I am doing research on C-reactive protein coding gene and how its
polymorphisms affect CRP levels and atherosclerosis genesis. I am
using PCR and a restriction enzyme MaeIII to resolve patients'
genotypes (GG, GC or CC).

But alas! for the last month I have not been able to get any results,
before that I managed to resolve approx. 20 cases. Most of the samples
on 1% DNA Agar gel show DNA smears, and some samples show very thin
bands (I have not used the restriction enzyme because it is so
expensive and the PCR is not working efficiently enough at the
moment).

PCR optimisation guides tell that when there is a lot of smearing, one
should try to reduce the amount of DNA in the samples. However, while
those few bands are as thin as they are, they become even more thinner
after DNA reduction.

In the beginning everything worked out just fine, the bands were thick
and clear. Nothing else has changed but some of the reactants have
been renewed and I am vortexing the samples more.

I know that this is rather a vague description of my problem and that
I am merely a second year medical student, but can anyone give me some
clues on what to seek in troubleshooting?

Thank you