Thanks for the help. I am using a 95 C denaturing step prior to the 45 C denaturing step. The
deletion is a perfect 87 bp or 29 amino acids in length. It starts and ends in a valine
residue, thus maintaining frame. i have used a positive control sense RNA of the full length
and the mutant deleted forms and they gave the expected results. Also, the intensities of the
two bands on total Brain RNA is similar suggesting to me at least that the shorter band from
the deletion must be real or a big artifact.