Question

Why internal secondary structures are not preferred for primers?

(a) Internal structures are very bulky and thus elongation is not preferred

(b) Because of it, primer may fold back on itself and won’t be available for template

(c) Internal secondary structures require more amount of template

(d) If internal structures are present, no proof reading would be observed

This question was posed to me in homework.

My doubt stems from Primers topic in chapter Polymerase Chain Reaction of Genetic Engineering

Answer 1

Right option is (b) Because of it, primer may fold back on itself and won’t be available for template

To elaborate: Internal structures are not preferred because if they are present the primer may fold back on itself. As the primer folds back on it, it is not available for the template. As an intramolecular reaction, self annealing is preferred over intermolecular annealing of primer to the template.