https://www.researchgate.net/post/How_to_purify_contaminated_DNA  

Check this out.. it may be helpful

Thanks a lot K.Suresh

Hi  Abdulrahman,

1. What do you mean by 'copy' DNA? Did you mean to 'amplify' a DNA fragment?

2. You did not explain what is the difference between the first gel and the second gel.

3. It seems that the first gel have some single band. But you may need to optimize the gel running conditions a bit. Add a DNA marker in the first gel, and read your gel to see what is the size of these bands.

 Dear in your second image there appears to be DNA in wells but it appears to move upwards away from the wells in wrong direction.

First check the anode cathode arrangement which you use because opposite settings results in dna movement in wrong direction.

Secondly try to use different dna extraction protocol for tomato seeds.

what concentration of agarose are you using and what is the amplicon size (or size of pcr product).

Moreover when you extract dna from tomato seeds have you run it on agarose gel?

Dear Abdulrahman,

you can check some websites/ forums like

http://www.protocol-online.org/biology-forums/extraction.html

But, why are you trying to isolate DNA from the seeds, its always difficult. See you want DNA not RNA, and DNA is same in all tissues and cells of any organisms. So, better strategy to isolate DNA is always to germinate your seeds, preferably in dark (away from light, so that chlorophyll is not developed which interfers with DNA isolation), harvest the saplings or young plantlets and isolate DNA from them using standard CTAB method.

Once you get pure or clean DNA, you can proceed with the marker study.

Dear Abdulrahmman

Follow these steps

1. Incubation of DNA with Proteinase K for 1 hour at 45 C

2. Add chloroform (v/v) to DNA and nix it

3. Centrifuge and take the aqueous phase

4. Add ammonuim acetate and ethanol (100%)

5. Incubation at -20C for overnight

6. Centrifuge at 10000 rpm at 4 C for 20 min

7. re-suspend of pellet in TE

best wishes