Do you observe any streaks in the lanes? Sometimes if your buffers have any nuclease contamination the DNA degrades and you might observe streaks on the gel rather than bands.

Don't use an old vial of enzyme or the buffer, they are often the  cause of non specific cleavages and DNA degradation.

Make sure, you are putting enough DNA to visualize on gel. If you don't see anything in your aliquot, then run everything at once. If nothing is visible, get a new vial of your restriction enzyme.

Dear Hussain

The given information is not complete. Though, confirm first whether your product having restriction sites. If yes which are they. Have you observed any smear or anything else in Gel.

If possible provide gel picture. 

as far as the activity of restriction system is concerned, you can check it by digesting your plasmid vector.

second, are you sure about your PCR product. In my experience a faint PCR band is always useless for any further process.

third, may be your restriction reaction is not appropriate. These kind of results were observed by me when restriction enyzyme was used at a very high final concentration. 

first check the restriction enzyme you are using (try to adhere to the protocol), how many restriction sites are there in your sequence (use the appropriate one for your experiment). use 1,5 % to 2% agarose gel and don't run it so much (30 min. is enough). please also try to give more useful information about your experiment in order to give you a specific answers.  

If you can attach a picture of your pre-digest gel and post-digest gel, I think you would get better advice. Also, what is the final concentration of your restriction enzyme?

Can it be that the enzyme has star activity and is just degrading everything? For how long are you incubating? All suggestions above are useful. When I have mysterious digestions like these, I run the undigested product, the product just with the digestion buffer, and finally the digested product. Just in case the buffer is contaminated, even if it is a new vial (your pipettes might be contaminated somehow, maybe running it with filter tips once just in case?)

In my opinion, your digestion is not working.

I think you actually have problem with digestion, as suggested above, in result your DNA degraded. Better way - revise all steps, replace the enzyme and buffer to another and repeat the experiment. Be sure to use the control.

You can do one thing.....Carefully see how much restriction enzymes you are adding and how much u supposed to be...Titration of restriction enzyme is very important. Besides, are you adding any BSA?... some buffers or enzyme activity requires BSA...Fianally, what is your incubation period? If you are incubating for 1h then you try for overnight incubation for enzymes that are generally old...Hop it helps

First thing, I can't understand the picture of the gel. No markers and no indication of lanes (which is which), so honestly I can't comment on that.

Well, the size of the bands you see on gel, are they of the right size? As mentioned earlier, please check your enzyme with your plasmid if its working properly, perhaps run it side by side with your PCR product so you give equal treatment to both samples.

This sounds very much as if your enzyme or one of the other reagents is contaminated with DNase. Including a small plasmid such as pUC13 as a digestion control would be a good way of checking this. 

Hi Hussain,

I propose to cut enough of DNA and run your digestion product on polyacylamide gel and non in agarose. 

You can prepare 10% Acrylamid Gel us follow:

- 3 ml Acrylamid 40%

- 1,2 ml TBE10x

- 120µl Ammonium persulfate

- 10µl TEMED

- 7,67 ml H2O

Good luck

As "Andrew Jenkins" suggested I would first run a control for DNase contamination and to identify the source of contamination such as your buffer, water etc. 

well . if you sure that you have your specific product :

make sure that you load a sufficient quantity of your digested  DNA .

for example : if you load 5ul of your PCR product in this gel image . in this case you need to digest at lest 10 ul of your PCR product and then load all the digestion mixture to the gel .

best....