The gDNA is much too big to go through the structure of the agarose. what u see above is the template u have used.

Genomic DNA that has not been subjected to any sort of shearing can easily be >10kb average fragment size (fragmented a little bit during lysis and from sample processing). Thus, it would be stuck in the well due to size exclusion. 

Are those wells in which you are trying to run out the gDNA? Or are they PCR reaction samples that you are loading? 

If they are PCR samples, can you tell us how much template you are using?

As said above, gDNA is much to large to travel through your gel. If you're interested in just a certain region, you should PCR just that area.

It could happen due to one or more of the following reasons:

1. The well surface is uneven: It retains (adheres) some of the migrating DNA

2. Concentration of DNA must be equivalent/almost equal, if not same. Else varying concentration will show some differences in migration pattern.

3. Size exclusion (as mentioned above by Dr Nathaniel)

 Thanks for the suggestion. Nathaniel I am loading the PCR product and template concentration is 20 ng, but the problem is that with same condition i am observing the band of my intersest in PCR reaction in the DNA template from the whole adult worm as seems in the picture in first two wells, DNA stucking problem is with DNA template of the larvae. Non template control is working fine.

What's the concentration of Agarose u r using? For visualization of gDNA best concentration of agarose is in between 0.8-1.0 %. lambda phage DNA should be run along with gDNA for approx. size estimation like we run appropriate molecular marker with PCR products.

It all depends on your downstream usage. If you want to run a PCR for example it is often not necessary to worry about your DNA too much.

If you really want it to enter the gel try this:

1) Go down to a 0,5%-0,6% agarose gel.

2) Lower the voltage to 2-3 V/cm.

3) Allow your DNA to dissolve in TE over night at 4°C.

4) Check for carbohydrate contamination.

5) Check your 230/260 ratios.

6) Lower the concentration you put on the gel.

7) Try to reprecipitate the DNA.

8) Add additional purification steps, like Proteinase K treatment.

Dear Paramjit Kaur,

Decrease Agarose concentration in to 1 or 0.8% then run in 150 volt for 10-15 minutes. In case of higher concentrated DNA you may get some struck DNA in the well side, it happen normally as you are doing a short time run and sometime smooth wall well retain much lower then rough surface well surface in gel.

Better to dilute your sample DNA in to 4X or 10X then load, hope this problems will be eliminated.

Sometimes high protein contain in extracted DNA also shows such condition. Check 260/280 ratio. Specially 280 nm, protein in DNA samples give absorbance

Good Luck !

Genomic DNA has migrated into the gel only slightly. Its exactly what you expect. But you used truly MASSIVE amounts of DNA for the PCR (I think your estimate of 20ng is wrong by a factor of 10 or even 100). I suggest you make serial 1:10 dilutions of just one sample of the gDNA and carry out PCR again. Don't run the gel too long: its reassuring when you see the primers at the bottom -it at least confirms that you added them!

Genomic DNA is too big for your Agarose concentration. You can try to reduce the agarose concentration (less than 1% should work). Since it was PCR products, try to use less gDNA to lessen the gDNA band intensity so the amplicons band can have better resolution. Good luck

I also extracted DNA and ran the gel electrophoresis, the DNA remained in the well. My gel concentration was at 1%. Do you think reducing the gel concentration to 0.8% would be of any effect to that gDNA movement?