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From design to validation of CRISPR/gRNA primers towards genome editing


Mohd Rizwan Jameel1,2,3, Zubaida Ansari2 & Mohammad Irfan Qureshi1



1Department of Biotechnology, Jamia Millia Islamia, New Delhi - 110025, India; 2Centre for Interdisciplinary Research in Basic Science, Jamia Milia Islamia, New Delhi - 110025, India; 3International Centre for Genetic Engineering and Biotechnology, New Delhi ˗ 110067, India;



Mohd Rizwan Jameel - E-mail: mohdrizwanjameel@gmail.com (+91-9718723180)

Zubaida Ansari - E-mail: zaansari@jmi.ac.in

M. Irfan Qureshi - E-mail: miqureshi@jmi.ac.in


Article Type

Research Article



Received April 14, 2022; Revised May 31, 2022; Accepted May 31, 2022, Published May 31, 2022



CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR-associated system) is used to edit specific genomic sequences with precision and efficacy. There are many online platforms/software for the design of gRNAs and related primers. However, there are concerns in design regarding off-site deletions besides knocking out sequences in the target genes. Nonetheless, a well known robust platform for CRISPR/gRNA primers design is CRISPRdirect. We demonstrate the use of this tool in the design of CRISPR/gRNA primers for soluble starch synthases (SSS) II-1, 2, and 3 genes in the Oryza sativa genome followed by the PCR-mediated amplification of SSS genes with corresponding confirmation towards genome editing having improved phenotype features.



CRISPR, CRISPdirect, primers, knock out, and soluble starch synthase (SSS)



Jameel et al. Bioinformation 18(5): 471-477 (2022)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.