2
Topology in Biology: From DNA Mechanics
to Enzymology
S.D. Levene
Summary.The focus of this contribution is on biological applications of topology
to the study of DNA structure and to understanding protein–DNA interactions that
involve alterations of DNA topology.
We review basic aspects of DNA structure and the tertiary organization of cir-
cular DNA by supercoiling, knotting, and catenation (linking). This is followed by a
review of our current understanding of the topology of chromosomal DNA. Finally,
we discuss some topological and structural aspects of DNA site-specific recombina-
tion by the yeast enzyme FLP.
2.1 Overview
The focus of this contribution is on biological applications of topology to the
study of DNA structure and to understanding protein–DNA interactions that
involve alterations of DNA topology. Control of DNA topology is an essential
aspect of the existence of every living cell because of the extraordinary degree
to which the genomes of free-living organisms are confined. Moreover, changes
in DNA topology accompany a wide range of enzyme-mediated processes on
DNA such as replication, recombination, and repair. In higher organisms the
interconversion of DNA between an inert state contained within chromatin
fibers and an active state characterized by greater, but not necessarily com-
plete, accessibility, provokes many questions about how DNA topology and
its regulation provides both challenges and opportunities to the cell.
We first review basic aspects of DNA structure and the tertiary organiza-
tion of circular DNA by supercoiling, knotting, and catenation (linking). This
is followed by a review of our current understanding of the topology of chro-
mosomal DNA. Finally, we discuss some topological and structural aspects of
DNA site-specific recombination by the yeast enzyme FLP.