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bioRxiv · 10.1101/2022.02.24.481677

A nucleation-and-growth model for the packaging of genome in linear virus-like particles: impact of multiple packaging signals

de Bruijn, R.·Wielstra, R. P.·Calcines Cruz, C.·van Waveren, T.·Hernandez-Garcia, A.·van der Schoot, P.
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Abstract

Inspired by recent experiments on the spontaneous assembly of virus-like particles from a solution containing a synthetic coat protein and double-stranded DNA, (1) we put forward a kinetic model that has as main ingredients a stochastic nucleation and a deterministic growth process. The efficiency and rate of the packaging of the DNA turn out to strongly increase by introducing proteins onto the DNA template that are modified using CRISPR-Cas techniques to bind specifically at predesignated locations, mimicking assembly signals in viruses. Our model shows that treating these proteins as nucleation-inducing diffusion barriers is sufficient to explain experimentally observed increase in encapsulation efficiency, but only if the nucleation rate is sufficiently high. We find an optimum in the encapsulation kinetics for conditions where the number of packaging signals is equal to the number of nucleation events that can occur during time required to fully encapsulate the DNA template, presuming that the nucleation events can only take place adjacent to a packaging signal. Our theory is in satisfactory agreement with the available experimental data. SIGNIFICANCEThe rate and efficiency of the encapsulation of double-stranded DNA by synthetic coat proteins was recently found to be strongly enhanced by the presence of specifically positioned protein molecules on the DNA that mimic so-called packaging signals. We present a kinetic theory based on the initial stochastic nucleation and subsequent deterministic elongation of the protein coat with the aim to explain these findings. We find that equidistantly placed nucleation sites that also act as diffusion barriers on the DNA have profound and non-trivial effects, and they can either slow down or speed up encapsulation, depending on how fast nucleation is on the time scale of the elongation process. Our findings may contribute to the rational design of linear virus-like particles.

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de Bruijn, R., Wielstra, R. P., Calcines Cruz, C., van Waveren, T., Hernandez-Garcia, A., van der Schoot, P.. 2022-02-25. A nucleation-and-growth model for the packaging of genome in linear virus-like particles: impact of multiple packaging signals. https://doi.org/10.1101/2022.02.24.481677

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