You can run on 2% of agarose gel with about 90 volt for about one hour and can you check each 0.5 h and can increase voltage depending on the resolution of your fragmented bands and comparing with ladder.

I hope this helpful

1% gel with TAE buffer worked best for me. You may try to start running it at low voltage (~80-90V) for about 15 min to allow DNA to smoothly enter the gel and then increase voltage up to 120-130V and run it for about another 30 min - this is for a medium-size gel box (~150ml).

Also, you may check the water you use for your PCR-cocktail. Super 'fresh' and clean water gives the best 'clean' gel picture (otherwise there might be some smearing).

Hope it helps! Best of luck!

Dear Francois Kroll

I know that you asked for agarose gel but you can also try a capillary-based electrophoresis (ABI sequencer). One of your primers (e.g. forward) has to be fluorescent-labeled (e.g. FAM). Fragment analysis with size standard (e.g. LIZ) shows you the exact length of your PCR product. You can compare a control sample and sample with expected deletion with a high accuracy.

Regards,

Marcela

What the point? from "

- Run the gel backwards for the first 10-15 min"

run low electroendosmosis grade agarose at low temperature and ideally in a cold room to stop thermal diffusion and band broadening. Also check that the deletion may make/destroy a restriction enzyme site and cut the pcr product before running the gel. If this is not the case then cut the pcr product with another enzyme ( or amplify with primers giving a smaller product) as small changes of size show better with small fragments. If the deletion is perhaps 3bp in 100bases or more then agarose is not ideal and use polyacrylamide gels

You can run on 2% of agarose gel with about 90 volt for about one hour and can you check each 0.5 h and can increase voltage depending on the resolution of your fragmented bands and comparing with ladder.

I hope this helpful