What do you mean by DNA degraded after extraction? Do you mean you run the extracted DNA on gel and it looks degraded on the gel? What did it look like? No band at the target size region but have faint smearing at bottom of gel? (your DNA may not be eluted) or very clear smearing at bottom of gel? this means your DNA is degraded but as far as I know, there is low possibility of DNA clean up from gel or PCR getting degraded.

Tips on getting better results on DNA gel extraction:

1. Try to minimize exposure of gel to UV when excising, meaning that excise the band as fast as you can, as longer exposure to UV will damage DNA

2. when excising bands from gel, cut off as much gel as you can from the side of the band, since you use very high gel percentage, too much gel might clog the column

3. Double or triple the NTI buffer and make sure that the gel is totally dissolved. Try not to put more than 200mg of gel for each column. Ensuring these can reduce possibility of column clogging

4. During the elution step, you can try incubate for 5-10 min instead of 1 min.

Hope this helps, Good luck!

Dear Wong Ling Chie, thanks for your nice answer. I did not run another gel, as a matter of fact. I just checked the quantity of DNA extracted by Qubit, which shows a concentration between 0.144-0.146 ng/micrliter. I also checked with the bioanalyzer 2100 using DNA high sensitivity kit. Both assays indicate no DNA in the samples.