PCR - Primers and Their Design

Practice flashcards based on lecture notes about PCR primers and their design.

What role do PCR primers play in DNA replication?

PCR primers confer specificity and directionality to DNA replication.

What is the typical length of PCR primers?

PCR primers have a typical length of 18-24 bases.

What is the ideal G/C content for PCR primers?

The ideal G/C content for PCR primers is 40-60%.

What is the melting temperature (Tm) range for effective PCR primers?

The melting temperature (Tm) of PCR primers should be between 50-60°C.

What should be considered to avoid complementary regions in primer design?

Primer pairs should not have complementary regions to prevent non-specific binding.

What is the significance of the 3’-ends of hybridized primers?

The 3’-ends of hybridized primers should point towards each other.

What happens if the annealing temperature is too high during PCR?

If the annealing temperature is too high, primer binding is inhibited.

What are primer dimers and why are they a concern?

Primer dimers occur when primers bind to each other, leading to non-specific amplification.

How does GC content affect primer binding strength?

G and C bases bind more strongly than A and T, making GC content a major determinant of binding strength.

What is a degenerate primer?

A degenerate primer is a population of primers with similar sequences that cover all possible nucleotide combinations for a given protein sequence.

Why is it important for primer pairs to have similar melting temperatures?

Primer pairs should have similar Tm values to ensure they anneal at the same temperature.

What problems arise from primers being too short or too long?

Too short primers (

What can happen when primers have significant secondary structures?

Significant secondary structures can inhibit the interaction of primers with their target sequence in the template DNA.

What is the purpose of using conserved sequences in designing PCR primers?

Conserved sequences are important for ensuring broad applicability in nested PCR.

What is the consequence of having mismatches between primer and template sequences?

Mismatches may increase the number of potential priming sites, leading to non-specific products.