Top figure is an example of a purine (Adenine) where the edges are known as Watson-Crick, Hoogsteen, and Sugar Edges. Since the structures of the canonical Watson-Crick and non-canonical Hoogsteen base pairs were determined, many other types of non-canonical base pairs have been presented and described.įigure 2: Base pairing edge of nucleobases. Ultimately, after years of studying both Watson-Crick and Hoogsteen base pairs, it has been determined that both occur naturally in DNA, and that they exist in equilibrium with one another the conditions in which the DNA exists ultimately determine which form will be favored. The G-C Hoogsteen base pair was first observed via X-ray crystallography years later, in 1986, by co-crystallizing DNA with triostin A (an antibiotic). Five years after Hoogsteen proposed the A-T Hoogsteen base pair, optical rotary dispersion spectra which provided evidence for a G-C Hoogsteen base pair were reported. Ten years later, in 1963, Karst Hoogsteen reported that he had used single crystal X-ray diffraction to investigate alternative base pair structures, and he found an alternative structure for the nucelobase pair adenine-thymine in which the purine (A) takes on an alternative conformation with respect to the pyrimidine (T). James Watson and Francis Crick published the double helical structure of DNA and proposed the canonical Watson-Crick base pairs in 1953. The presence of non-canonical base pairs in double stranded DNA results in a disrupted double helix.

They are typically less stable than standard base pairings. pairing of G with U), and in tRNA recognition.

Non-canonical base pairings commonly occur in the secondary structure of RNA (e.g. The first discovered non-canonical base pairs are Hoogsteen base pairs, which were first described by American biochemist Karst Hoogsteen.

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. 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 (which are adenine (A) - thymine (T) in DNA, adenine (A) - uracil (U) in RNA, and guanine (G) - cytosine (C) in both DNA and RNA).

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