What happens to the duplex structures under high stringency conditions?

Under high stringency conditions, duplex structures, which are formed by the hybridization of complementary nucleic acid strands, are maintained primarily when the strands are perfectly matched. These conditions typically involve a more stringent environment—such as higher temperatures or the use of more selective buffers—that allows only those duplexes with high complementarity to remain stable.

When the conditions are stringent, mismatched or partially matched duplexes do not have the necessary stability to be preserved, leading them to dissociate. This results in the phenomenon where only perfectly matched duplexes are retained, allowing researchers to increase the specificity of nucleic acid detection methods. Thus, the stability of the duplex is contingent upon the fidelity of base pairing; perfectly complementary strands can withstand the high stringency, whereas those with mismatches cannot. This concept is critical for applications such as PCR, hybridization assays, and other molecular diagnostics techniques where sensitivity and specificity are paramount.