Watson-Crick pair

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

Santamaria, R., Charro, E., Zacarias, A., Castro, M., 1999, Vibrational Spectra of Nucleic Acid Bases and Their Watson-Crick Pair Complexes , J. Comput. Chem., 20, 511. 

The liberation of the third, newly formed strand is of great importance in this process it is made possible by adding free dodecameric purine oligonucleotides, which can bond to the newly-formed pyrimidine matrix by Watson-Crick pairing. 

The symbol denotes Watson-Crick pairing, while - means Hoogsteen pairing CH+ is protonated C (cytosine). 

Nucleic acids which contain only adenosine, guanosine and uridine are able to form A-U Watson-Crick pairs and G-U wobble pairs. They should be able to build up complex secondary and tertiary structures. 

Sarai, A., and M. Saito. 1985. Theoretical Studies on the Interaction of Proteins with Base Paris. II. Effect of External H-Bond Interactions on the Stability of Guanine-Cytosine and Non-Watson-Crick Pairs. Int. J. Quantum Chem. 28, 399-409. 

I I I I I Watson-Crick pairs G-U wobble base pair /WWW exon... 

Fig. 7 The two-stage folding scheme for the hammerhead ribozyme, as proposed by Tilley s group [77-80]. The arrow indicates the cleavage site. The scheme consists of two steps to generate the Y- or y-shaped ribozyme/substrate complex. The higher affinity of Mg is related to formation of domain II (structural scaffold non-Watson-Crick pairings between G12-A9, Ais-Gg and A14-U7 forming a coaxial stack between hehces II and III that runs through G12A13A14) and the lower affinity of Mg to formation of domain I (catalytic domain formation by the sequence C3U4G5A6 and the C17 with the rotation of helix I around into the same quadrant as helix II) [78]...

Electronic Coupling within Watson-Crick Pairs... 

The wobble (or third) base of the codon contributes to specificity, but, because it pairs only loosely with its corresponding base in the anticodon, it permits rapid dissociation of the tRNA from its codon during protein synthesis. If all three bases of a codon engaged in strong Watson-Crick pairing with the three... 

For example, Hoogsteen proposed an alternative A-T pairing using the 6-NH2 and N-7 of adenine.34 Here the distance spanned by the base pair, between the C-T sugar carbons, is 0.88 nm, less than the 1.08 ran of the Watson-Crick pairs. Duplexes of certain substituted poly (A) and poly (U) chains contain only Hoogsteen base pairs35 and numerous X-ray structure determinations have established that Hoogsteen pairs... 

Another pairing that occurs in tRNAs allows guanine to pair with uracil, e.g., G4 with U69. This was originally proposed to account for codon-anticodon interactions betweentRNA molecules and messenger RNA (Chapter 29). It is commonly called wobble pairing because the uracil must wobble away from its orientation in the normal Watson-Crick pair.27 37... 

Special structural features may be found at junctions between different types of DNA, e.g., between A-DNA and B-DNA.284-286 However, the most interesting junctions are branched.287 29° For example, Fig. 5-28 shows a four-way junction in which all of the bases form Watson-Crick pairs. This junction is better known as a Holliday junction because it was proposed by Holliday in 1964 as an intermediate in genetic recombination.291 As shown at the top of Fig. 5-28A the junction is formed from two homologous DNA duplexes. These are identical except for the boxed and shaded base pairs. The ends of the first duplex are marked I and II and those of the second III and IV. The Holliday junction appears to arise by cleavage of one strand of each duplex with rejoining of the strands as indicated by the green arrows. Rotation gives the untwisted Holliday junction structure... 

Draw the structures of the Watson-Crick base pairs guanine-cytosine (GC) and adenine-thymine (AT). Also draw the GU pair, which is not a Watson-Crick pair. 

Figure 29-8 Pairing of inosine with cytosine (a Watson-Crick pair) and of inosine with adenine and uracil (wobble pairs).

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