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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This survey covers the following topics: (1) Theoretical calculation of the total multitude of the energetically permitted regular DNA helices. These findings give rise to three general problems: (1) Theoretical description of total conformational possibilities of the double helix. In particular, it would be desirable to learn what "place" among all potentially possible structures the known forms have and to learn if one can expect to discover new complementary helices radically different from the known ones.Owing to the rigidity of DNA, a separate consideration of the transitions within the regular helices and the problem of DNA bending is justified physically. So, another task is calculating the DNA helix flexibility, in particular, examining the anisotropy of bending.(2) Experimental study of the conformational polymorphism of the double helix and its dependence on the external factors and the nucleotide sequence with the aim of revealing conditions and physical mechanisms of the the conformational transitions within the double-stranded state. In particular, it would be interesting to obtain the thermodynamic parameters for the interfamily B-A transition.( 3 ) Biological applications of the conformational changes occurring within the framework of the double-stranded state.

The synthesis of N4-methyl-2'-deoxycytidine and its fully protected mononucleotide, suitable for the oligonucleotide synthesis by phosphotriester method is described. A set of octanucleotides - d(CGCGCGCG), d(CG5mCGCGCG), d(CG4mCGCGCG) and dodecanucleotides - d(GGACCCGGGTCC), d(GGA5mCCCGGGTCC), d(GGA4mCCCGGGTCC) has been synthesized in a solution. Physical characterization of the oligonucleotide duplexes by means of UV and CD spectrometry provides the evidence that 4mC similarly to 5mC favours the B--greater than Z transition, although both of these methylated cytosines inhibit the B--greater than A conformational change. N4-Methylcytosine in contrast to 5-methylcytosine reduces the DNA double helix thermal stability.