COMPONENT

VOLUME

FINAL CONCENTRATION

1.autoclaved ultra-filtered water (pH 7.0)

20.7µL

-

2.10x PCR Buffer*

2.5µL

1x

3.dNTPs mix ( 25 mM each nucleotide)

0.2µL

200 µM (each nucleotide)

4.primer mix (25 pmoles/µL each primer)

0.4µL

0.4 µM (each primer)

5.Taq DNA polymerase (native enzyme)

0.2µL

1 Unit/25 µL

6.genomic DNA template (100 ng/µL)

1.0µL

100 ng/25 µL

QUESTIONS

SOLUTIONS

1. I get (many) longer unspecific products. What can I do?

Decrease annealing time Increase annealing temperature Decrease extension time Decrease extension temperature to 62-68º C Increase KCl (buffer) concentration to 1.2x-2x, but keep MgCl2 concentration at 1.5 -2mM . Increase MgCl2 concentration up to 3 -4.5 mM but keep dNTP concentration constant. Take less primer Take less DNA template Take less Taq polymerase If none of the above works: check the primer for repetitive sequences (BLAST align the sequence with the databases) and change the primer(s) Combine some/all of the above

2. I get (many) shorter unspecific products. What can I do?

Increase annealing temperature Increase annealing time Increase extension time Increase extension temperature to 74-78º C Decrease KCl (buffer) concentration to 0.7-0.8x, but keep MgCl2 concentration at 1.5 -2mM Increase MgCl2 concentration up to 3 -4.5 mM but keep dNTP concentration constant Take less primer Take less DNA template Take less Taq polymerase If none of the above works: check the primer for repetitive sequences (BLAST align the sequence with the databases) and change the primer(s) Combine some/all of the above

3. Reaction was working before, but now I can't get any product.

Make sure all PCR ingredients are taken in the reaction (buffer, template, Taq, etc) Change the dNTP solution (very sensitive to cycles of thawing and freezing, especially in multiplex PCR) If you just bought new primers, check for their reliability (bad primer synthesis ?) Increase primer amount Increase template amount Decrease annealing temperature by 6-10º C and check if you get any product. If you don't, check all your PCR ingredients. If you do get products (including unspecific ones) reaction conditions as described above. Combine some/all of the above

4. My PCR product is weak. Is there a way to increase the yield?

Gradually decrease the annealing temperature to the lowest possible. Increase the amount of PCR primer Increase the amount of DNA template Increase the amount of Taq polymerase Change buffer (KCl) concentration (higher if product is lower than 1000bp or lower if product is higher than 1000bp) Add adjuvants. Best, use BSA (0.1 to 0.8 µg/µL final concentration). You can also try 5% (v/v, final concentration) DMSO or glycerol. Check primer sequences for mismatches and/or increase the primer length by 5 nucleotides Combine some/all of the above

5. My two primers have very different melting temperatures (Tm) but I cannot change their locus. What can I do to improve PCR amplification?

An easy solution is to increase the length of the primer with low Tm. If you need to keep the size of the product constant, add a few bases at the 3' end. If size is not a concern, add a few bases at either the 3' or the 5' end of that primer.

6. I have a number of primer pairs I would like to use together. Can I run a multiplex PCR with them?. How?