Destabilization of the duplex and the high-salt Z-form of poly(dG-methyl 5dC) by substitution of ethyl for the 5-methyl group

The B-to-Z conformational transition of poly(dG-dC) is highly promoted by 5-methyl substitution of the dC moiety, i.e. in poly(dG-methyl 5dC). By the synthesis of a new poly(dG-dC) analogue, poly(dG-ethyl 5dC), the effect of a longer alkyl-chain substituent of dC on structure and conformation has been studied with ultraviolet absorption melting profiles and circular dichroism spectroscopy. The 5-ethyl substituent in poly(dG-ethyl 5dC) destabilizes the duplex structure against thermal denaturation compared with both poly(dG-methyl 5dC) and poly(dG-dC). C.d. studies also reveal that for the high-salt B-Z transition of poly(dG-ethyl 5dC) a higher NaCl concentration is required than for that of poly(dG-methyl 5dC), although much lower than for poly(dG-dC). However low-salt Z-DNA in poly(dG-ethyl 5dC) shows unique features, e.g. it needs no divalent cations to be stable. The low-salt B-Z transition of poly(dG-ethyl 5dC) can also be observed by the absorption-temperature melting profile, in constrast to both poly(dG-methyl 5dC) and poly(dG-dC). The effects of MgCl 2 concentration, temperature, acid pH and trifluorethanol on the conformation of poly(dG-ethyl 5dC) have also been determined.