Pyrimidine-purine dinucleosides

Fig. 2 (A, top). Induced CD spectra of ethldlum bromide upon addition of CpG cuid dC-dG in a l-mm thermostatted cell at 3"C. Utie samples were 0.75 mM EB and 2.3 mM CpG and 0.75 and EB and 3.2 mM dC-dG. Both samples were dissolved in a D2O potassium phosphate buffer (5 mM) pD = 7.4 (pH meter + 0.4). The 6 values are direct readings from the recorder. Note that the scale of the ordinate has been expeuided below the zero level. (B, bottom figure). Induced CD spectra of ethidium bromide in the presence of equimolar mixtures of the complementary (UpG + CpA and GpU + ApC) and non-complementary ribodinucleoside monophosphates at -3 C. Note that only the complementary mixture of pyrimidine-purine dinucleosides UpG + CpA gives rise to the characteristic induced CD spectrum under the present e3q)erimental conditions.

Sobell and his coworkers (Tsai et. al., 1975 Jain et. al., 1977) utilized our initial experiments with ethidium bromide as guidance in selecting to cocrystallize ethidium with the ribodinucleoside monophosphates. The pyrimidine-purine sequence dinucleosides UpA and CpG were easily cocrystallized with ethidium and formed 2 2 complexes. 

Sequence Specificity Optical studies on the binding of intercalative drugs to dinucleoside monophosphates demonstrated that actinomycin exhibits a purine(3 -5 )pyrimidine specificity (57-60) while ethidium exhibits a pyrimidine(3 -5 )purine (61-63)... 

The pyrimidine nucleobases have the highest quantum yields for photoreactivity, with thymine uracil > cytosine. The purine nucleobases have much lower quantum yields for photochemistry, but can be quite reactive in the presence of oxygen. As can be seen from Figure 9-3, thymine forms primarily cyclobutyl photodimers (ToT) via a [2ir + 2tt cycloaddition, with the cis-syn photodimer most prevalent in DNA. This is the lesion which is found most often in DNA and has been directly-linked to the suntan response in humans [65]. A [2Tr + 2Tr] cycloaddition reaction between the double bond in thymine and the carbonyl or the imino of an adjacent pyrimidine nucleobase can eventually yield the pyrimidine pyrimidinone [6 1]-photoproduct via spontaneous rearrangement of the initially formed oxetane or azetidine. This photoproduct has a much lower quantum yield than the photodimer in both dinucleoside monophosphates and in DNA. Finally, thymine can also form the photohydrate via photocatalytic addition of water across the C5 = C6 bond. 

The discovery of these base pairs, which imply the double helical structure of DNA, stimulated a series of crystal structural studies not only of complexes of purines and pyrimidines, but of other complexes involving related molecules and their derivatives. Although we can formulate a large number of possible heterocombinations in matrix form, as shown below these complexes are reluctant to crystallize even when there is spectroscopic evidence of hetero-complex formation in solution. This is presumably because self-(homo)-association is energetically more favorable and only in rare cases were crystals of hetero complexes actually formed. Because of their three hydrogen bonds, G-C complexes form and crystallize more readily. There have been many attempts to crystallize the Watson-Crick A-U base pair, but none was successful and it only formed when the dinucleoside phosphate adenylyl-3,5,-uridine (ApU [536]) or higher oligomers were crystallized (see Part III, Chapter 20). 

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