Question

What is the average length of oligonucleotide primers used in PCR? a) 6 nucleotides b) 10 nucleotides c) 20 nucleotides d) 50 nucleotides

Answer 1

C) 20 nucleotides

20 nucleotides is the optimum length for designing a PCR primer with average GC content of 50% and zero repetitive sequences.

6 or 10 nucleotides long primers are too short to anneal to a specific DNA location in the genome, since more than one loci in the genome can have same sequence which is as short as 6 or 10 nucleotides leading to non-specific amplifications.

50 nucleotides long sequence although would bind more specifically but would have annealing temperatures too high, they will have more chances of self annealing and secondary structure formation plus non-specific partial binding in the genome at lower temperatures.