Application of quantitative RT-PCR to the analysis of dopamine receptor mRNA levels in rat striatum.

A quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) procedure has been developed which selectively amplifies and quantifies the two isoforms of the dopamine D2 receptor. Variability is corrected by the inclusion of a D2 dopamine receptor mRNA standard within each reaction. The internal standard was generated by introducing a point mutation within a D2 cDNA clone that created a unique restriction site within the amplified region. An in vitro transcribed RNA for the internal mutant control is added to the RNA isolated from brain tissue and the mixture is subjected to RT-PCR, digestion with the restriction enzyme, separation of the products by PAGE, and quantification by direct analysis of radioactivity incorporated during the PCR step. The standard is amplified, in the same reaction as the experimental RNA, using the same primers and RT-PCR conditions. In this manner, the effects of contaminants of the RNA preparation which could affect the amplification procedure are assessed. To insure that the amplification is linear, the number of PCR cycles is minimized. This adaptation avoids 'competitive PCR' and provides for a linear response. Moreover, to obviate non-specific co-amplification, primer annealing steps are performed at or above the melting temperature for the primers, thus increasing signal-to-noise ratios. Finally, primer pairs have been designed which permit amplification of specific fragments for each of the five rat dopamine receptor subtypes. These fragments have unique sizes and so can be differentiated when simultaneously amplified in the same RNA preparations.