Hi:) Why do you think that any of them is contaminated. Contamination could be caused by any of the reaction components of aerosol in the pipette. The easiest way to solve this problem is to use the fresh solution of everything and filter tips.

I might add to Maja's answer: Do wash your pipette, ESPECIALLY the interior of the outlet, after you disassemble the whole thing.

1)water+soap

2)light (!!!) solution of NaOH (no more than 0,5M). This will ensure remowal of contaminating DNA. Washing with ethanol would only precipitate it more.

Primer will not easily contaminated. Generally master mix will get contamination, kindly check master mix. 

In my opinion do a fresh dilution of your working primers if you think so. But i think you should check your water which you are using during PCR master mix preparations. In these type of situations you have to check each and every components individually by adding or subtracting in you PCR reactions.

Hi Abhischek, unfortunately every component of your reaction mix could be contaminated, not necessarily your primers. Washing your pipette regularly as colleagues suggest is always good practice (mostly if your template is in plasmids you work with using the same pipettes), and using plugged tips for PCR also helps a lot. Anyway, it is very good practice to always aliquot all your costly reagents for PCR, including the Taq polymerase itself (you can probably risk not aliquoting the buffer and the MgCl2), so that you don't pipette from the same tube more than 5-10 times and you can afford throwing everything away if you get contamination.

In practice to solve your problem you should change ALL your reagents, including water, which is anyway safer just to take fresh from a MilliQ system every time you start a PCR.

Thank you all for your contribution. But may be I didnot explained it properly.

Actually, I have already changed and manupulated all other reagents of PCR and then came to know that the primers are the main culprit. Now, its confirmed that my primary stock solution of primer is already contaminated somehow. So, my question is, that how to know which one is contaminated already, as I have to purchase a fresh one for that particular primer. 

If you have another set of primers that you know aren't contaminated then you could set up two mastermixes, one with the potentially contaminated primer A as an extra addition, and a second with the other questionable primer as an extra addition. Obviously though the new mastermixes should have primers which you know are sterile (you can set up controls to ensure this of course), and be able to target the contamination in the questionable primers, i.e. have the same target. Or of course have two mastermixes, one of the questionable primers with a known sterile one in each.

Out of curiousity, when you say the primers are the "main culprit", what do you mean? Are there contamination issues elsewhere? If so you should try to eliminate these fo certain before purchasing (and potentially contaminating) new primer.

And as Pietro has said, always aliquot out your stocks to avoid having to throw out whole samples in future if contamination arises (plus helps with reagent integrit). Good luck.

Did you get amplification with other primers in the negative control or water-control? As for checking which primer(s), maybe you can take OD using nanodrop at OD260nm. Your original primer tube should have the number of moles which you would have dissolved to get the primer to 100uM, so you can try and see if you get anything beyond 100uM with your primers. 

I would do a PCR with different primers, which works properly and add to one reaction tube "contaminated" primer 1 and to the second tube "contaminated" primer 2. Maybe that will help. (hopefully no primer dimer or stg similar)

Good suggestion from Monika, really addressing the question... but if you only have one pair of primers it's easier and cheaper to just order them newly synthesized... and for the future make a stock dilution, typically 100 uM, and then, using plugged tips, prepare your working 10-20 uM dilutions.

Good luck.