In primer design, self-complementarity results in
Self-complementarity in primers, particularly at 3' termini, enables undesirable interaction between two primer molecules or identical molecules, generating primer-dimer artifacts. During annealing, complementary bases pair transiently, and polymerase extends each primer using the other as template, creating short double-stranded products that accumulate exponentially and compete aggressively with target amplicon for reagents. This reduces overall yield, generates low-molecular-weight bands on gels, and interferes with quantitative assays like real-time PCR and melt curve analysis. Effective design avoids self-complementary stretches and evaluates 3' complementarity scores using specialized software.
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.