Lidstrom:QuikChange Site-Directed Mutagenesis

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The zillion kits

Kit	PCR: min/kb	# of cycles	Dpn1 digetstion time	Mutations @ multiple sites?	Manual link	10 reaction kit item #	30 reaction kit item #
QuikChange (original kit: don't buy)	1 min?		1 hr	one pair of primers --> mutations in one DNA region		200519. $263.	200518. $700
QuikChange II	1 min	12-18	1 hr	one pair of primers --> mutations in one DNA region	QuikChange II manual	200523. $263	200524. $700
QuikChange MULTI	1 min?		1 hr	YES. priming w/ multiple primers & primers aren't paired w/ reverse compliment		Academic: 200515. $370	200514 = academic kit = $886.50.
QuikChange Lightning	30 seconds		5 minutes	one pair of primers --> mutations in one DNA region		210518. $253	210519. $673
QuikChange Lightning MULTI	30 seconds	30 cycles	5 minutes	YES. priming w/ multiple primers & primers aren't paired w/ reverse compliment	Manual for Catalog # 210513 and #210515	Academic: 210515. $357	Academic: 210513. $948.
QuikChange, XL (large templates)	FAST (30 sec/kb PCR, "5 min" Dpn1)	one pair of primers --> mutations in one DNA region	1 min?		1 hr ?	200517. $263.	200516. $700
QuikChange II, XL (large templates)	1 min?		1 hr?	one pair of primers --> mutations in one DNA region	XL manual	200521. $263.	200522. $700
QuikChange II + Electroporation cells (not chem. comp)	1 min?		1 hr	one pair of primers --> mutations in one DNA region	QC + electroporation manual	200555

Manuals

• QuikChange II: use 2 oligos (reverse compliments) and only do mutations at one priming site
• QuikChange II Lightning: use 1 oligo, and can introduce mutations at multiple sites

QuikChange Basics

• You can buy a kit from Agilent or use your own ingredients (not true for multi kit though).
• The marketing term "lightning" refers to an improved Dpn1, that degrades template (unmutated template) more efficiently.
• If you buy the kits, 10uL rxns are plenty (this is ~4x less than the protocol suggests) and transformations using 10uL of competent cells are suitable. If you are introducing mutations with multiple priming sites, you could consider transforming more.

Quik Solution

• Quik Solution is probably pure DMSO.

Two (main) QuikChange kits are available

• QuikChange Lightning.
  • For mutations contained within a single primer
• QuikChange Lightning Multi
  • For mutations contained in >1 primer
  • Can be used for mutations contained in 1 primer, but this kit is more expensive than the single kit and likely has lower efficiency.
• Both kits:
  • come with chemically competent XL10-Gold. This is perhaps the most valuable part of the kit.

Primer Design

• Use online primer design tool. Account required.
• Use guidelines in the manual:

  • 

    primer design instructions from the manual

Reaction Recipes

• Regular (2 reverse compliment primers)

  • File:Quik change lightning NOT-multi kit reaction recipe.jpg

    reaction recipe instructions from the non-multi Lightning manual

• Lightning:

  • 

    reaction recipe instructions from the Lightning manual

  • QuikSolution (DMSO) can be added: 0 - 0.75uL per 25uL of reaction.
  • ds-DNA template = 50ng per 25uL for <5 kb, or 100 ng per 25uL if for >5 kb.
    • 2ng/uL works fine for 6kb plasmids. -Janet Matsen 9/2014
  • primers:
    • our lab usually dilutes primers to 10uM, and the recipes are for ng. Usually 10uM is ~100ng/uL.
    • Add ~0.5uL of primer per 8uL of reaction. *Janet Matsen 9/2014

Thermocycling

• Regular LIGHTNING Kit (but not multi LIGHTNING kit)

  • 

    thermocycling protocol from NOT-multi manual

• Multi Lightning Kit

  • 

    thermocycling protocol from Multi + Lightning manual

Tips

• Though the lightning Dpn1 enzyme claims to be effective in 5 minutes, you might as well incubate it for 30 minutes, just in case it lowers your unmutated background further.
• If you want to use one priming site to introduce mutations, it is about the same price to order 1 oligo and do it with the multi kit, or order 1 pair of complementary oligos and do it with the non-multi kit. If ordering less primers is appealing, go for it. A small decrease in efficiency might be seen, but it shouldn't be a problem based on JM's use of one primer to introduce 24 different mutations. (The first colony screened had the desired mutation in 90+% of the sequenced plasmids and the efficiency was quite high.)
• From the manual:
  • Thaw the dNTP mix once, prepare single-use aliquots, and store the aliquots at –20°C. Do not subject the dNTP mix to multiple freeze-thaw cycles
• Make your kit last longer by doing 8uL reactions, not 25uL. You only transform 1uL per reaction so this is always plenty.