Guanine-cytosine pairing

An interesting feature was discovered by Sharma and co-workers494,495 in the crystal structure of isocytosine. Two tautomers of isocytosine (42 and 43) exist in an exact 1 1 ratio in the crystal. The tautomers are hydrogen-bonded to each other in a manner analogous to that proposed by Watson and Crick496,497 for the guanine-cytosine pair in DNA. It is worth underlining that the base pair of isocytosine was not obtained by expedient cocrystallization of the two components. It seems therefore probable that both forms 42 and 43 of isocytosine are of approximately equal stability and are present in comparable amounts in solution. 

In two papers, the energies of the molecular orbitals of the guanine-cytosine pair have not been given. The evaluation could be made only from the correlation diagram of the molecular orbitals. 

DFT calculations for the 16-atom model of a Watson-Crick guanine-cytosine pair have been reported in Ref. They also suggest positive sign of J(NH) and J(NN) couplings, although the method of calculation is less sophisticated than in Ref. since only FC terms are calculated. 

E. Clementi, J. Mechl, and W. V. Niessen, J. Chem. Phys., 54, 508 (1971). Study of the Electronic Structure of Molecules. XII. Hydrogen Bridges in the Guanine-Cytosine Pair and in the Dimeric Form of Formic Acid. 

Fig. 12.3. Adenine-thymine hydrogen-bonded pairs (a) found by Hoogsteen in a 1 1 complex of 3-N-methyllhymine and 9-Af-methyladenine (b) postulated by Watson and Crick (current version refined by Arnott) for part of the structure of DNA. Guanine-cytosine pairs (c) Hoogsteen type (d) Watson-Crick type (Wilkins and Arnott, 1965). (From Mahler and Cordes, 1966.)...

As an example of a property related to the base pairs we may consider the qualification resonance stabilization through H bonds which heavily underlined points to the H bonds of the guanine-cytosine pair and therefore means that the stabilization through hydrogen bonding is predicted to be greater for the G-C pair than for the A-T pair. 

Scheme 29 Adenine-thymine and guanine-cytosine pairs with remote substituents.

Scheme 31 Supramolecular substituents In adenine—thymine and guanine—cytosine pairs. Reproduced from (2006MI) with kind permission from Springer Science and Business Media.

We think that there is no doubt that the guanine-cytosine pair involves three hydrogen bonds, and we may conclude that the difference between this pair and the adenine-thymine pair, with two hydrogen bonds, is such as to introduce greater specificity in the action of a polynucleotide as a template than was indicated by the considerations of Watson and Crick, who had assumed that two hydrogen bonds are formed in each case. 

The density of one molecule of DNA rich in guanine-cytosine pairs is greater than that of a DNA rich in adenine-thymine pairs. Thus, if a DNA suspension composed of a mixture of two different DNA s—one rich in AT pairs and another rich in CG pairs—is centrifuged in gradient concentrations of cesium chloride, the two types of DNA band separately at the end of the centrifugation. The position of the band depends on the bouyant density of the DNA molecule. The bouyant density of the DNA molecule was shown to be directly proportional to the amount of CG pairs present. The determination of the bouyant density of DNA has thus provided a convenient method for establishing quickly the base composition of small amounts of DNA. 

Figure 34. pH dependence of guanine-cytosine pairing in the allc yianosyl series, and its d ndence on the base-pair sequence [14]. 

Figure 39. The altropyianosyl series does not differ from the allopyianosyl smes (fig. 34) with regard to the weakness and pH dependence of the guanine-cytosine pairing [16].

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