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Three dinucleoside monophosphates containing 8-bromoguanosine (br8G), (2'-5')C-br8G, (3'-5')C-br8G, and dC-br8G, were synthesized and characterized by UV absorption, CD, and 1H NMR spectroscopy. The 1H NMR data show that all the br8G residues in these dimers take a syn glycosidic conformation. At low dimer strand concentration (5 X 10(-5) M), the UV hypochromicity data suggest that the degree of base stacking decreases in the following order, (2'-5')C-br8G greater than C-G approximately equal to dC-br8G greater than (3'-5')C-br8G. The CD data also suggest little stacking in (3'-5')C-br8G. At high dimer strand concentration (5 X 10(-3) M), only (3'-5')C-br8G shows duplex formation in 0.1 M NaCl. The duplex is assumed to take a left-handed helical structure similar to that of Z-DNA. The Tm of this duplex is surprisingly high for a dimer (about 35 and 45 degrees C at 5 X 10(-3) and 10(-2) M dimer strand concentration, respectively). The above results and the similarity between the CD spectra of (3'-5')C-br8G and poly(G-C) suggest the possible existence of Z-form structure in ribooligo- and ribopolynucleotides with alternating purine-pyrimidine sequences.

The conformational properties of purine-pyrimidine and pyrimidine-purine dinucleoside monophosphates in which the glycosidic torsion is fixed to congruent to 120 degree by the formation of a covalent link between the base and the sugar ring are explored by 1H NMR spectroscopy in order to obtain information about the spatial configuration of high anti nucleic acids. The intramolecular stack of the high anti dimers were found to be left handed, in contrast to that (right handed) for natural oligomers, which are low anti. Even though both the high anti pyrimidine-purine and purine-pyrimidine dimers have similar backbone torsion angles, they display widely different relative geometry between the bases; thus in the former there is extensive base-base overlap in the stack, and in the latter there is negligible intramolecular base-base overlap. In addition it was found that purine-pyrimidine systems form miniature double helices in which there is substantial interstrand purine-purine interaction; on the other hand the pyridine-purine high anti dinucleosides have no proclivity to form such base-paired complexes in solution. Mathematical polymerization of the conformation of the high anti purine-pyrimidine dinucleoside monophosphates generates a left handed helix for high anti polynucleotides. This also means that the double helix for high anti-nucleic acids containing purine-pyrimidine repeated units may also be left handed, as had been suggested [Sundaralingam, M., & Yathindra, N. (1977) Int. J. Quantum Chem., Quantum Biol. Symp. 4, 285]. It is suggested that the plasticity in the structure of genomic DNA is such that, if under certain conditions of interactions the sugar-base torsion of certain domains assume high anti values, that domain will become left handed, and this in turn can be a mechanism for the control of expression by genomic DNA.