A.cntdot.T and C.cntdot.C+ base pairs can form simultaneously in a novel multistranded DNA complex

Publisher Website
Google Scholar
Abstract
Previous experiments have established that in certain synthetic oligomeric DNA sequences, including mixtures of d(AACC)5 with d(CCTT)5, adenine-thymine (A.cntdot.T) base pairs form to the exclusion of neighboring protonated cytosine-cytosine (C.cntdot.C+) base pairs [Edwards, E., Ratliff, R., and Gray, D. (1988) Biochemistry 27, 5166-5174]. In the present work, circular dichroism and other measurements were used to study DNA oligomers that represented two additional classes with respect to the formation of A.cntdot.T and/or C.cntdot.C+ base pairs. (1) One class included two sets of repeating pentameric DNA sequences, d(CCAAT)3-6 and d(AATCC)4,5. For both of these sets of oligomers, an increase in the magnitude of the long-wavelength positive CD band centered at about 280 nm occurred as the pH was lowered from 7 to 5 at 0.1 and 0.5 M Na+, indicating that C.cntdot.C+ base pairs formed. Even though it may have been possible for these oligomers to form duplexes with two antiparallel A.cntdot.T base pairs per pentamer, no A.cntdot.T base pairing was detected by monitoring the CD changes at 250 nm. Thus, spectral data showed that as few as 40% C.cntdot.C+ base pairs were stable in two sets of oligomers in which A.cntdot.T base pairs did not form adjacent to, or in place of, C.cntdot.C+ base pairs. (2) Another class of oligomer was represented by d(C4A4T4C4), which was studied by CD, HPLC, and centrifugation experiments. We confirmed previous work that this sequence was able to form both types of base pairs as the pH and temperature were lowered [Gray, D., Cui, T., and Ratliff, R. (1984) Nucleic Acids Res. 12, 7565-7580]. We further established that at low pH, where both A.cntdot.T and C.cntdot.C+ base pairs formed concurrently in d(C4A4T4C4), there was an increase in molecular weight above that expected for a duplex. Our interpretation of all these data is that those sequences that formed only A.cntdot.T base pairs had an antiparallel-strand orientation while those that formed only C.cntdot.C+ base pairs probably had a parallel-strand orientation. We propose that d(C4A4T4C4) at low pH adopted a multistranded structure that contained both parallel-stranded C.cntdot.C+ base pairs and antiparallel-stranded A.cntdot.T base pairs.
Keywords