DNA bands disappear

[wishmaes]

Hi..
My PCR product is 190 bps.. it becomes faint and disappears during electrophoresis
Can anyone tell me possible reasons

[Aga]

It is possible that you load to little DNA so after some time of migration the band stretches and disappears. Or you use too little ethidium bromide to stain it.

[Moleecule]

You might be running the gel too long- EtBr runs out of the lower gel portion first. Or gel percentage is too low and the fragment runs as a diffuse band..

[butters]

@wishmaes, can u show us the gel?

DNA migration is from black to red. etbr is from red to black thus longer u ran the gel the less etbr will be at red part of the tank. That is the part where ur low molecular weight DNA will be at the end of the run. It occured when u ran a pre-stain gel. the easiest way is to look at ur ladder. does the 100bp or 200bp is faint and almost disappear? However if the ladder band for 100bp or 200bp is very strong thus it is not related to etbr or running too long. so if possible show us the gel with the ladder beside the pcr product and tell us how much u load. thank!

[ramnivas]

You should use atleast 2 % gel and run it with less voltage. Then you may see the bands.

[Drekketh]

Originally Posted by butters

@wishmaes, can u show us the gel?

DNA migration is from black to red. etbr is from red to black thus longer u ran the gel the less etbr will be at red part of the tank. That is the part where ur low molecular weight DNA will be at the end of the run. It occured when u ran a pre-stain gel. the easiest way is to look at ur ladder. does the 100bp or 200bp is faint and almost disappear? However if the ladder band for 100bp or 200bp is very strong thus it is not related to etbr or running too long. so if possible show us the gel with the ladder beside the pcr product and tell us how much u load. thank!

I will agree with you totally. Prolonged run of a gel, means that you EtBr will migrate off your gel, and QQ then for your bands. In that case you might be able to restain your gel with EtBr, though is not recommended. Also check the intensity of your UV lamps. It has been reported that prolonged exposure of a DNA gel under a strong UV lamp may diffuse and ultimately disappear your DNA bands.