A kinetic model for the impact of packaging signal mimics on genome encapsulation

• Published in: Biophysical journal Vol. 121; no. 13; pp. 2583 - 2599
• Main Authors: de Bruijn, René, Wielstra, Pieta Cornelia Martha, Calcines-Cruz, Carlos, van Waveren, Tom, Hernandez-Garcia, Armando, van der Schoot, Paul
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05.07.2022; The Biophysical Society
• Subjects: DNA; DNA Packaging; Kinetics; Proteins - genetics; Virus Assembly - genetics
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2022.05.040

Inspired by recent experiments on the spontaneous assembly of virus-like particles from a solution containing a synthetic coat protein and double-stranded DNA, we put forward a kinetic model that has as main ingredients a stochastic nucleation and a deterministic growth process. The efficiency and rate of DNA packaging strongly increase after tiling the DNA with CRISPR-Cas proteins at predesignated locations, mimicking assembly signals in viruses. Our model shows that treating these proteins as nucleation-inducing diffusion barriers is sufficient to explain the 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 signal mimics is equal to the number of nucleation events that can occur during the 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.