Thymine pairs

As found for other stacked base pairs, in the stacked thymine-thymine pair changes in the interaction energy upon rotation of one thymine unit are almost completely compensated for by solvation effects [99JPC(B)884]. The adenine-thymine (A-T) base pair, which possesses a significant degree of conformational... 

The tt-SCF MO calculations on the pair and on the isolated molecules show that the molecular orbitals of the adenine-thymine pair are slightly perturbed with respect to adenine or thymine (compare the... 

A wide assortment of different possible geometries for the uracil dimer were examined [127] in 1998. The most stable of all these contained a pair of NH- -O bonds, but another was identified, only slightly less stable than the others, in which one of these conventional H-bonds was replaced by CH- -O = C. There was no way of estimating the energetic contribution of this particular interaction, as it was secondary to the stronger NH- -O bond. A study of the adenine thymine pair [128] noted a blue shift of the C-H stretching frequency, an indication of a H-bond, but the authors did not attempt to extract an interaction energy. 

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. 

It is interesting that the surface denaturation of dh DNA is inhibited by the formation of covalent interstrand cross-links formed in DNA by bifunctional platinum coordination complexes - cis-diamminedichloro-platinum (II) and its trans-isomer [115]. The half-time of the interfacial denaturation of dh DNA in alkaline medium of ionic strength of 0.5 is c. 20 s [102] and is lowered with decreasing ionic strength [112]. The experiments carried out on dh DNAs of various base content indicate that the segments in dh DNA rich in adenine.thymine pairs are more susceptible to this kind of denaturation than those rich in guanine-cytokine pairs [115]. The surface denaturation at the mercury electrode has also been observed in dh RNA and dh complexes of synthetic polydeoxy- and polyribonucleotides [112, 116]. 

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