Past exam of the biochemistry and Molecular Biology course of the University of Cambridge / 2025 / Paper 2 / Section C / 14 / b

Two desirable properties are similar primer melting temperatures, allowing one annealing condition to support both primers efficiently, and specific binding with little self-complementarity or mutual complementarity, especially at the $3^{\prime }$ ends, to reduce off-target products and primer dimers. Suitable length and a balanced GC content help achieve these goals. A long homopolymer, strong hairpin or repeated genomic binding site would compromise a candidate even if its calculated melting temperature looked acceptable.