Which characteristic is essential for an ideal primer in PCR?

The essential characteristic for an ideal primer in PCR is the absence of secondary priming sites in the template. This is crucial because when primers bind to unintended sites on the template DNA, it can lead to non-specific amplification, resulting in unwanted PCR products. This non-specific binding can further complicate the interpretation of results and reduce the fidelity of the amplification process.

By ensuring that primers do not have significant complementarity to other regions of the template, the specificity of the PCR reaction is enhanced. This characteristic allows the reaction to amplify only the desired target sequence, thereby increasing the yield of the specific product and making it easier to analyze the desired genetic material.

High melting temperature (Tm) is important for primer stability but is not the sole defining factor for primer design. Similarly, hairpin formations can hinder the effectiveness of primers. While high specific binding at the 3' end is beneficial for ensuring extension by DNA polymerase, it does not address the critical issue of preventing non-specific binding, which is the reason why the absence of secondary priming sites is essential for an ideal primer in PCR.