DATA ANALYSIS PROBLEM

Boles, T.C., J.H. White, and N.R. Cozzarelli. 1990. Structure of plectonemically supercoiled DNA. J. Mol. Biol. 213:931–951.

Question 9.18

The structural parameters of plectonemically supercoiled DNA in solution were first examined by Cozzarelli and coworkers. Using a combination of electron microscopy and gel electrophoresis, they examined the properties of plasmid DNAs with different superhelical densities (σ). DNAs were spread for electron microscopic examination. DNA twists on itself to form a superhelix. The length of the superhelical axes of the entire molecule can be determined by measuring and adding up the lengths of the axes of all segments and branches. In the example shown below, there are five segments with three branch points. The superhelix is seen as the crossing of the DNA as it winds about itself, with the crossing points on the DNA defined as nodes.

  1. How many nodes are there in this DNA? Each node is roughly equivalent to a supercoil.

  2. If one assumes that each supercoil results from an underwinding of the DNA by one turn, and the DNA has a length of 7,000 bp, calculate σ.

The investigators found a linear relationship between the number of nodes (n) and ΔLk, such that n = −0.89 ΔLk (implying that most, but not all, of the change in linking number results from changes in the writhe or twist of the DNA helix axis on itself).

  1. With this in mind, calculate the σ for this molecule.

  2. Is there any evidence of solenoidal supercoiling?

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