Primer with hairpin structure is
Ideal primers must remain linear to efficiently hybridize with template DNA. A hairpin structure arises when a primer contains internal self-complementary sequences that fold back, forming intra-molecular base pairing and a loop. This conformation sequesters primer, reduces effective concentration available for template binding, impedes polymerase extension, and lowers reaction efficiency. Primer design software therefore penalizes palindromic sequences, especially involving 3' end, and targets minimal self-complementarity. Avoiding hairpin formation ensures maximal accessibility and improves
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.