[PDF][PDF] Production of PCR mimics for any semiquantitative PCR application

SA Ali, I Sarto, A Steinkasserer - Biotechniques, 1997 - Taylor & Francis
Biotechniques, 1997Taylor & Francis
Semiquantitative polymerase chain reaction (PCR) is a powerful tool for determining DNA
and RNA copy numbers in biological samples (4, 5, 8). Essentially, the technique involves
amplification of the target with specific primers and comparison of the signal intensity with
that of a standard that was amplified within the same tube after separation of the products by
gel electrophoresis. Signal intensity is proportional to target copy number in semiquantitative
PCR. The standard can either be an endogenous sequence (eg housekeeping genes such …
Semiquantitative polymerase chain reaction (PCR) is a powerful tool for determining DNA and RNA copy numbers in biological samples (4, 5, 8). Essentially, the technique involves amplification of the target with specific primers and comparison of the signal intensity with that of a standard that was amplified within the same tube after separation of the products by gel electrophoresis. Signal intensity is proportional to target copy number in semiquantitative PCR. The standard can either be an endogenous sequence (eg housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase [GAPDH]; see References 16 and 17) or be added prior to amplification at a specific copy number (14). An optimal competitor sequence should be amplified at a similar efficiency as the target gene. Therefore, it should use the same primers as the target DNA and have similar size, nucleotide composition and secondary structure. Hence, optimal competitior ‘mimics’ tend to be constructed from the cloned target gene. Several strategies exist to do this. Restriction enzymes can be used to create a deletion within the target gene or permit insertion of a stuffer fragment (9). However, in the absence of suitable restriction sites, this approach is not feasible. A recent publication describes the application of inverse polymerase chain reaction (IPCR) to generate PCR mimics without the requirement of restriction enyzmes (18). This method is rapid and simple, but does have one major drawback. If the plasmid containing the target gene is large, then amplification of the entire plasmid can be difficult unless the target gene is first subcloned into a smaller vector. We present an application of PCR-ligation-PCR (PLP) mutagenesis (2, 3) for the production of an ideal mimic sequence for any semiquantitative PCR application. Like the IPCR method, this method is rapid and does not require the use of restriction sites at the point of the deletion. However, unlike IPCR, there is no requirement for amplifica-
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