Question

1. An experimental multiplex PCR examines the flagellin genes expressed by several strains of Salmonella enterica Typhimurium; Type X, Y, or Z.

(a) You design two sets of primers per flagellin type you want to amplify. The following primers were designed for Type X. Assuming the bases were appropriate to the DNA region of interest, would (either / both / none) of the primer sets be appropriate to your test? Explain your choice in less than 30 words.

Primer set 1 a. 5’CCATAACGT b. 5’GTTATGGTG

Primer set 2 c. 5’AACGTCCAT d. 5’GCTCAAGCT

Answer 1

Answer: Primer set 1

Reason: While conducting multiplexing, common primers are generally used having a substantial amount of GC content as well as at least a single set of a triplet of adenine-thymine residues which help in strong binding. Although both primer sets have a substantial amount of GC content, primer set 1 seems more promising as it contains a good sequence of ATAAC which helps in strong yet random binding.