3.4 Leaf Squish & PCR

Salk genotyping: Leaf Squish & PCR

See revised instructions handout below.


correct PCR cycle. should be

  • 98C 15s
  • 60C 30s
  • 72C 1min 32-40 cycles

Goal for this lab: Genotype Salk line plants, looking for homozygous mutants.

the RP is always on the side of the flanking sequence, that is, RP is always on the 3' end of the insertion. Therefore, the PCR reaction should always be set up as LB+RP for HM and LP+RP for WT. http://signal.salk.edu/tdnaprimers.2.html

Use 3 primers in a single reaction (GSP1, GSP2, LBP) OR

Run 2 separate gels

LB 195

LBb1.3 ATTTTGCCGATTTCGGAAC (111 bp from left border)

Should be on a long-lab day! If it can't be on the long day, it should stop at DNA extraction, then do PCR plus gel the next period!

Set out the 24-tube microcentrifuges. They have 13 samples.


(See materials for Lab 1.1)

ingredient mL per rxn x 26 rxn x 19 pairs
DEB 0.6 15.6 296.4
KOAc 0.25 6.5 123.5
Isoprop 0.6 15.6 296.4
70% EtOH 1.4 36.4 691.6
T10E5 0.225 5.85 111.15
NaOAc 0.025 0.65 12.35
100%EtOH 0.5 13 247
T10E1 0.05 1.3 24.7

Put out 3 double block dry baths at 65C

salkprimerlabels2013.doc59 KB
lab3-4-redo.docx208.99 KB
lab_3-4-leafsquish.docx138.66 KB
2015-phire-genotyping.docx172.64 KB


DNA yield from leaf punch

The yield is low - many student get no bands at all. Not much better than when we used the older quick squish buffer.

One pair repeated the experiment with quick squish and did no better.

Check primers first?