Two Perspectives on the Twist of DNA

TL;DR

This paper explores the mathematical and structural aspects of DNA supercoiling, deriving expressions for twist and writhe, and discusses how these measures can reveal chiral distortions caused by protein binding.

Contribution

It provides new mathematical expressions for DNA twist and writhe consistent with modern structural biology and compares different notions of twist to analyze protein-induced DNA distortions.

Findings

Derived expressions for DNA twist and writhe.

Identified differences between step-parameter twist and supercoiling twist.

Proposed using twist comparisons to study protein effects on DNA structure.

Abstract

Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked single-stranded rings. Two closed space curves have long been known by mathematicians to exhibit a property called the linking number, a topologically invariant integer, expressible as the sum of two other quantities, the twist of one of the curves about the other, and the writhing number, or writhe, a measure of the chiral distortion from planarity of one of the two closed curves. We here derive expressions for the twist of supercoiled DNA and the writhe of a closed molecule consistent with the modern view of DNA as a sequence of base-pair steps. Structural biologists commonly characterize the spatial disposition of each step in terms of six rigid-body parameters, one of which, coincidentally, is also called the twist. Of interest is the difference in the mathematical properties between this step-parameter twist and the twist of supercoiling associated with a given base-pair step. For example, it turns out that the latter twist, unlike the former, is sensitive to certain translational shearing distortions of the molecule that are chiral in nature. Thus, by comparing the values for the two twists for each step of a high-resolution structure of a protein-DNA complex, the nucleosome considered here, for example, we may be able to determine how the binding of various proteins contributes to chiral structural changes of the DNA.