page_title: Non-canonical base pairing
section_title: Tertiary
hierarchical_section_title: Non-canonical base pairing / 3-D Structure / Tertiary
caption_attribution_description: English: structure of a pseudoknot of pdb-file 1YMO. (A) sticks (B) backbone Deutsch: Struktur eines Pseudoknots aus pdb-Datei 1YMO. (A) sticks (B) Rückgrat Colors: A U C G
context_page_description: Non-canonical base pairing occurs when nucleobases hydrogen bond, or base pair, to one another in schemes other than the standard Watson-Crick base pairs. There are three main types of non-canonical base pairs: those stabilized by polar hydrogen bonds, those having interactions among C−H and O/N groups, and those that have hydrogen bonds between the bases themselves. The first discovered non-canonical base pairs are Hoogsteen base pairs, which were first described by American biochemist Karst Hoogsteen.
  Non-canonical base pairings commonly occur in the secondary structure of RNA, and in tRNA recognition. They are typically less stable than standard base pairings. The presence of non-canonical base pairs in double stranded DNA results in a disrupted double helix.
context_section_description: Three-dimensional structures are formed through the long-range intra-molecular interactions between the secondary structures. This leads to the formation of pseudoknots, ribose zippers, kissing hairpin loops, or co-axial pseudocontinuous helices. The three-dimensional structures of RNA are primarily determined through molecular simulations or computationally guided measurements. An example of a Pseudoknot is given in Figure 8.
caption: Figure 8: An example of a Pseudoknot three-dimensional structure.
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