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SynDesign: web-based prime editing guide RNA design and evaluation tool for saturation genome editing

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Title
SynDesign: web-based prime editing guide RNA design and evaluation tool for saturation genome editing
Author(s)
Jinman Park; Goosang Yu; Sang-Yeon Seo; Jinyeong Yang; Hyongbum Henry Kim
Publication Date
2024-07
Journal
Nucleic Acids Research, v.52, no.W1, pp.W121 - W125
Publisher
Oxford University Press
Abstract
Saturation genome editing (SGE) enables in-depth functional evaluation of disease-associated genes and variants by generating all possible single nucleotide variants (SNVs) within a given coding region. Although prime editing can be employed for inducing these SNVs, designing efficient prime editing guide RNAs (pegRNAs) can be challenging and time-consuming. Here, we present SynDesign, an easy-to-use webtool for the design, evaluation, and construction precision pegRNA libraries for SGE with synonymous mutation markers. SynDesign offers a simple yet powerful interface that automates the generation of all feasible pegRNA designs for a target gene or variant of interest. The pegRNAs are selected using the state-of-the-art models to predict prime editing efficiencies for various prime editors and cell types. Top-scoring pegRNA designs are further enhanced using synonymous mutation markers which improve pegRNA efficiency by diffusing the cellular mismatch repair mechanism and serve as sequence markers for improved identification of intended edits following deep sequencing. SynDesign is expected to facilitate future research using SGE to investigate genes or variants of interest associated with human diseases. SynDesign is freely available at https://deepcrispr.info/SynDesign without a login process. Graphical Abstract
URI
https://pr.ibs.re.kr/handle/8788114/15309
DOI
10.1093/nar/gkae304
ISSN
0305-1048
Appears in Collections:
Center for Nanomedicine (나노의학 연구단) > 1. Journal Papers (저널논문)
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