Evidence map›Paper›PMID 35642255›Full record

ArticleBiophysical journal2022

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

René de Bruijn, Pieta Cornelia Martha Wielstra, Carlos Calcines-Cruz, Tom van Waveren, Armando Hernandez-Garcia, Paul van der Schoot

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biophysical journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.2field-weighted citation impact, top 44% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 2 institutions in 2 countries.

René de BruijnDepartment of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands. Electronic address: r.a.j.d.bruijn@tue.nl.
Pieta Cornelia Martha WielstraDepartment of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands.
Carlos Calcines-CruzDepartment of Chemistry of Biomacromolecules, Institute of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico.
Tom van WaverenDepartment of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands.
Armando Hernandez-GarciaDepartment of Chemistry of Biomacromolecules, Institute of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico.
Paul van der SchootDepartment of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands.
Eindhoven University of Technology · NLUniversidad Nacional Autónoma de México · MX

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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, 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.

Indexed as

DNA PackagingVirus AssemblyDNAKineticsProteinsDNAProteins

Identifiers

PMID35642255
PMCPMC9300666
OpenAlexW4281975417

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.