A NOVEL INTACT CIRCULAR DSDNA SUPERCOIL

A novel intact circular dsDNA supercoil is proposed as an alternative to the conventional DNA supercoil, so that the two complementary stran ds of ssDNA circles are separable without any covalent bond breakage. This new structure can be visualized by using two tubings: one black a nd one clear. Twist the black tubing a number of times and connect its two ends. Do the same for the clear tubing. Then wrap the two tubings together. This forms the separable or novel supercoil. On the other h and, the conventional supercoil can be modeled by twisting the black a nd clear tubings together and then connect their respective ends, so t hat the two tubings are not separable unless one of them is cut. Exper imentally, in the absence of any enzyme, many intact plasmid dsDNA cir cles give two bands on agarose gel electrophoresis under a certain giv en condition, while the same plasmid molecules after cutting once by a restriction enzyme give only one band under the same condition. In th e case of intact pUC19 plasmids, these two bands can then be recovered and sequenced separately, using two primers in opposite directions. E ach band gives mostly one sequence which is complementary to that of t he other band. The combination of the above theoretical model and expe rimental results strongly suggests that there is an alternative struct ure of DNA which does not have the usual difficulty of unwinding, rewi nding and requiring numerous covalent bond breakages and ligations dur ing semiconservative replication. (C) 1996 Society for Mathematical Bi ology