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Grna oligonucleotides

Manufactured by Merck Group

GRNA oligonucleotides are synthetic RNA molecules designed for use in research and laboratory applications. They are composed of a guide RNA (gRNA) sequence that can be programmed to target specific DNA sequences. GRNA oligonucleotides are commonly used in gene editing and other molecular biology techniques.

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5 protocols using grna oligonucleotides

1

Constructing Retroviral Vectors for Gene Expression

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Addgene plasmid #102919 (https://www.addgene.org/102919/) was used to express ABE7.10 for the in vitro experiments. For U6-sgRNA expression plasmids, five different gRNA oligonucleotides were synthesised (Sigma) and cloned into the pU6gRNA vector using the BsmBI restriction site (Supplementary Table 2). To generate the retroviral construct for the GFP switch-on system, gfp was PCR-amplified from pSERS11 SF GFP24 (link) and modified by using a long primer containing Gly-Ser stretch, the stop codon TAG and the restriction site for NcoI (Sigma; P1 and P2 in Supplementary Table 1). The backbone and the PCR product were digested using NcoI and NotI (NEB) and ligated with T4 ligase (NEB).
Similarly, to generate the retroviral construct for the HFE-GFP switch-on system, gfp was PCR-amplified from pSERS11 SF GFP using a long primer containing 20 bp of the HFE sequence, carrying the stop codon TAG, a Gly-Ser stretch and the restriction site for NcoI (Sigma; P3 and P2 in Supplementary Table 1). The backbone and the PCR product were digested using NcoI and NotI (NEB) and ligated with T4 ligase (NEB). Amplification of plasmids was performed in One Shot™ Stbl3™ Chemically Competent E. coli (C737303, Invitrogen).
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2

Generating Myc-targeting CRISPR guides

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The guide RNAs (gRNAs) were designed using the R package CRISPRseek (58 ). The three highest-ranking gRNAs were chosen. Among these was guide Myc.87 (5′-GCTGTACGGAGTCGTAGTCG-3′), a gRNA that targets Myc in the first exon. The gRNA oligonucleotides were purchased from Sigma-Aldrich, and phosphorylated and annealed according to previously published protocols (59 (link)). The duplex oligonucleotides were subsequently cloned into the lentiCRISPR_V1 plasmid (Addgene #49535), replacing the 2 kb filler.
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3

CRISPR guide design and cloning

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The guide RNAs (gRNAs) were designed as previously described, and the highest-ranking gRNAs were chosen (Nowak et al., 2015 (link)). Anti-IPO11 guides were: g.1, 5′-CACAGCAGTATCCTGACTGG-3′; g.2, 5′-CCCTTGATATAAATGTACGG-3′; g.3, 5′-ATGGGATTGATCGTTACTGG-3′; and g.4, 5′-GAAAAGTCAACATTGCGTGC-3′. The gRNA oligonucleotides were purchased from Sigma-Aldrich, phosphorylated, and annealed according to previously published protocols (Cong et al., 2013 (link)). The duplex oligonucleotides were subsequently cloned into the lentiCRISPRv2 plasmid (plasmid 52961; Addgene), replacing the 2-kb filler as previously described (Sanjana et al., 2014 (link); Nowak et al., 2015 (link)).
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4

Cloning and Viral Transduction Protocol

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We obtained the pET28aLIC (Plasmid #26094) and pL-CRISPR.efs.gfp (plasmid # 57818) plasmids from Addgene and the pLVXTRE3GZsGreen1 vector from Clontech. We amplified the coding sequence of the NT5C2 cDNA from pLOC-NT5C2 (Tzoneva et al., 2013 ) and cloned it into the pET28aLIC vector using In-fusion cloning using the In-Fusion HD Cloning Kit (Clonetch) following manufacturer guidelines. We cloned the NT5C2 S408-D415 loop deletion mutation into the pET28aLIC and pLVXTRE3GZsGreen1 vector using Gibson Assembly using the Gibson Assembly Master Mix (New England Biolabs) following manufacturer guidelines. We cloned a truncated active form of NOTCH1 ΔE-NOTCH1 (Schroeter et al., 1998 (link)) into the pMSCV-pBabeMCS-IRES-RFP retroviral vector (Addgene plasmid # 33337). We generated lentiviral vectors expressing CAS9 and gRNAs targeting the arm segment of mouse Nt5c2 by cloning the corresponding gRNA oligonucleotides (Sigma-Aldrich) into pL-CRISPR.efs.gfp as reported (Shalem et al., 2014 (link)).
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5

Construction of NT5C2 Mutant Plasmids

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We obtained the pET28aLIC (Plasmid #26094) and pL-CRISPR.efs.gfp (Plasmid #57818) plasmids from Addgene and pLVXTRE3GZsGreen1 vector from Clontech. We amplified the coding sequence of the NT5C2 cDNA from pLOC-NT5C2(7 (link)) and cloned it into the pET28aLIC and pLVXTRE3GZsGreen1 vectors using In-fusion cloning using the In-Fusion HD Cloning Kit (Clontech) following manufacturer guidelines. We generated lentiviral vectors expressing CAS9 and gRNAs targeting exon 3 or 8 of Nt5c2 by cloning the corresponding gRNA oligonucleotides (Sigma-Aldrich) into pL-CRISPR.efs.gfp as reported(42 (link)). We cloned NT5C2 R238W, K359Q, R367Q, L375F, D407A, K217R, K217Q, K344R, K344Q, S418A, S418D, S502A, S502D, D229A and D229S mutations into the pLOC-NT5C2(7 (link)) or pET28aLIC-NT5C2 by site directed mutagenesis using the QuikChange II XL Site-Directed Mutagenesis kit (Agilent Technologies) according to manufacturer’s guidelines.
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