did your agarose checker gel show clean bands for these samples or did they look the same in agarose?

The bands on the agarose gel were clean

Pity. In that case possibly a change in the smeary sequences may be capable of forming 2 conformations both of which are not stable at the ren temperature and are flicking between the 2 conformations sometimes running fast and sometimes running slow depending on the conformation and the final result is a smear. This is a guess. I have no reference to quote as to whether this does happen.

Thank you for your explanation, I appreciate it.

Thank you @Paul Rutland. I actually have challenges in getting my DGGE to work. The ladder I used showed but the sample did not. I have attached the PCR Gel picture and the DGGE gel picture here

This question is probably best in open forum where many can see it Akadiri Olalekan Oladimeji but as a starting point a very strong clean amplificaion is needed since the band may split into many different size bands during dgge if there are snps and mutations in the amplimer. Also the amplimer needs a high GC tail to ensure that the band does not completely melt into single stranded dna and not show any sequence differences. Also your gel looks like PAG stained with ETBR which is a weak stain in PAG. Silver staining is much more sensitive and will often show even weak bands

Thank you @Paul Rutland

As you rightly pointed out, the faint band on the AGE shows its not a very strong clean amplificaion. I will try to optimise the PCR process.

I will also try to stain with silver next time

Thanks for your time Sir

@Paul Rutland

I am still not getting it right ..... I already optimised PCR with another master mix. I got a clearer band on AGE. But my DGGE still turned out to be aweful. I made a 6% gel with 30%-60% gradient. All buffer and reagents used were freshly prepared with molecular grade reagents too. What could I be doing wrongly?

btw ...I couldn't lay my hands on silver stain due to the low fund in my lab.

Thanks for your time