSM intern at the Office of Equity and Inclusion. Nour- Saïda loves computers and the probability of finding her at the ITS Helpdesk at any given time of the day is very close to 1. Now, let’s viral jam!

To see last year’s poster: https://harzallahnoursaida1.wixsite.com/mysite

Abstract: Viruses exist as a protein shell called a capsid. It encloses single or double stranded DNA which codes for the virus elements. In order to reproduce and survive, a virus tightly packages its genetic material then ejects it into a host cell. The infected cell, whose functions are now under the virus’ control, becomes a viral reproductive machine. Through coarse grained computer simulations, we create a model for packaging of DNA into the phi29 bacteriophage. We simulate three initial configurations in which the viral genome adopts a different conformation: a toroid, a rod, and an unorganized cluster of DNA beads. DNA-DNA interactions are purely attractive to mimic a high cationic concentration of the environment. We then initiate the packaging process by applying an upward force, analogous to the force induced by the ATP-driven motor found in phi29 phages, to the beads at the mouth of the viral feeding tube. We collect thermodynamic data and record the number of beads packaged. Packaging proceeds smoothly for DNA initially in a toroidal conformation. However, our simulation results indicate stalling for rod and unorganized cluster conformations. Stalling patterns are in accordance with experimental data where packaging is studied in positively charged environments with high cationic concentration. We speculate that the DNA jamming recorded experimentally is due to jamming outside of the capsid, rather than inside. We hypothesize that this DNA jamming is due to the conformation adopted by the DNA prior to packaging. The packaging force is strong enough to unravel toroidal conformations but unable to overcome the strong attractive DNA-DNA interactions in other conformations. We anticipate our findings to be a steppingstone towards higher level simulations. As we further understand DNA packaging, its limitations, and parameters, we can invent ways of countering these processes or applying them towards biomedical applications such as drug delivery or viral assembly inhibition.

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Live Poster Session: Zoom Link
Thursday, July 30th 1:15-2:30pm EDT

1 thought on “Molecular Simulation of DNA Packaging into the Phi29 Bacteriophage”

  1. I enjoyed your video on viral packaging! I am curious: what do the colored beads represent? How much viral DNA does each segment represent? I am presuming this is some sort of elastic rod model. Very nice poster!

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