Helical repeat of DNA in solution

Abstract

The helical repeat of DNA in solution has been measured directly by analyzing the gel electrophoretic patterns of pairs of covalently closed DNAs with length differences between 1 and 58 base pairs, out of a total length of about 4350 base pairs per DNA molecule. The method is based on the observation that for a covalently closed DNA of a fixed size of n base pairs (n of the order of several thousand), under appropriate conditions, two topological isomers (topoisomers) differing by 1 in their linking numbers are well resolved by gel electrophoresis. If the size of the DNA is increased to n + x base pairs, unless x is an integral multiple of the helical repeat h, the bands of the topoisomers with n + x base pairs per molecule are all shifted relative to the bands of the topoisomers with n base pairs per molecule. The magnitude of the shift is directly related to the nonintegral residual of x/n. Analysis of the set with x ranging from 1 to 58 gives the DNA helix repeat in solution as 10.4 base pairs per turn under physiological conditions, with an estimated probable error of +/- 0.1. This result strongly supports the double helix structure of DNA and rejects the side-by-side model of Rodley et al. [Rodley, G.A., Scobie, R.S., Bates, R.H. T & Lewitt, R.M. (1976) Proc. Natl. Acad. Sci. USA 73, 2959-2963]. The helical repeat of DNA measured in solution is significantly different from the value 10.0 base pairs per turn for the B form fiber structure.