Watson-Crick geometry

It has been found that 6-aminopyrazinone (Scheme 2), when incorporated as a pyrimidine base analog into an ohgonucleotide, might participate in a nonstandard base pair that retains Watson-Crick geometry [14],... 

One of the most prominent hydrogen-bonded systems is DNA. Despite numerous experimental and theoretical investigations on vibrational spectra of nucleic acid bases [7-13], information on inter- and intramolecular interactions in base pairs and DNA oligomers is still limited [14-25]. A recent example is the work on single adenine-uracil (AU) base pairs in the Watson-Crick geometry in solution, which showed an enhancement of vibrational energy... 

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]. 

The associations of DNA with proteins and drugs introduce additional deformations of Watson-Crick geometry. Several examples, which are illustrated in Fig. 4, demonstrate the functional importance of the base-pair deformations discussed above. 

Figure 13 Structures and base pairing of the modified nucleoside lysidine (k C). (a) The neutral form of lysidine. The lysidine base has a pKa of approximately 12, and therefore the base would be charged at pH = 7 along with a zwitterionic form for the side chain, (b) Protonated form of lysidine allowing pairing with A in a Watson-Crick geometry, (c) and (d) Alternative protonated forms of lysidine that would be less favorable for A-pairing.

Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A (2012) KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat Chem Biol 8(7) 612-614. doi 10.1038/nchembio.966... 

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