Watson-Crick Base Pair Geometry

The Structure of DNA and RNA Double Helices is Determined by Watson-Crick Base-Pair Geometry... 

The wobble base pairs are displayed in Fig. 20.4. In comparison with Watson-Crick base pairs, the positions of the glycosyl links differ, but their directions are more or less retained so that the short codon-anticodon double helix is smooth. Pyrimidine-pyrimidine base pairs U - U and U - C, which could also form (Part II, Chap. 16) are considered to be unlikely since their C(l,) -C(r) distances are about 2 A shorter than the 10.5 A in a Watson-Crick base pair. The long A-1 base pair with C(l ) -C(r) distance of about 13.5 A, as actually observed in a comparable crystalline base-pairing complex [678], is too long to be accommodated in a smooth double helix. It has been suggested therefore that inosine in syn form could mimic the Watson-Crick geometry [679]. 

Table 2 Average hydrogen-bonding geometry of Watson-Crick base pairs in high-resolution DNA structures ...

Figure 1.66 Illustrations of the specific Watson-Crick base pairings, dG.dC and dA.dT involving complementary deoxynucleoside residues. Overlay structure provides visual demonstration of the dG.dC/dA.dT isomorphous geometry.

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. 

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