DNA Super coiling: 

Cellular DNA, as we have seen, is extremely compacted,
implying a high degree of structural organization. The
folding mechanism not only must pack the DNA but also
must permit access to the information in the DNA. Before
considering how this is accomplished in processes
such as replication and transcription, we need to examine
an important property of DNA structure known as Supercoiling.

         “Supercoiling” means the coiling of a coil. A telephone
cord, for example, is typically a coiled wire. The
path taken by the wire between the base of the phone
and the receiver often includes one or more supercoils.
DNA is coiled in the form of a double helix,

with both strands of the DNA coiling around an axis.
The further coiling of that axis upon itself 
produces DNA supercoiling. As detailed below, DNA supercoiling
is generally a manifestation of structural
strain. When there is no net bending of the DNA axis
upon itself, the DNA is said to be in a relaxed state.
We might have predicted that DNA compaction involved
some form of supercoiling. Perhaps less predictable
is that replication and transcription of DNA also
affect and are affected by supercoiling. Both processes
require a separation of DNA strands—a process complicated by the helical interwinding of the strands.

That a DNA molecule would bend on itself and become
supercoiled in tightly packaged cellular DNA
would seem logical, then, and perhaps even trivial, were
it not for one additional fact: many circular DNA molecules
remain highly supercoiled even after they are extracted
and purified, freed from protein and other
cellular components. This indicates that supercoiling is
an intrinsic property of DNA tertiary structure. It occurs
in all cellular DNAs and is highly regulated by each cell. Several measurable properties of supercoiling have
been established, and the study of supercoiling has provided
many insights into DNA structure and function.
This work has drawn heavily on concepts derived from a
branch of mathematics called topology, the study of
the properties of an object that do not change under
continuous deformations. For DNA, continuous deformations
include conformational changes due to thermal
motion or an interaction with proteins or other molecules;
discontinuous deformations involve DNA strand
breakage. For circular DNA molecules, a topological
property is one that is unaffected by deformations of the
DNA strands as long as no breaks are introduced. Topological
properties are changed only by breakage and
rejoining of the backbone of one or both DNA strands.
We now examine the fundamental properties and
physical basis of supercoiling. 

                           Figure: Relaxed and supercoiled plasmid DNAs. The molecule in the leftmost
electron micrograph is relaxed; the degree of supercoiling increases from left to right.

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