ABSTRACT:

Objective and Method – To investigate the effect of single - base difference (C- G) at the 3′–end of a primer on the diagnosis of a particular disease, if any. Our study involving a pair of the primers which represented a plieotropic gene- a transcription repressor gene on chromosome 1 that codes for a component of MeCP1 protein complex. The primer taken as standard, was an amplification of a 126 (base pair) region of a human gene P66beta. Due to trinucleotide (CAG) expansion, this gene is reported to be associated with disease schizophrenia in many population studies and thus PCR amplification of DNA of this gene demands precision for identification.  Results – The primers with the C-G difference gave absolutely different PCR amplification -product results at all the different annealing temperatures (50-58^oC) tested than expected. The primers having single C-G difference at the 3'- end produced specific polymerase chain reaction (PCR) fragment at some of the annealing temperatures used, absolutely in contradiction with the expected ones identified as standard to diagnose the disease. Conclusion – We conclude that human genome possess many plieotropic genes corresponding to multiple phenotypic expressions in which even a single -base difference can create an absolute diagnostic error in identification. This makes the exact and proper primer sequence essential especially of those primers which are to be used in sensitive diagnostic techniques for identifying of molecular diseases as schizophrenia.