Publisher Summary This chapter discusses the basic concepts and methods by which the
topological structure of DNA molecules is determined. Knotting and catenation are the true …

Although linking number is an effective topological invariant for describing supercoiled DNA,
it is inadequate for the additional interwinding in catenated or knotted DNA. We explain how …

Supercoiling, knotting, and catenation are three common higher-order structures involving
coiling of the axis of double-stranded DNA. These forms appear as a result of a number of …

Agarose gel electrophoresis is by far the most widely used method for characterizing the
topological state of DNA molecules. Although this technique has been used for more than 30 …

Processes of DNA rearrangement such as recombination or replication frequently have as
products different subsets of the limitless number of distinguishable catenanes or knots. The …

Large amounts of DNA are wound up and packed into the average cell. In fact, there is
enough DNA in a 2 m. human body to stretch from the earth to the sun and back 50 times …

To understand, at the molecular level, the mechanism of enzymes that act on DNA, it is
highly informative to know the topology of their substrates and products. To describe fully the …

We describe a two-dimensional agarose gel electrophoresis procedure that improves the
resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA …

The characterization of knots formed in duplex DNA has proved useful to infer biophysical
properties and the spatial trajectory of DNA, both in free solution and across its …

DNA as the genetic material is a topic of intense interest in the 21st century, with the
genomes of many organisms having been sequenced. The double helix structure …