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Tetramethylammonium chloride plays two main roles in Random Amplified Polymorphic DNA (RAPD) analysis of poplar trees: enhancing PCR specificity and increasing the stability of amplified products.

♥ Enhancing specificity: Tetramethylammonium chloride, as a cationic surfactant, improves the efficiency of DNA primer annealing during PCR. By adding Tetramethylammonium chloride to the PCR system, the stability of hybridization between the primers and template DNA is increased, thereby enhancing PCR specificity. Specificity is crucial in RAPD analysis, as this technique uses random primers to amplify specific regions of the genomic DNA, generating DNA fragments of specific lengths that reflect genetic diversity among individuals. The presence of TMAC improves the specific binding of primers, reducing the likelihood of non-specific amplification.

♥ Increasing stability of amplified products: Tetramethylammonium chloride helps prevent DNA degradation during PCR. As an additive, it inhibits the activity of DNA-degrading enzymes, thereby increasing the stability of amplified products. RAPD analysis requires long PCR amplification reactions, and DNA is prone to enzymatic degradation during PCR, resulting in the failure to generate specific-length amplified products. By adding TMAC, DNA is protected from enzymatic degradation, leading to higher success rates and stability of PCR reactions.

In summary, Tetramethylammonium chloride in RAPD analysis of poplar trees enhances PCR specificity and increases the stability of amplified products, thereby improving the accuracy and repeatability of RAPD analysis.