GeneTargeter: Automated In Silico Design for Genome Editing in the Malaria Parasite, Plasmodium falciparum
Name
crispr.2021.0069.pdf
Description
Published version
Size
7.7 MB
Format
Adobe PDF
Checksum (MD5)
95bf43220f2c2be4419934ca5aa1ea67
Author(s)
Cárdenas, Pablo
Esherick, Lisl Y
Chambonnier, Gaël
Dey, Sumanta
Turlo, Christopher V
Nasamu, Armiyaw Sebastian
Niles, Jacquin C
Date Issued
2022
Journal
The CRISPR Journal
Publisher
Mary Ann Liebert Inc
Citation
Cárdenas, Pablo, Esherick, Lisl Y, Chambonnier, Gaël, Dey, Sumanta, Turlo, Christopher V et al. 2022. "GeneTargeter: Automated In Silico Design for Genome Editing in the Malaria Parasite, Plasmodium falciparum." The CRISPR Journal, 5 (1).
Version
Final published version
Abstract
Functional characterization of the multitude of poorly described proteins in the human malarial pathogen, Plasmodium falciparum, requires tools to enable genome-scale perturbation studies. Here, we present GeneTargeter (genetargeter.mit.edu), a software tool for automating the design of homology-directed repair donor vectors to achieve gene knockouts, conditional knockdowns, and epitope tagging of P. falciparum genes. We demonstrate GeneTargeter-facilitated genome-scale design of six different types of knockout and conditional knockdown constructs for the P. falciparum genome and validate the computational design process experimentally with successful donor vector assembly and transfection. The software's modular nature accommodates arbitrary destination vectors and allows customizable designs that extend the genome manipulation outcomes attainable in Plasmodium and other organisms.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1089/CRISPR.2021.0069
