Two distinct conformers coexist in a synthetic DNA poly(dA-dT).Poly(dA-dT) in low-salt aqueous solution.

Circular dichroism spectroscopy (CD) sensitively reflects even slight alterations of the base stacking geometry in DNA (Tinoco et al. 1980; Johnson et al. 1981). However, the alterations cannot be unambiguously interpreted in conforma­ tional terms so that, for example, the question concerning the origin of the relatively extensive temperature-induced changes in the CD spectrum of a synthetic DNA poly(dA-dT). poly(dA-dT) still remains unanswered (Gennis and Cantor 1972; Studdert et al. 1972; Brahms et al. 1976). These changes are interesting from the biological point of view because some proteins participating in gene expression cause the same changes in the CD spectrum of poly(dA-dT). poly(dA-dT) as do temperature alterations (Shimer et al. 1988; Schnarr and Daune 1984). We report two new results relevant to this problem, obtained from comparative CD analysis of a number of poly(dA-dT). poly(dA-dT) analogs. A careful analysis of the CD spectra of poly(dA-dT). poly(dA-dT) recorded at different temperatures suggests that they intersect in isodichroic points loc­ ated at about 241 and 278.5 nm (Fig. 1). This possibility is interesting because isodichroic points point to the presence of two distinct species in solution (Kypr and Vorličková 1986), in this case two polynucleotide conformers. The tem­ perature-induced changes are fast, completely reversible, and the isodichroic points slightly shift if NaCl concentration in the polynucleotide solution is increased (not shown). We synthesized a number of poly(dA-dT). poly(dA-dT) analogs differing from the parent polynucleotide by the base pair exocyclic substituents, and examined the temperature dependences of their CD spectra. Figure 1 shows CD spectra of poly(dA-ethyl 5 dU) .poly(dA-ethyľdU) obtained at different temperatures. In this case, the existence of the insodichroic points (at 224 and 272 nm) is even more evident than with poly(dA-dT). poly(dA-dT). We conclude from these experiments that two distinct B-DNA type conformers with slightly different base stacking geometries coexist in poly(dA-dT). poly (dA-dT) and poly(dA-ethyl 5 dU). poly(dA-ethyl'dU) and that the relative sta