### Secondary structures

The secondary structure of single-stranded DNA describes the spatial composition of DNA. The secondary structure of DNA is coined by long-range interactions between nucleotides (i.e. nucleotides that are not close in the primary sequence) leading to more complex structures such as bulges and hairpins. The formation of secondary structures affects the energetic profile of DNA and therefore greatly influences the interactions between primers and templates. A primer that is highly complementary to a template sequence in its coil form might not be able to bind at all when it exhibits secondary structures precluding possible base pairings. Moreover, it may be beneficial to also check the template target regions for possible structures.

To guarantee that complementary primers can actually hybridize to their corresponding template sequences, it is advised to check whether the primers could form secondary structures. Primers forming secondary structures should be excluded, because they typically cannot hybridize to their target sequences.

openPrimeR uses The ViennaRNA Package to predict DNA secondary structures.