<P> 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 . The secondary structures of biological DNA's and RNA's tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complicated base - pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar . </P> <P> 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 . </P> <P> In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). In the canonical Watson - Crick base pairing, adenine (A) forms a base pair with thymine (T) and guanine (G) forms one with cytosine (C) in DNA . In RNA, thymine is replaced by uracil (U). Alternate hydrogen bonding patterns, such as the wobble base pair and Hoogsteen base pair, also occur--particularly in RNA--giving rise to complex and functional tertiary structures . Importantly, pairing is the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation . Some DNA - or RNA - binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes . Hydrogen bonding is the chemical mechanism that underlies the base - pairing rules described above . Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably . DNA with high GC - content is more stable than DNA with low GC - content, but contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly and stabilization is mainly due to stacking interactions . </P> <P> The larger nucleobases, adenine and guanine, are members of a class of doubly ringed chemical structures called purines; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of singly ringed chemical structures called pyrimidines . Purines are only complementary with pyrimidines: pyrimidine - pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine - purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion . The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond . The GU wobble base pair, with two hydrogen bonds, does occur fairly often in RNA . </P>

Can rna exist in a variety of secondary structures