Non-Watson-Crick base pairing

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.

Non-Watson-Crick base pairs, 17 614, 616 Nonwood fibers, 21 16-20... 

Figure 10.7. Schematic representation of the Rev protein, emphasizing its two key functional domains. The secondary structure of the RRE, highlighting the Rev biding site, is shown. Residues essential for RRE are in bold. The intervening bulge contains two non-Watson-Crick base pairs, G48 G71 and G47 A73, and a bulged base U72. ...

Bartel, D.P., Zapp, M.L., Green, M.R. and Szostak, J.W. (1991) HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell, 67, 529-536. 

In nature, base pairs of the Watson-Crick type prevail [674] as described in the previous sections. However, there are some well-documented structures where other base pairs occur. In one type, illustrated in Fig. 20.4, the bases are in the canonical keto/amino forms but base pairs are in mismatch configurations called wobble base pairs [675]. They occur even systematically in interactions between messenger RNA (mRNA) and transfer RNA (tRNA), and appear to play a role in mutation processes during DNA replication. Another type of non-Watson-Crick base pairs is found if the bases occur in rare enol/imino forms. These are also believed to be involved in mutation processes, albeit by a mechanism other than wobble base pairs, vide infra. 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

The potential for RNA to act as a catalyst is dictated by its structure as a linear polymer of the four common ribonucleotides. Like DNA, RNA can form double stranded, antiparallel helices via traditional Watson-Crick base pairing. However, the backbone of nucleic acid is highly flexible and RNA can form complex tertiary structures that often involve non-Watson-Crick base pairing to create active site crevices for catalysis. The phosphodiester backbone is charged negatively and interacts electrostatically as well as by direct coordination with solution divalent cations. Ribose, purines, and pyrimidine bases contain both H-bond donors and acceptors that help stabilize higher-order stmcture and provide for substrate positioning, as well as participate in active site interactions. 

Leontis, N.B., Stombaugh, J., Westhof, E. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 2002, 30, 3497-531. 

An alternative to these two tautomer models for point mutations assumes non-Watson-Crick base pairing schemes between normal tautomer forms in which the glycosidic bonds are displaced relative to their normal position in DNA. In other words, incorporation of these wobble mispairs requires appropriate adjustment of the DNA backbone resulting in glycosidic distances different from the usual 10.7 A. 

The replicative DNA polymerases themselves are able to correct many DNA mismatches produced in the course of replication. For example, the subunit of E. co/i DNA polymerase III functions as a 3 -to-5 exonuclease. This domain removes mismatched nucleotides from the 3 end of DNA by hydrolysis. How does the enzyme sense whether a newly added base is correct As a new strand of DNA is synthesized, it is proojread. If an incorrect base is inserted, then DNA synthesis slows down owing to the difficulty of threading a non-Watson-Crick base pair into the polymerase. In addition, the mismatched base is weakly bound and therefore able to fluctuate in position. The delay from the slowdown allows time for these fluctuations to take the newly synthesized strand out of the polymerase active site and into the exonuclease active site (Figure 28.41). There, the DNA is degraded, one nucleotide at a time, until it moves back into the polymerase active site and synthesis continues. 

Internal loops occur where two helices are separated by non-Watson-Crick base pairs. Bulges refer to cases where all bases on one strand can base pair while one or more bases on the opposite strand cannot (Fig. 1.1). Both bulges and internal loops are potential, and often used, targets for site-specific recognition of the RNA. 

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. 

Mismatches, or non-Watson-Crick base pairs in a DNA duplex, can arise through the following... 

Figure 1.67 Structures of non-Watson-Crick base pairings involving deoxyadenosine. Original dA.dT Watson-Crick base pairing is shown (red, top left) for comparison.

The x-ray crystal structures of several RNA oligomers incorporating symmetric internal loops have been determined. Four internal loop motifs are observed in the crystal structure of the P4-P6 domain of the group I intron. Three of these four internal loops are asymmetric. The x-ray crystal structures show the geometry of the non-Watson-Crick base pairs formed in the internal loops, the importance of bound water and metal ions, the distortion introduced into the RNA helix, and the mobility of the residues in and out of the internal loop. 

Internal Loops in RNA Oligomer Crystals. The first crystal structure of an RNA internal loop was solved in 1991(8). The dodecamer rGGACUUCGGUCC (internal loop underlined) forms a duplex in the crystal with an internal loop of consecutive U-G, U-C, C-U and G-U mismatches as shown in Figure 2. The chains of the double helix show two-fold symmetry in the crystal, thus the U-G and U-C pairs are identical to the C-U and G-U pairs. As can be seen, the internal loop generally continues the double helices which surround it by formation of non-Watson-Crick base pairs. The major groove of the A-form helix is opened with respect to a canonical RNA helix. 

Figure 5 (a-g). Non-Watson-Crick base pairs found in the internal loops of RNA oligomers. Water molecules integral to the base pairing are indicated (5c, 5e). Hydrogen bonds are represented by dashed lines. 

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