Difference between revisions of "Designing and Generating CRISPR-Cas Mutants"

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==Overview==
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__NOTOC__
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We are using the double-nickase mutation strategy.  This involves the generation of two CRISPR-Cas plasmids per mutation, each of which nicks a different strand, spaced apart by about 40 nt.  To generate a point mutant, you can also include a piece of DNA containing the mutation and allow for homologous recombination.
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[[ Category: Cloning ]]
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[[ Category: Molecular Biology ]]
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[[ Category: Genome Editing ]]
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[[ Category: CRISPR ]]
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==Designing the Targeting Strategy==
 
==Designing the Targeting Strategy==
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* Determine where you want to target the gene and copy that DNA sequence.  It needs to be the genomic DNA from that particular species that is targeted, so if your region of interest spans several introns, you need to copy the genomic DNA not the mRNA sequence.
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* Determine where you want to target the gene and copy that DNA sequence.  It needs to be the genomic DNA from that particular species that is targeted, so if your region of interest spans several introns, you need to copy the genomic DNA not the mRNA sequence.  In other words, if you can design your CRISPR pairs to be within one exon that is best.  In that case submit the exon to the CRISPR tool.  If your target site is close to an exon boundary then you need to submit the genomic sequence around that exon.  You do not want your CRISPR pairs to span an intron.  
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* Paste this sequence into the CRISPR tool at http://crispr.mit.edu/ and select your target species.  When complete select Double Nickase Design
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* Paste this sequence into the CRISPR tool at http://crispr.mit.edu/ and select your target species.  When complete select Double Nickase Design for Guides and Off-Targets for non-Nickase
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* Based on where you want to cut the DNA select the two guide DNA sequences.
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* Based on where you want to cut the DNA select the one or two guide DNA sequences.  Name those sequences based on the nucleotide it cuts after (see cuts after position in the CRISPR tool output).  Use the actual nucleotide from the reference mRNA sequence, not the nucleotide based on the arbitrary region that you pasted into the CRISPR tool.  
 
* Print out, or sketch all of the targeting information into your notes.
 
* Print out, or sketch all of the targeting information into your notes.
  
 
==Generating the CRISPR-Cas Plasmids==
 
==Generating the CRISPR-Cas Plasmids==
  
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You will need to generate two nickase plasmids using the pX335 backbone.  Below is a schematic of the cloning taken from http://www.addgene.org/42335/
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You will need to generate two nickase plasmids using the pX335 backbone, or a single gDNA using the pX459 backbone.  Below is a schematic of the cloning taken from http://www.addgene.org/42335/
  
 
[[File:pX335.png | 700px]]
 
[[File:pX335.png | 700px]]
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===Desigining and Ordering Primers===
 
===Desigining and Ordering Primers===
 
* For each guide DNA sequence you need to order a pair of primers to make this gDNA sequence.   
 
* For each guide DNA sequence you need to order a pair of primers to make this gDNA sequence.   
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* To make the forward primer copy the sequence but remove the NGG site at the end.  Add CACC to the 5' end of it to generate the appropriate overhang.
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* To make the forward primer copy the sequence but remove the NGG site at the end.  Add CACC to the 5' end of it to generate the appropriate overhang. If the gDNA does not start with a 'G' also add a G (CACCG-gDNA)
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* To make the reverse primer reverse transcribe the copied sequence (removing the NGG and the end, and not including the CACC at the other end).  Add AAAC to the 5' end of that reverse transcribed sequence to make the appropriate overhang.
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* To make the reverse primer reverse transcribe the copied sequence (removing the NGG and the end, and not including the CACC at the other end).  Add AAAC to the 5' end of that reverse transcribed sequence to make the appropriate overhang. If you had to add a G to the forward primer, end this primer with a 'C'
 
* Name the primers as follows: '''mm-Pygm-gDNA-62-FWD''' where mm = species; Pygm = your gene name, 62 = where this nickase cuts, and FWD or REV is whether the primer is forward or reverse.
 
* Name the primers as follows: '''mm-Pygm-gDNA-62-FWD''' where mm = species; Pygm = your gene name, 62 = where this nickase cuts, and FWD or REV is whether the primer is forward or reverse.
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===Cloning===
 
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* First digest pX335 vector by adding to a PCR tube:
 
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** 1 ug of pX335,
 
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** 1uL of 10X NEB Buffer 2.1
 
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** 1 uL of CIAP
 
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** 1 uL of BbsI
 
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** water up to 10 uL
 
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** Digest for 1h in, gel purify the fragment from an agarose gel.
 
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* Next prepare the insert by annealing and phosphorylating the primers in a PCR tube:
 
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** ADD ANNEALING INFO
 
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** Run on ANNEALING CYCLE
 
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** Phosphorylate the primers by adding:
 
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*** X uL of ligase buffer
 
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*** 1 uL of T4 PNK
 
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*** Incubate at 37C for 30 mins then 60C for 20 mins to heat inactivate PNK
 
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* Combine the ligation mixture in an eppendorf tube:
 
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** 50 ng of vector (~100 pmoles of vector)
 
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** X uL of insert (~300 pmoles of Insert)
 
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** 2.5 uL of 4X ligation buffer
 
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** 1 uL of T4 DNA Ligase
 
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** Water to 10 uL
 
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* Incubate for 10 min at RT
 
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* Transform into competent cells (see [[Transformation of Bacteria]])
 

Latest revision as of 12:48, 14 July 2015



Designing the Targeting Strategy

  • Determine where you want to target the gene and copy that DNA sequence. It needs to be the genomic DNA from that particular species that is targeted, so if your region of interest spans several introns, you need to copy the genomic DNA not the mRNA sequence. In other words, if you can design your CRISPR pairs to be within one exon that is best. In that case submit the exon to the CRISPR tool. If your target site is close to an exon boundary then you need to submit the genomic sequence around that exon. You do not want your CRISPR pairs to span an intron.
  • Paste this sequence into the CRISPR tool at http://crispr.mit.edu/ and select your target species. When complete select Double Nickase Design for Guides and Off-Targets for non-Nickase
  • Based on where you want to cut the DNA select the one or two guide DNA sequences. Name those sequences based on the nucleotide it cuts after (see cuts after position in the CRISPR tool output). Use the actual nucleotide from the reference mRNA sequence, not the nucleotide based on the arbitrary region that you pasted into the CRISPR tool.
  • Print out, or sketch all of the targeting information into your notes.

Generating the CRISPR-Cas Plasmids

You will need to generate two nickase plasmids using the pX335 backbone, or a single gDNA using the pX459 backbone. Below is a schematic of the cloning taken from http://www.addgene.org/42335/

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Desigining and Ordering Primers

  • For each guide DNA sequence you need to order a pair of primers to make this gDNA sequence.
  • To make the forward primer copy the sequence but remove the NGG site at the end. Add CACC to the 5' end of it to generate the appropriate overhang. If the gDNA does not start with a 'G' also add a G (CACCG-gDNA)
  • To make the reverse primer reverse transcribe the copied sequence (removing the NGG and the end, and not including the CACC at the other end). Add AAAC to the 5' end of that reverse transcribed sequence to make the appropriate overhang. If you had to add a G to the forward primer, end this primer with a 'C'
  • Name the primers as follows: mm-Pygm-gDNA-62-FWD where mm = species; Pygm = your gene name, 62 = where this nickase cuts, and FWD or REV is whether the primer is forward or reverse.
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