Hoogsteen base pair reversed

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). 

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

Free energy calculations have been used to examine Hoogsteen base-pairing and reversed... 

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).

Fig. 10 A possible molecular packing and hydrogen bond scheme for (a) the heteroassembly formed from an equimolar mixture of 14a and 15a and (b) the homoassembly from 16a. (a, b) Top view of a layered structure composed of linear polymolecular arrays ( reversed Hoogsteen base pair configuration is employed here for the thymine-adenine heteroassociation), (c) Front view showing 2-D complementary and 1-D amide hydrogen bond network, (d) Side view of the polymolecular arrays. In (d), the one-dimensional amide hydrogen bond chain contributes to the stabilization of the base stacking and the formation of complementary hydrogen bonds. Reprinted with permission from J Am Chem Soc 2001, 123, 5947...

In three dimensions, tRNAs fold into an L-shaped structure in which the acceptor stem and T C arm coaxially stack to form one part of the L known as the minihelix, and the D and anticodon arms likewise stack to form the other part of the molecule. This structure is facilitated and stabilized by tertiary interactions at the corner of the L that bring together the D and variable loops. The nucleotides involved in these interactions are typically invariant or semi-invariant, indicating that the tRNA L shape is universal. While most base pairs in tRNA helices are canonical Watson-Crick pairs, the tertiary interactions at the corner of the L make use of some unusual hydrogen-bonding conformations. For example, nearly all tRNAs contain a U8 A14 reverse Hoogsteen base pair, and several base triples (where three bases are paired together) are also typically present at the core of the structure. 

FIGURE 1.7 Base pairing schemes of Watson-Crick and non-Watson-Crick types. Among the non-Watson-Crick base pairs, wobble pairs are formed by H-bonds between tautomeric forms of hydroxyl (OH) and imino (NH) groups. Non-Watson-Crick base pairs also comprise Hoogsteen base pairs and reverse Watson-Crick base pairs which form the basal structural units in triplex DNA and In parallel-stranded DNA (psDNA), respectively. 

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.

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