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PNA probes have no direct interaction with DNA polymerase. However, PNAs can terminate the elongation of oligonucleotide primers by binding to the template or competing with the primers. This strategy of PNA directed PCR clamping uses PNAs to inhibit the amplification of a specific target by direct competition of the PNA targeted against one of the PCR primer sites and the conventional PCR primer. This PNA–DNA complex formed at one of the primer sites effectively blocks the formation of the PCR product. The procedure is so powerful that it can be used to detect single base-pair gene variants for mutation screening and gene isolation. The peptide nucleotide acid (PNA) blockers can be used to block amplification from the internal transcribed spacer. For example, the PCR can include peptide nucleotide acid (PNA) blockers targeting the plant plastid and mitochondria rRNA gene for 16S rRNA gene amplifications (GGCAAGTCTTCTTCGGA and GGCTCAACCCTGGACAG) and PNA targeting plant nuclear rRNA genes for ITS2 region (CGAGGGCACGTCTGCCTGG) to reduce amplification of plant material.
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