scholarly journals CRISPR-offinder: a CRISPR guide RNA design and off-target searching tool for user-defined protospacer adjacent motif

2017 ◽  
Vol 13 (12) ◽  
pp. 1470-1478 ◽  
Author(s):  
Changzhi Zhao ◽  
Xiaoguo Zheng ◽  
Wubin Qu ◽  
Guanglei Li ◽  
Xinyun Li ◽  
...  
Keyword(s):  
Guide Rna ◽  
Protospacer Adjacent Motif ◽  
Target Searching ◽  
Rna Design

Flexible guide-RNA design for CRISPR applications using Protospacer Workbench

2015 ◽  
Vol 33 (8) ◽  
pp. 805-806 ◽  
Author(s):  
Cameron Ross MacPherson ◽  
Artur Scherf
Keyword(s):  
Guide Rna ◽  
Rna Design

scholarly journals Enhancement of target specificity of CRISPR–Cas12a by using a chimeric DNA–RNA guide

2020 ◽  
Vol 48 (15) ◽  
pp. 8601-8616 ◽  
Author(s):  
Hanseop Kim ◽  
Wi-jae Lee ◽  
Yeounsun Oh ◽  
Seung-Hun Kang ◽  
Junho K Hur ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Engineering ◽  
Target Genes ◽  
Target Sequence ◽  
Energy Potential ◽  
Guide Rna ◽  
Sequence Recognition ◽  
Protospacer Adjacent Motif ◽  
Effective Manner ◽  
Target Dna

Abstract The CRISPR–Cas9 system is widely used for target-specific genome engineering. CRISPR–Cas12a (Cpf1) is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cas12a has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and off-target cleavage issues may become more problematic when Cas12a activity is improved for therapeutic purposes. Therefore, we investigated off-target cleavage by Cas12a and modified the Cas12a (cr)RNA to address the off-target cleavage issue. We developed a CRISPR–Cas12a that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR–Cas12a and SpCas9 nickase effectively work in the intracellular genome is suggested. Chimeric guide-based CRISPR- Cas12a genome editing with reduced off-target cleavage, and the resultant, increased safety has potential for therapeutic applications in incurable diseases caused by genetic mutations.

Guide RNA Design for CRISPR/Cas9-Mediated Potato Genome Editing

2018 ◽  
Vol 479 (1) ◽  
pp. 90-94 ◽  
Author(s):  
A. V. Khromov ◽  
V. A. Gushchin ◽  
V. I. Timerbaev ◽  
N. O. Kalinina ◽  
M. E. Taliansky ◽  
...  
Keyword(s):  
Genome Editing ◽  
Potato Genome ◽  
Guide Rna ◽  
Rna Design

scholarly journals DeepCRISPR: optimized CRISPR guide RNA design by deep learning

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Guohui Chuai ◽  
Hanhui Ma ◽  
Jifang Yan ◽  
Ming Chen ◽  
Nanfang Hong ◽  
...  
Keyword(s):  
Deep Learning ◽  
Guide Rna ◽  
Rna Design

scholarly journals GuideScan software for improved single and paired CRISPR guide RNA design

2017 ◽  
Vol 35 (4) ◽  
pp. 347-349 ◽  
Author(s):  
Alexendar R Perez ◽  
Yuri Pritykin ◽  
Joana A Vidigal ◽  
Sagar Chhangawala ◽  
Lee Zamparo ◽  
...  
Keyword(s):  
Guide Rna ◽  
Rna Design

scholarly journals Complete guide RNA design for CRISPR-mediated regulation of human long noncoding RNA transcription

2018 ◽  
Author(s):  
Amir Saberi ◽  
Renjun Zhu ◽  
Chulan Kwon
Keyword(s):  
Noncoding Rna ◽  
Large Fraction ◽  
Guide Rna ◽  
Transcription Start Sites ◽  
Common Reference ◽  
Functional Studies ◽  
Short Palindromic Repeat ◽  
Genome Annotations ◽  
Rna Design ◽  
Genome Scale

AbstractTranscription inhibition and activation of long noncoding RNAs (lncRNAs) mediated by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology provides potential advantages in high-throughput functional genomics studies over RNA interference or overexpression platforms. In this work, we identify over 90,000 lncRNA transcription start sites (TSSs) based on the MiTranscriptome human genome annotation and design single guide RNA (sgRNA) libraries with strong predicted activities and low off-target effects for CRISPR-mediated inhibition and activation (CRISPRi/a) of their transcription. A large fraction of these TSSs correspond to putative genes that are not annotated in common reference genome annotations and have never been functionally studied. Our CRISPRi/a libraries, or their context-dependent subsets, are potentially useful in genome-scale functional studies of human lncRNAs.

scholarly journals kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9

2019 ◽  
Author(s):  
Mahmudur Rahman Hera ◽  
Amatur Rahman ◽  
Atif Rahman
Keyword(s):  
Genome Editing ◽  
Design Tool ◽  
Target Region ◽  
Guide Rna ◽  
Guide Rnas ◽  
Rna Design ◽  
Reference Genomes ◽  
Target Effects

AbstractGenome editing using the CRISPR/Cas9 system requires designing guide RNAs (sgRNA) that are efficient and specific. Guide RNAs are usually designed using reference genomes which limits their use in organisms with no or incomplete reference genomes. Here, we present kRISP-meR, a reference free method to design sgRNAs for CRISPR/Cas9 system. kRISP-meR takes as input a target region and sequenced reads from the organism to be edited and generates sgRNAs that are likely to minimize off-target effects. Our analysis indicates that kRISP-meR is able to identify majority of the guides identified by a widely used sgRNA designing tool, without any knowledge of the reference, while retaining specificity.

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