Base reverse Hoogsteen

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.

Three classes of nucleic acid triple helices have been described for oligonucleotides containing only natural units. They differ according to the base sequences and the relative orientation of the phosphate-deoxyribose backbone of the third strand. All the three classes involve Hoogsteen or reverse Hoogsteen-like hydrogen bonding interaction between the triple helix form-... 

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. 

A reversed Hoogsteen base pair present in tRNA molecules... 

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). 

Fig. 16.10. Schematic description of A-U base pairs found in crystals and in double helical nucleic acids. AU62 Watson-Crick A(JS2 reversed Watson-Crick AU32 Hoogsteen AU22 reversed Hoogsteen...

Triplex formation with natural bases is limited by several important structural requirements. Recognition of any sequence in one of the WC strands is achieved by the formation of specific sets of hydrogen bonds (Hoogsteen or reverse Hoogsteen) with complementary base pairs in the other strand (Figure 7). 

Reverse Hoogsteen/Watson-Crick triplex base pairs... 

Cheng, Y.-K., Pettitt, B. M. (1992). Hoogsteen versus reversed-Hoogsteen base pairing DNA triple helices, J. Am. Chem. Soc., 114 4465. 

Figure 3.1 Hydrogen bond formation in G-tetrad, parallel triplexes consisting of T X a-T and C x g-C triads, A-motif, and i-motif (Watson-Crick basepairing is shown with dashed bonds, and Hoogsteen or reversed Hoogsteen base-pairing is shown with hashed bonds).

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