Circular dichroism spectra of DNA oligomers show that short interior stretches of C.cntdot.C+ base pairs do not form in duplexes with A.cntdot.T base pairs

Publisher Website
Google Scholar
Abstract
Circular dichroism (CD) experiments were carried out on a series of DNA oligomers to determine if short internal stretches of protonated cytosine-cytosine (C .cntdot. C+) base pairs could coexist with adenine-thymine (A .cntdot. T) base pairs. (1) C .cntdot. C+ base pairs did form in the absence of A .cntdot. T base pairs in the individual oligomers d(AACC)5 and d(CCTT)5, as indicated by the appearance of a long-wavelength CD band centered at 282-284 nm, when the pH was lowered to 6 or 5 at 0.5 M Na+. A comparison of measured with calculated spectra showed that d(CCTT)5 at pH 5, 0.5 M Na+, 20.degree. C, likely adopted a structure with a central core of stacked C .cntdot. C+ base pairs and looped-out thymines. Under the same conditions, it appeared that C .cntdot. C+ base pairs also formed in d(AACC)5, but with the adenines remaining intrahelical. Each of these oligomers showed a cooperative transition for formation of C .cntdot. C+ base pairs as the temperature was lowered, with C .cntdot. C+ base pairs forming at a higher temperature in d(CCTT)5 than in d(AACC)5. A .cntdot. T base pairs formed in equimolar mixtures of d(AACC)5 plus d(CCTT)5 as monitored by an increase in the negative magnitude of the 250-nm CD band. However, a large increase did not appear at about 285 nm in CD spectra of the mixtures, showing that there were no stacked C .cntdot. C+ base pairs in the d(AACC)5 .cntdot. d(CCTT)5 duplex even though they formed under the same conditions in the individual strands. Thus, in this duplex, A .cntdot. T base pairs prevented the formation of neighboring internal C .cntdot. C+ base pairs. (2) CD measurements were also made of d(A10C4T10). At pH 5 there was evidence for formation of a duplex with A .cntdot. T base pairs, but no C .cntdot. C+ base pairs were detected. (3) Finally, we found that the individual oligomers d(A6C6A6) and d(T6C6T6) were able to form C .cntdot. C+ base pairs, but only A .cntdot. T base pairs were present in 1:1 mixtures of the two strands, even at pH values below the pKa for C .cntdot. C+ base pair formation in the individual strands. Thus, short internal stretches of 2, 4, or 6 C .cntdot. C+ base pairs were incompatible with A .cntdot. T base pairs in complexes of these oligomers under the conditions studied.