Hoogsteen/Watson-Crick base pairs

Fig. 8. Non-Watson-Crick base pairs occurring in double-stranded RNA where — represents the site of attachment to the sugar (a) A—U reverse-Watson-Crick (b) G—C reverse-Watson-Crick (c) A—U Hoogsteen (d) A—U reverse-Hoogsteen (e) G—U wobble and (f) G—U reverse-wobble.

Fig. 4.3 Triplex invasion by homopyrimidine PNA oligomers. One PNA strand binds via Watson-Crick base pairing (preferably in the antiparallel orientation), while the other binds via Hoogsteen base pairing (preferably in the parallel orientation). It is usually advanta-...

Hoogsteen pairs were first observed in nature in transfer RNA molecules (Fig. 5-31). These molecules contain mostly Watson-Crick base pairs but there are also two reversed Hoogsteen pairs. One of them, between U8 and A14, is invariant in all tRNAs studied. Hoogsteen pairing also occurs in four-stranded DNA, which has important biological functions. A G quartet from a DNA tetraplex held together by Hoogsteen base pairs is shown in Fig. 5-8. 

While tRNAs consist largely of loops and stems containing Watson-Crick base pairs, they also contain Hoogsteen pairs, wobble pairs, and triplets such as the following. 

Low resolution Fourier syntheses of electron density with phases calculated from an approximate but erroneous model may nevertheless indicate another model and thus provide an unusually compelling indication that the phasing model is imperfect. This strategy has been used to reject Hoogsteen in favor of Watson-Crick base-pairing in DNA (60,61), to eliminate 10-fold in favor of 11-fold helicies in A-RNA (62), to favor nested chains rather than double helices in the case of one form of sodium hyaluronate (40). 

Fig. 9. Base triplets formed between a Watson-Crick base pair G C and a third base G or C Hoogsteen-pairing) (left) or a transplatin-modified G or C (right)...

Combination AU62 is the Watson-Crick base pair, AUS2 is called reversed Watson-Crick (Fig. 16.10, left). AU32 is the base pair discovered by Hoogsteen, and AU22 is the reversed Hoogsteen base pair (Fig. 16.10, right). 

Both Watson-Crick and other forms of base pairing are found in parts of RNA molecules. One alternative form of base pairing is known as Hoogsteen pairing and other forms are generally known as non-Watson-Crick base pairs. 

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