Coaxial stacking

Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer.RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional tertiary structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structure motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized.

The double helix is the dominant tertiary structure for biological DNA, and is also a possible structure for RNA. Three DNA conformations are believed to be found in nature, A-DNA, B-DNA, and Z-DNA. The "B" form described by James D. Watson and Francis Crick is believed to predominate in cells.James D. Watson and Francis Crick described this structure as a double helix with a radius of 10 Å and pitch of 34 Å, making one complete turn about its axis every 10 bp of sequence. The double helix makes one complete turn about its axis every 10.4-10.5 base pairs in solution. This frequency of twist (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain. Double-helical RNA adopts a conformation similar to the A-form structure.

Other conformations are possible; in fact, only the letters F, Q, U, V, and Y are now available to describe any new DNA structure that may appear in the future. However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems.

The minor groove triple is a ubiquitous RNA structural motif. Because interactions with the minor groove are often mediated by the 2'-OH of the ribose sugar, this RNA motif looks very different from its DNA equivalent. The most common example of a minor loop triple is the A-minor motif, or the insertion of adenosine bases into the minor groove (see above). However, this motif is not restricted to adenosines, as other nucleobases have also been observed to interact with the RNA minor groove.

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