Self-complementary oligoribonucleotides: Effects of helix defects and guanylic acid-cytidylic acid base pairs

Oligonucleotides consisting of a sequence of adenylic acid and a sequence of uridylic acid separated by one eytidylic or guanylic acid or by a cytidilic-guanylic pair (C · G) have been synthesized and their associating properties studied. When G or C is inserted between the blocks the stability of the bimolecular, helical complex is reduced. C is the more destabilizing, reducing T_m from 10 to 17 deg. C equivalent to the removal of 2 adenylic-uridylic (A · U) pairs. Several observations suggest that, in contrast to C, the duplex rearranges to accommodate G opposite a U residue. Equimolar mixtures of oligomers differing only in that one contains C between the blocks and the other G are found to form bimolecular helices of enhanced stability. In a decamer the effect of one G · C pair replacing an A · U pair is to raise T_m by 8.5 deg. C. Double this effect is observed for the helical duplexes which are formed by (Ap)_nCpG(pU)_n. The stabilizing effect of G · C pairs is probably dependent on their location in the helix and nearest neighbors. In this case their effect on T_m is greater than that found for natural polymeric bihelical RNA, i.e. 0.9 deg. C per percentage increase in G + C rather than 0.75 deg. C. The greater enthalpy of formation of a G · C pair over an A · U pair can only be roughly estimated.