synopsisConformation of two-stranded DNA in HzO-methanol, H20-ethanol, HzO-isopropanol, and HzO-dioxane solutions a t different concentrations of alkaline ions has been studied with the aid of circular dichroism. The following conclusions are drawn:The conformation of DNA in HzO and HZO-methanol belongs to a family of B forms (B, C, T forms are the representatives of the family). The magnitude of the winding angle between adjacent base pairs (0) is determined by the concentration and type of the cations. In HZ0 the cation action is nonspecific and leads to an increase in 8 value. In 80% methanol the ions act specifically, Cs+ being to stabilize a form with a greater e value, and Lif being with a lesser one. The total e change is likely within the limits At high content of ethanol, isopropanol, or dioxane (-SO%), but not with methanol, and in low ionic strength the conformation of DNA belongs to a family of A forms (A form is one of the members of the family) and is specified by the concentration and type of cation involved. The two-stranded regions of RNA in HzO are also of A type and winds with the rise of cation concentration. The range of e variation is not narrower than30" 6 e 6 33".The conformational transitions within the families (induced by ions) are of noncooperative pattern, wheras the transitions between the families (induced by nonpolar component) are of cooperative pattern. The effect of cations, when specific, is discussed on the basis of steric correspondence between the width of DNA narrow groove and the size of a hydrated cation.of330 < e 6 45".

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Self-complementary decadeoxynucleotides, CCGATATCGG, CCAGATCTGG, CCCTGCAGGG, GGGGGCCCCC, were designed and synthesized to estimate the A-philic free energy of CC/GG contacts. First, regions of temperature-stability of the double-stranded conformation were determined for each 10-mer. Then, circular dichroism spectra were recorded for the B-family forms at different temperatures, counter-ion concentrations and trifluoroethanol contents. A cooperative change typical of the B-A transition is observed in the CD spectra at a trifluoroethanol content specific for each duplex. The positions of half-transition points were functions not only of the nucleotide sequence but of the duplex length as well: the B to A transitions were hindered in these 10-mers in comparison with a lengthy DNA. The B-phility value was estimated to be 3 kcal/mol of 10-mer. The B-A transition point was shown to drop with an increase in the number of CC/GG contacts in a duplex. The designed 10-mers made it possible to estimate quantitatively the A-phility of CC/GG contact as compared with an average DNA: (FA-FB)CC = 0.2 Kcal/mol, (FA-FB)DNA = 0.7 Kcal/mol.

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The transition of the 14-meric deoxyoligonucleotide duplex d-(ACCCCCTTTTTTTG).d-(CAAAAAAAGGGGGT) from the B- to the A-conformation in water/trifluorethanol (TFE) solution was studied with the use of circular dichroism. An increase in the fraction of TFE induces a two-step B-A transition. In the first step, up to 73% TFE, the A-form is generated from the GC-rich part; in the second step, 73-82% TFE, the AT-rich part shifts to the A-form. By this we suggest the existence of a B/A junction near 73% TFE. Emergence of the B/A junction has been directly confirmed with the use of distamycin A and netropsin, ligands known to selectively bind to AT stretches of B-DNA. It can be shown that both ligands suppress formation of the A-form in the B-philic part. The free energy value for the B/A junction was estimated to be 2.1 kcal/mol, which agrees well with known data for polymeric DNAs. The obtained results may have biological relevance in connection with recently published x-ray data about the occurrence of the B/A junction in the complex of DNA with reverse transcriptase of HIV.

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spnopsisThe additiou of reducing agents, i.e., ascorbic acid or sodium borohydride, to a DNA solution containing Cu*+ ions causes changes in the DNA absorption spectra which are due to a new absorption band with a maximum a t 280 assigned to a DNA base-CuI + complex. The stoichiometry of the complex is one Cul+ ion per four bases of DNA. The DNA-Cd + complex has an increased melting temperature and rather different circular dichroism curve as compared with DNA itself. It is inferred that the above effects are caused by proton transfer along the hydrogen bond from guanine to cytosine under complexing of Cul+ ions with t~he h77 atom of the guanine of DNA.