Nurturing Life Sciences
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#Unit 13. Methods in Biology
The sequence of the target DNA itself can affect PCR efficiency. The GC-rich sequences in target DNA may form secondary structures in the single strands produced by denaturation; this could reduce PCR efficiency.
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7-dcaza guanosine triphosphate (7-deaza OTP) can be used in place of OTP; it reduces hairpin loop formation without affecting the Watson-Crick base pairing required for annealing and primer extension.
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Addition of certain proteins, such as, bovine serum albumin enhances efficiency by protecting the DNA polymerase and by binding to PCR inhibitors.
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5′ nuclease assay (TaqMan assay). PCR is undertaken with a fluorescence reporter/quencher pair (called RQ probe).
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During extension by Taq polymerase, the probe is cleaved owing to the nuclease activity of the polymerase.
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Due to release of the reporter, there is a detectable increase in fluorescence, which is monitored in real-time PCR experiments.