Final answer:
The use of shorter and more variable primers in PCR could lead to non-specific amplification, inefficient binding, and lower yield of the desired DNA product. This is due to their lower melting temperature and increased likelihood of binding at multiple unintended sites on the template.
Step-by-step explanation:
If the primers used in a PCR reaction were shorter and more variable, it would likely have several effects on the PCR reaction. Short primers may bind non-specifically to multiple sites on the DNA template leading to non-specific amplification. This is because shorter primers have a lower melting temperature and can anneal to the template at several unintended sites, given that less sequence is required for stable hybridization. Furthermore, the variability in primer sequences could further exacerbate the issue of non-specific binding.
During the second cycle of PCR amplification, the annealing temperature plays a crucial role in the specificity of primer binding. If primers are shorter and more variable, their binding might be less reliable, and thus the desired PCR product may be synthesized at lower efficiency. The annealing step typically at 55°C might not be optimal for such primers, and the specificity of the PCR needs to be monitored closely to ensure amplification of the intended product.
The concentration of the primer is usually between 0.05µM to 0.1µM, which allows for efficient binding to the template DNA. However, if the primers are shorter and their binding is variable, the efficiency of the PCR reaction might decrease, and the yield of the desired DNA product could be compromised. In short, shorter and more variable primers could lead to less efficient and less specific PCR amplifications, potentially resulting in a mixture of non-target products.