Nucleic acid secondary structure

This article is about secondary structure in nucleic acid. For the article about secondary structure in protein, see Protein secondary structure.
Nucleic acid primary structureNucleic acid double helixStem-loopPseudoknotNucleic acid tertiary structureNucleic acid quaternary structure
The image above contains clickable links
The image above contains clickable links
Interactive image of nucleic acid structure (primary, secondary, tertiary, and quaternary) using DNA helices and examples from the VS ribozyme and telomerase and nucleosome. (PDB: ADNA, 1BNA, 4OCB, 4R4V, 1YMO, 1EQZ​)


Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule.[1] The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar.[citation needed]

In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures for DNA nanotechnology and DNA computing, since the pattern of basepairing ultimately determines the overall structure of the molecules.

  1. ^ Dirks, Robert M.; Lin, Milo; Winfree, Erik & Pierce, Niles A. (2004). "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392–1403. doi:10.1093/nar/gkh291. PMC 390280. PMID 14990744.