1. Computational and Systems Biology
Download icon

A molecular view on the escape of lipoplexed DNA from the endosome

Short Report
  • Cited 5
  • Views 2,745
  • Annotations
Cite this article as: eLife 2020;9:e52012 doi: 10.7554/eLife.52012

Abstract

The use of non-viral vectors for in vivo gene therapy could drastically increase safety, whilst reducing the cost of preparing the vectors. A promising approach to non-viral vectors makes use of DNA/cationic liposome complexes (lipoplexes) to deliver the genetic material. Here we use coarse-grained molecular dynamics simulations to investigate the molecular mechanism underlying efficient DNA transfer from lipoplexes. Our computational fusion experiments of lipoplexes with endosomal membrane models show two distinct modes of transfection: parallel and perpendicular. In the parallel fusion pathway, DNA aligns with the membrane surface, showing very quick release of genetic material shortly after the initial fusion pore is formed. The perpendicular pathway also leads to transfection, but release is slower. We further show that the composition and size of the lipoplex, as well as the lipid composition of the endosomal membrane, have a significant impact on fusion efficiency in our models.

Data availability

All raw data of fusion experiments and analysis software amount to TBs of data, so are available upon request. A data package has been prepared and deposited to Dryad, under the DOI 10.5061/dryad.fqz612jq4

The following data sets were generated

Article and author information

Author details

  1. Bart Marlon Herwig Bruininks

    Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5136-0864
  2. Paulo C T Souza

    Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
  3. Helgi Ingolfsson

    Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
  4. Siewert-Jan J Marrink

    Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
    For correspondence
    s.j.marrink@rug.nl
    Competing interests
    Siewert-Jan J Marrink, S.J.M acknowledges funding from the ERC through an Advanced grant COMP-MICR-CROW-MEM".".
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8423-5277

Funding

H2020 European Research Council (COMP-MICR-CROW-MEM)

  • Siewert-Jan J Marrink

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Michael M Kozlov, Tel Aviv University, Israel

Publication history

  1. Received: September 20, 2019
  2. Accepted: February 24, 2020
  3. Accepted Manuscript published: April 16, 2020 (version 1)
  4. Version of Record published: April 17, 2020 (version 2)

Copyright

© 2020, Bruininks et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,745
    Page views
  • 336
    Downloads
  • 5
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease
    Michael Sheinman et al.
    Research Article

    Horizontal Gene Transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93 481 bacterial genomes identified 138 273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than 3 orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.

    1. Cell Biology
    2. Computational and Systems Biology
    Ina Lantzsch et al.
    Research Article

    The female meiotic spindles of most animals are acentrosomal and undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of acentrosomal spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic C. elegans spindles undergoing the transition from metaphase to anaphase. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over on second time scales. The results show that the transition from metaphase to anaphase correlates with an increase in the number of microtubules and a decrease in their average length. Detailed analysis of the tomographic data revealed that the length of microtubules changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for those microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the observed large-scale reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those that are closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe alone. In anaphase, even microtubules close to the chromosomes show no signs of cutting. This suggests that the most prominent drivers of spindle rearrangements from metaphase to anaphase are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on the presence of katanin.