Interlocked DNA rings. II. Physicochemical studies

Several species of topologically interlocked λb2b5c DNA rings (catenanes) have been prepared in vitro . The sedimentation behavior of dimeric catenanes containing 0, 1, or 2 covalently closed duplex rings has been studied as a function of the superhelical density of the covalently closed ring or rings. In general, if XtpY represents rings X and Y topologically interlocked, the sedimentation coefficient of this species, S XtpY, is related to the sedimentation coefficients S X and S Y of the component rings by the empirical relationship S XtpY/ S Y = [( M X + M Y )/ M Y ] [1 + ( M X / M Y ) 1.78 ( S Y/ S X) 1.78 ] −0.56 This equation can also be extended to the case where three monomeric rings are topologically linked in a chain. For two topologically interlocked monomeric rings with neither ring covalently closed, the sedimentation coefficient is 1.35 times that of the monomeric ring. This is different from results reported for mitochondrial and P22 catenanes by others. Several possibilities are discussed to account for this discrepancy. The sedimentation coefficient of a species containing one covalently closed duplex ring and a single‐stranded ring was also measured in an alkaline medium. This species, which can be easily derived from a dimeric catenane containing two covalently closed duplex rings, is particularly useful for the identification of covalently closed dimeric catenanes. Some electron microscopic studies of these interlocked rings are presented in an accompanying paper.