Dear, Hanamant,

You better store them at 4°C in the fridge. Don´t freeze them because the freezing and thawing causes breaks.

You might have a nuclease contamination in one of your reagents. Are you cleaning up the reactions after PCR and storing products in buffer containing EDTA?

Hi Hanamant,

Like Govinda suggested, it sounds like you have DNAase contamination. That is, I expect that you've proven to yourself that your products are good before you freeze them?

One way to address DNAase contamination is to store your products in a buffer such as TE, a high Tris-EDTA buffer at pH 8. The higher pH and EDTA are meant to inhibit nucleases. Heidelinde is correct in suggesting that repetitive freeze-thaw of your DNA will cause degradation. However, it takes several instances of freeze/thaw for this to happen and it can be avoided by making aliquots of your products so that you don't have to repetitively unfreeze your one stock. I would highly recommend keeping your products at -20C or below. 

Thank you all,,,,, ya i m storing them in Tris-EDTA buffer PH 8 but i stored without purification

careful handling, clean environment , physiological buffer (tis pH 7.2-8) for storage at -20 but in aliquotes will give you better result.