SYNTHETIC SPECTROSCOPIC MODELS RELATED TO COENZYMES AND BASE PAIRS .2. EVIDENCE FOR INTRAMOLECULAR BASE-BASE INTERACTIONS IN DINUCLEOTIDE ANALOGS

In order to study interactions of bases found in nucleic acids in the absence of complicating factors associated with hydrogen bonding or the usual carbohydrate and phosphodiester linkages, we have synthesized a series of 12 dinucleotide analogs in which the bases are connected by a trimethylene chain: B-(CH2)3-B' or B-C3-B’, where B and B' are 9-substituted adenine or guanine or 1-substituted cytosine, thymine, or uracil residues. These compounds were studied optically at concentrations low enough to preclude formation of intermolecular complexes so that the perturbations associated with the 1:1 interaction of a pair of bases could be characterized, namely, by ultraviolet spectra in aqueous solution at room temperature and by emission spectra in 1:1 ethylene glycol-water glass in the vicinity of 77 °K. In the series of B-C3-B’, the order of interaction in neutral aqueous solution is purine-purine > purine-pyrimidine > pyrimidine-pyrimidine, as judged by hypochromism [decrease in integrated ultraviolet absorption intensity of B-Cn-B' compared with equimolar B-(CH2)2CH3 + B′-(CH2)2CH3], The divisions between the categories were not sharp, but the trend was unmistakable. The same order of interaction was confirmed by low-temperature fluorescence emission studies. Emission from singlet excimer states was observed for analogs with relatively strong base-base interaction, while pyrimidine-pyrimidine pairs had fluorescence emission similar to that characteristic of isolated chromophores. The fluorescence emission of 9,9′-trimethylenebisadenine (Ad-C3-Ad), for example, was characteristic of an eximer state, the emission of Ad-C3-Cy and Gu-C3-Th occurred from both eximer states and from excited singlet states, and the fluorescence emission of Th-C3-Th, Cy-C3-Th, and Cy-C3-Cy occurred only from excited singlet states similar to those found for the isolated chromophores of the molecules. Both hypochromism and excimer formation decreased when the pH was varied so as to result in ionization of the bases. Base-base interaction, as judged by hypochromism, was greatly diminished when 95% ethanol was substituted for water as the solvent. In a series of 9,9′-polymethylenebisadenines, the order of interaction deduced from hypochromism and emission studies was n = 3 > 2 and 6. Reduced interaction at n = 2 reflected the impossibility of this molecule assuming folded, parallel-plane conformations which would allow maximal interaction, as in Ad-C3-Ad. An entropy effect was probably responsible for decreased interaction in the n = 6 compound relative to n = 3. The phosphorescence emission from all neutral dinucleotide analogs is characteristic of the base with the lower lying triplet state. This shows that the triplet energy transfer is an efficient mechanism in these molecules and confirms the order of the triplet levels of the bases, which is (in decreasing energy) C, G, A, T. 1,1 ‘-Trimethylenebisthymine (Th-C3-Th) underwent intramolecular photodimerization at 3.5 times the rate for TpT, presumably reflecting a greater time-average separation of the thymine rings in the latter case. The greater hypochromisms of the analogs compared with the corresponding ribodinucleoside phosphates in general suggest that average base-base separation is smaller in our analogs. The accumulated data indicate that the B-(CH2)3-B' analogs serve as useful spectroscopic models for situations in which the nucleic acid bases are held in relatively close proximity, such as in aggregates of bases in aqueous solutions or in the native forms of nucleic acids. © 1968, American Chemical Society. All rights reserved.