Quantitative PCR (Q-PCR or qPCR) also known as real-time PCR is used to quantify starting amounts of nucleic acid template by analysing the amount of DNA produced during each cycle of PCR. The detection techniques include SYBR Green and probe. The cycling step is often preceded by reverse transcription to detect RNA via their cDNA.
Amplification of DNA is exponential in the early and middle cycles of a PCR (i.e. it is linear on a logarithmic scale). This property can be exploited to infer the starting amount of PCR template (see diagram in Hunt tutorial).
- pair towards 3' end (often more specific, some cDNAs don't contain)
- pair separated by an exon-exon boundary (reduces genomic background) e.g. last exon & penultimate
- amplified region must be no biger than 200 bp; usally 60-150 bp
- GC content: 50-60%
- min length: 18, max length 24 (best: 20 nt)
- melting temperature: min 60, max 63, best 60
- max Tm difference: 10 (shouldn't be more than 1 in final pair)
- max 3' self complementary: 1
- max poly-w: 3
Verify by blasting the primers sequences. Target gene should come out with the lowerst E value. No other gene should be close. Also check whether possible isoforms will be detected by the candidate primer pair.
RTPrimerDB is an excellent database storing known primer and probe sequences for popular techniques (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon). This can help you save the time of designing and testing your own primers. It is also intended to facilitate standardisation among different laboratories. The database is hosted by the Center for Medical Genetics, Gent, Belgium. Please submit you tested primer pairs.
RealTimePrimers.org is another such database but it contains only few primers.
See also: Designing primers
See also: PCR
A mRNA used as reference or standard of a Q-PCR (and other experiments) should have the following properties:
- expressed in all cells
- constant copy number in all cells
- medium copy number for more accuracy
Common reference mRNAs linked to known mouse primer pairs:
- β-actin (common cytoskeletal enzyme) , 
- glyceraldehyde-3-phosphate dehydrogenase GAPDH (common metabolic enzyme) , 
- ribosomal proteins (e.g. RPLP0) and RNAs (28S or 18S)
- cyclophilin mRNA
- MHC I (major histocompatibility complex I)
Search RTPrimerDB and check the literature before doing it from scratch.