Does extracted DNA degrade after a certain time period? For direct use as template in PCR runs. Chelex 100 5-10% w/v extraction. Without listing the whole protocol, in the end the supernate is decanted off and then stored at 4°C. I was under the impression that this could be stored and later used almost indefinately but two of four samples extracted several months back failed to produce a product (when it was known they should have). Assuming no mistakes were made and the reactions were the same, is there a technical reason the template would degrade to an unusable point? Is there a rule of thumb about how long it can reasonably be expected to last?

My rule of thumb for DNA samples (in TE or water) - if I have plans to use it that week, I store at 4C. If I plan on using it within a month, I store at -20C. If I'm not sure when I will use it, I keep multiple aliquots at -80C. DNA can degrade by acid hydrolysis in water, because of contaminating nucleases in the sample, and by multiple freeze/thaw cycles.