The use of PCR to probe calcium channel diversity

Voltage-dependent calcium channels are a diverse set of proteins that can be classified into at least 3 classes based on their electrophysiological and pharmacological behavior. Our studies have focused on the dihydropyridine-sensitive L-type class, which has two isoforms that have been cloned and expressed. In this report we describe the development of a polymerase chain reaction (PCR, Cetus) to probe for the expression of L-type calcium channel isoforms. We describe the optimization of the PCR reaction in terms of the following: methods for producing the template cDNA, concentration of primers, and magnesium concentration. In addition, we discuss our efforts to understand the factors involved in the design of oligonucleotides for PCR primers. These studies led to the following conclusions: 1) that primers should be less than 30 base pairs in length, 2) that the addition of extraneous polylinker sequences on the 5' end of the primer has no effect, 3) that the primer should not be located in regions where secondary structure may exist, and 4) that non-degenerate primers can be used to amplify homologous gene family members. We also present methods for subcloning PCR fragments, which allow the product of a single reaction to be subcloned and sequenced. We illustrate the use of all these techniques with RNA from mouse ovary, where we have discovered the expression of the cardiac isoform of the dihydropyridine-sensitive L-type calcium channel, and the expression of a novel sequence that we postulate to be an isoform of L-type calcium channels.