Maybe it is the polymerase... In some lanes you see something that looks like primer dimers and no amplification product is visible. Did you use the same templates in both sets of PCR reactions (good gel and bad gel)?

Cheers, Christian

@Christian and @Laurence, Template is crude genomic DNA and we used the same template on both the gels. But it is not possible that the DNA is degraded because they were freshly prepared only a month ago. Could polymerase really be the problem? because it was working just fine until last week.

Do you have plasmid DNA that contains the primer binding sites? Then you could perform a PCR with the plasmid as a template. If you get a fine signal here you can rule out that it is the polymerase (or another PCR component).

Good luck!

I agree with Laurence as i also got such results when my samples contained crude genomic DNA few months old samples

Hello.

If I were you , firstly I would make new TBE buffer for agarose gel and electrophoresis since ladder also looks like smear. If that doesn't work I would try with some other DNA samples.

Good luck!

Thanks all for the valuable inputs! @Laurance, I will keep your suggestions in mind and lets hope that it works.

Thanks again Laurence! will let you know

Hi Padmagiri..

Most probably it is degradation of your template DNA. One remote possibility is that their is quite an amount of RNA in your template. Check 260/280 ratio. It shall give you an idea about the RNA in your sample.

the bands in the new gel look much smaller than the original bands to me. I do not see a negative control ( no sample) but I wonder if you have some primer dimer contamination and the p-d is just taking over the reaction because dimer production is so efficient and the proper band is just not able to compete. do your negative controls also show this band.Can you move one of your primers outside the original position so using a different primer set