DNA supercoil

From Wikipedia, the free encyclopedia

DNA supercoiling refers to the over- or under-winding of a DNA

strand, and is an expression of the strain on that strand. Supercoiling is
important in a number of biological processes, such as compacting
DNA, and by regulating access to the genetic code, DNA supercoiling
strongly affects DNA metabolism and possibly gene expression.
Additionally, certain enzymes such as topoisomerases are able to change
DNA topology to facilitate functions such as DNA replication or
transcription[1]. Mathematical expressions are used to describe
supercoiling by comparing different coiled states to relaxed B-form
DNA.

Contents
1 Overview
2 Visualizing DNA supercoils: Intercalation-induced
supercoiling of DNA
3 Functions
3.1 Genome packaging Supercoiled structure of circular DNA
3.2 Gene expression molecules with low writhe. The
4 Mathematical description helical nature of the DNA duplex is
5 Effects on sedimentation coefficient omitted for clarity.
6 See also
7 References
7.1 General references

Overview
In a "relaxed" double-helical segment of B-DNA, the two strands twist
around the helical axis once every 10.4–10.5 base pairs of sequence. Supercoiled structure of linear DNA
Adding or subtracting twists, as some enzymes can do, imposes strain. molecules with constrained ends. The
If a DNA segment under twist strain were closed into a circle by joining helical nature of the DNA duplex is
its two ends and then allowed to move freely, the circular DNA would omitted for clarity.
contort into a new shape, such as a simple figure-eight. Such a
contortion is a supercoil. The noun form "supercoil" is often used in the
context of DNA topology.

Positively supercoiled (overwound) DNA is transiently generated during DNA replication and transcription,
and, if not promptly relaxed, inhibits (regulates) these processes. The simple figure eight is the simplest
supercoil, and is the shape a circular DNA assumes to accommodate one too many or one too few helical
twists. The two lobes of the figure eight will appear rotated either clockwise or counterclockwise with respect
to one another, depending on whether the helix is over- or underwound. For each additional helical twist being
accommodated, the lobes will show one more rotation about their axis. As a general rule, the DNA of most
organisms is negatively supercoiled.[2]

Lobal contortions of a circular DNA, such as the rotation of the figure-eight lobes above, are referred to as
writhe. The above example illustrates that twist and writhe are interconvertible. Supercoiling can be
represented mathematically by the sum of twist and writhe. The twist is the number of helical turns in the DNA
and the writhe is the number of times the double helix crosses over on itself (these are the supercoils). Extra
helical twists are positive and lead to positive supercoiling, while subtractive twisting causes negative
supercoiling. Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change
DNA topology. DNA of most organisms is negatively supercoiled.

In part because chromosomes may be very large, segments in the middle may act as if their ends are anchored.
As a result, they may be unable to distribute excess twist to the rest of the chromosome or to absorb twist to
recover from underwinding—the segments may become supercoiled, in other words. In response to
supercoiling, they will assume an amount of writhe, just as if their ends were joined.

Supercoiled DNA forms two structures; a plectoneme or a toroid, or a combination of both. A negatively
supercoiled DNA molecule will produce either a one-start left-handed helix, the toroid, or a two-start right-
handed helix with terminal loops, the plectoneme. Plectonemes are typically more common in nature, and this
is the shape most bacterial plasmids will take. For larger molecules it is common for hybrid structures to form –
a loop on a toroid can extend into a plectoneme. If all the loops on a toroid extend then it becomes a branch
point in the plectonemic structure. DNA supercoiling is important for DNA packaging within all cells, and
seems to also play a role in gene expression.[3][4]

Visualizing DNA supercoils: Intercalation-induced supercoiling of

DNA
Based on the properties of intercalating molecules i.e., fluorescing upon binding to DNA and unwinding of
DNA base-pairs, recently a single-molecule technique has been introduced to directly visualize individual
plectonemes along supercoiled DNA[5] which would further allow to study the interactions of DNA processing
proteins with supercoiled DNA. In that study, Sytox Orange (an intercalating dye), has been used to
induce supercoiling on surface tethered DNA molecules.

Functions
Genome packaging

DNA supercoiling is important for DNA packaging within all cells. Because the length of DNA can be
thousands of times that of a cell, packaging this genetic material into the cell or nucleus (in eukaryotes) is a
difficult feat. Supercoiling of DNA reduces the space and allows for DNA to be packaged. In prokaryotes,
plectonemic supercoils are predominant, because of the circular chromosome and relatively small amount of
genetic material. In eukaryotes, DNA supercoiling exists on many levels of both plectonemic and solenoidal
supercoils, with the solenoidal supercoiling proving most effective in compacting the DNA. Solenoidal
supercoiling is achieved with histones to form a 10 nm fiber. This fiber is further coiled into a 30 nm fiber, and
further coiled upon itself numerous times more.

DNA packaging is greatly increased during nuclear division events such as mitosis or meiosis, where DNA
must be compacted and segregated to daughter cells. Condensins and cohesins are structural maintenance of
chromosome (SMC) proteins that aid in the condensation of sister chromatids and the linkage of the centromere
in sister chromatids. These SMC proteins induce positive supercoils.

Supercoiling is also required for DNA/RNA synthesis. Because DNA must be unwound for DNA/RNA
polymerase action, supercoils will result. The region ahead of the polymerase complex will be unwound; this
stress is compensated with positive supercoils ahead of the complex. Behind the complex, DNA is rewound and
there will be compensatory negative supercoils. Topoisomerases such as DNA gyrase (Type II Topoisomerase)
play a role in relieving some of the stress during DNA/RNA synthesis.[6]

Gene expression
Specialized proteins can unzip small segments of the DNA molecule when it is replicated or transcribed into
RNA. But work published in 2015 illustrates how DNA opens on its own.[3][4]

Simply twisting DNA can expose internal bases to the outside, without the aid of any proteins. Also,
transcription itself contorts DNA in living human cells, tightening some parts of the coil and loosening it in
others. That stress triggers changes in shape, most notably opening up the helix to be read. Unfortunately, these
interactions are very difficult to study because biological molecules morph shapes so easily. In 2008 it was
noted that transcription twists DNA, leaving a trail of undercoiled (or negatively supercoiled) DNA in its wake.
Moreover, they discovered that the DNA sequence itself effects how the molecule responds to
supercoiling.[3][4] For example, the researchers identified a specific sequence of DNA that regulates
transcription speed; as the amount of supercoil rises and falls, it slows or speeds the pace at which molecular
machinery reads DNA.[3] It is hypothesized that these structural changes might trigger stress elsewhere along
its length, which in turn might provide trigger points for replication or gene expression.[3][4] This implies that it
is a very dynamic process in which both DNA and proteins each influences how the other acts and reacts.[3]

Mathematical description
In nature, circular DNA is always isolated as a higher-order helix-upon-
a-helix, known as a superhelix. In discussions of this subject, the
Watson-Crick twist is referred to as a "secondary" winding, and the
superhelices as a "tertiary" winding. The sketch at right indicates a
"relaxed", or "open circular" Watson-Crick double-helix, and, next to it,
a right-handed superhelix. The "relaxed" structure on the left is not
found unless the chromosome is nicked; the superhelix is the form
usually found in nature.

For purposes of mathematical computations, a right-handed superhelix

is defined as having a "negative" number of superhelical turns, and a
left-handed superhelix is defined as having a "positive" number of
superhelical turns. In the drawing (shown at the right), both the
secondary (i.e., "Watson-Crick") winding and the tertiary (i.e.,
"superhelical") winding are right-handed, hence the supertwists are Drawing showing the difference
negative (-3 in this example). between a circular DNA chromosome
(a plasmid) with a secondary helical
The superhelicity is presumed to be a result of underwinding, meaning twist only, and one containing an
that there is a deficiency in the number of secondary Watson-Crick additional tertiary superhelical twist
twists. Such a chromosome will be strained, just as a macroscopic metal superimposed on the secondary
spring is strained when it is either overwound or unwound. In DNA helical winding.
which is thusly strained, supertwists will appear.

DNA supercoiling can be described numerically by changes in the linking number Lk. The linking number is
the most descriptive property of supercoiled DNA. Lko, the number of turns in the relaxed (B type) DNA
plasmid/molecule, is determined by dividing the total base pairs of the molecule by the relaxed bp/turn which,
depending on reference is 10.4;[7] 10.5;[8][9] 10.6.[10]

Lk is merely the number of crosses a single strand makes across the other. Lk, known as the "linking number",
is the number of Watson-Crick twists found in a circular chromosome in a (usually imaginary) planar
projection. This number is physically "locked in" at the moment of covalent closure of the chromosome, and
cannot be altered without strand breakage.
The topology of the DNA is described by the equation below in which the linking number is equivalent to the
sum of TW, which is the number of twists or turns of the double helix, and Wr which is the number of coils or
'writhes'. If there is a closed DNA molecule, the sum of Tw and Wr, or the linking number, does not change.
However, there may be complementary changes in TW and Wr without changing their sum.

Tw, called "twist", refers to the number of Watson-Crick twists in the chromosome when it is not constrained to
lie in a plane. We have already seen that native DNA is usually found to be superhelical. If one goes around the
superhelically twisted chromosome, counting secondary Watson-Crick twists, that number will be different
from the number counted when the chromosome is constrained to lie flat. In general, the number of secondary
twists in the native, supertwisted chromosome is expected to be the "normal" Watson-Crick winding number,
meaning a single 10-base-pair helical twist for every 34 Å of DNA length.

Wr, called "writhe", is the number of superhelical twists. Since biological circular DNA is usually
underwound, Lk will generally be less than Tw, which means that Wr will typically be negative.

If DNA is underwound, it will be under strain, exactly as a metal spring is strained when forcefully unwound,
and that the appearance of supertwists will allow the chromosome to relieve its strain by taking on negative
supertwists, which correct the secondary underwinding in accordance with the topology equation above.

The topology equation shows that there is a one-to-one relationship between changes in Tw and Wr. For
example, if a secondary "Watson-Crick" twist is removed, then a right-handed supertwist must have been
removed simultaneously (or, if the chromosome is relaxed, with no supertwists, then a left-handed supertwist
must be added).

The change in the linking number, ΔLk, is the actual number of turns in the plasmid/molecule, Lk, minus the
number of turns in the relaxed plasmid/molecule Lko.

If the DNA is negatively supercoiled ΔLk < 0. The negative supercoiling implies that the DNA is underwound.

A standard expression independent of the molecule size is the "specific linking difference" or "superhelical
density" denoted σ, that represents the number of turns added or removed relative to the total number of turns
in the relaxed molecule/plasmid, indicating the level of supercoiling.

The Gibbs free energy associated with the coiling is given by the equation below[11]

The difference in Gibbs free energy between the supercoiled circular DNA and uncoiled circular DNA with N
> 2000 bp is approximated by:

or, 16 cal/bp.

Since the linking number L of supercoiled DNA is the number of times the two strands are intertwined (and
both strands remain covalently intact), L cannot change. The reference state (or parameter) L0 of a circular
DNA duplex is its relaxed state. In this state, its writhe W = 0. Since L = T + W, in a relaxed state T = L. Thus,
if we have a 400 bp relaxed circular DNA duplex, L ~ 40 (assuming ~10 bp per turn in B-DNA). Then T ~ 40.

Positively supercoiling:
 T = 0, W = 0, then L = 0
T = +3, W = 0, then L = +3
T = +2, W = +1, then L = +3

Negatively supercoiling:

T = 0, W = 0, then L = 0
T = -3, W = 0, then L = -3
T = -2, W = -1, then L = -3

Negative supercoils favor local unwinding of the DNA, allowing processes such as transcription, DNA
replication, and recombination. Negative supercoiling is also thought to favour the transition between B-DNA
and Z-DNA, and moderate the interactions of DNA binding proteins involved in gene regulation.[12]

Effects on sedimentation coefficient

The topological properties of circular DNA are complex. In
standard texts, these properties are invariably explained in
terms of a helical model for DNA, but in 2008 it was noted
that each topoisomer, negative or positive, adopts a unique
and surprisingly wide distribution of three-dimensional
conformations.[4]

When the sedimentation coefficient, s, of circular DNA is

ascertained over a large range of pH, the following curves
are seen. Three curves are shown here, representing three
species of DNA. From top-to-bottom they are: "Form IV"
(green), "Form I" (blue) and "Form II" (red).

"Form I" (blue curve) is the traditional nomenclature used

for the native form of duplex circular DNA, as recovered
from viruses and intracellular plasmids. Form I is
covalently closed, and any plectonemic winding which may
be present is therefore locked in. If one or more nicks are
introduced to Form I, free rotation of one strand with
Figure showing the various conformational changes
respect to the other becomes possible, and Form II (red
which are observed in circular DNA at different pH.
curve) is seen.
At a pH of about 12 (alkaline), there is a dip in the
Form IV (green curve) is the product of alkali denaturation sedimentation coefficient, followed by a relentless
of Form I. Its structure is unknown, except that it is increase up to a pH of about 13, at which pH the
persistently duplex, and extremely dense. structure converts into the mysterious "Form IV".

Between pH 7 and pH 11.5, the sedimentation coefficient s, for Form I, is constant. Then it dips, and at a pH
just below 12, reaches a minimum. With further increases in pH, s then returns to its former value. It doesn’t
stop there, however, but continues to increase relentlessly. By pH 13, the value of s has risen to nearly 50, two
to three times its value at pH 7, indicating an extremely compact structure.

If the pH is then lowered, the s value is not restored. Instead, one sees the upper, green curve. The DNA, now in
the state known as Form IV, remains extremely dense, even if the pH is restored to the original physiologic
range. As stated previously, the structure of Form IV is almost entirely unknown, and there is no currently
accepted explanation for its extraordinary density. About all that is known about the tertiary structure is that it
is duplex, but has no hydrogen bonding between bases.
These behaviors of Forms I and IV are considered to be due to the peculiar properties of duplex DNA which
has been covalently closed into a double-stranded circle. If the covalent integrity is disrupted by even a single
nick in one of the strands, all such topological behavior ceases, and one sees the lower Form II curve (Δ). For
Form II, alterations in pH have very little effect on s. Its physical properties are, in general, identical to those of
linear DNA. At pH 13, the strands of Form II simply separate, just as the strands of linear DNA do. The
separated single strands have slightly different s values, but display no significant changes in s with further
increases in pH.

A complete explanation for these data is beyond the scope of this article. In brief, the alterations in s come
about because of changes in the superhelicity of circular DNA. These changes in superhelicity are
schematically illustrated by four little drawings which have been strategically superimposed upon the figure
above.

Briefly, the alterations of s seen in the pH titration curve above are widely thought to be due to changes in the
superhelical winding of DNA under conditions of increasing pH. Up to pH 11.5, the purported "underwinding"
produces a right-handed ("negative") supertwist. But as the pH increases, and the secondary helical structure
begins to denature and unwind, the chromosome (if we may speak anthropomorphically) no longer "wants" to
have the full Watson-Crick winding, but rather "wants", increasingly, to be "underwound". Since there is less
and less strain to be relieved by superhelical winding, the superhelices therefore progressively disappear as the
pH increases. At a pH just below 12, all incentive for superhelicity has expired, and the chromosome will
appear as a relaxed, open circle.

At higher pH still, the chromosome, which is now denaturing in earnest, tends to unwind entirely, which it
cannot do so (because Lk is covalently locked in). Under these conditions, what was once treated as
"underwinding" has actually now become "overwinding". Once again there is strain, and once again it is (in
part at least) relieved by superhelicity, but this time in the opposite direction (i.e., left-handed or "positive").
Each left-handed tertiary supertwist removes a single, now undesirable right-handed Watson-Crick secondary
twist.

The titration ends at pH 13, where Form IV appears.

See also
Jerome Vinograd
Mechanical properties of DNA
Ribbon theory

References

1. Bar, A., Mukamel, D., & Kabakçoǧlu, A. (2011). Denaturation of circular DNA: Supercoil mechanism. Physical
Review E - Statistical, Nonlinear, and Soft Matter Physics, 84(4), <xocs:firstpage xmlns:xoc s=""/>.
2. Champoux J (2001). "DNA topoisomerases: structure, function, and mechanism". Annu Rev Biochem. 70: 369–413.
PMID 11395412 (https://www.ncbi.nlm.nih.gov/pubmed/11395412). doi:10.1146/annurev.biochem.70.1.369 (https://doi.
org/10.1146%2Fannurev.biochem.70.1.369).
3. Singer, Emily (5 January 2016)."How Strange Twists in DNA Orchestrate Life"(https://www.quantamagazine.org/2016
0105-supercoiled-dna/). Quanta Magazine. Retrieved 2016-01-07.
4. Irobalieva, Rossitza N.; Zechiedrich, Lynn; et al. (12 October 2015)."Structural diversity of supercoiled DNA"(http://w
ww.nature.com/ncomms/2015/151012/ncomms9440/full/ncomms9440.html) . Nature Communications. 6 (8440).
PMC 4608029 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608029) . PMID 26455586 (https://www.ncbi.nlm.ni
h.gov/pubmed/26455586). doi:10.1038/ncomms9440(https://doi.org/10.1038%2Fncomms9440). Retrieved 2016-01-07.
5. Ganji, Mahipal; Kim, Sung Hyun; van der T orre, Jaco; Abbondanzieri, Elio; Dekker,Cees (2016-07-13)."Intercalation-
Based Single-Molecule Fluorescence Assay T o Study DNA Supercoil Dynamics"(http://dx.doi.org/10.1021/acs.nanolet
t.6b02213). Nano Letters. 16 (7): 4699–4707. ISSN 1530-6984 (https://www.worldcat.org/issn/1530-6984).
doi:10.1021/acs.nanolett.6b02213(https://doi.org/10.1021%2Facs.nanolett.6b02213).
 6. Albert AC, Spirito F, Figueroa-Bossi N, BossiL, Rahmouni AR (1996)."Hyper-negative template DNA supercoiling
during transcription of the tetracycline-resistance gene in topA mutants is lar
gely constrained in vivo" (https://www.ncb
i.nlm.nih.gov/pmc/articles/PMC146055). Nucl Acids Res. 24 (15): 3093–3099. PMC 146055 (https://www.ncbi.nlm.nih.
gov/pmc/articles/PMC146055) . PMID 8760899 (https://www.ncbi.nlm.nih.gov/pubmed/8760899).
doi:10.1093/nar/24.15.3093(https://doi.org/10.1093%2Fnar%2F24.15.3093).
7. Shimada, Jiro; Yamakawa, Hiromi (1984), "Ring-closure probabilities for twisted wormlike chains. Application to
DNA", Macromolecules, ACS Publications,17 (4): 689–698, doi:10.1021/ma00134a028(https://doi.org/10.1021%2Fm
a00134a028)
8. Essevaz-Roulet, Baptiste and Bockelmann, Ulrich and Heslot, Francois (1997), "Mechanical separation of the
complementary strands of DNA",Proceedings of the National Academy of Sciences, National Acad Sciences,94 (22):
11935–11940, PMC 23661 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC23661) , PMID 9342340 (https://www.nc
bi.nlm.nih.gov/pubmed/9342340), doi:10.1073/pnas.94.22.11935 (https://doi.org/10.1073%2Fpnas.94.22.11935)
9. Lavery, Richard and Lebrun, Anne and Allemand, Jean-François and Bensimon, David and Croquette, Vincent (2002),
"Structure and mechanics of single biomolecules: experiment and simulation", Journal of Physics: Condensed Matter,
IOP Publishing, 14 (14): R383–R414, doi:10.1088/0953-8984/14/14/202(https://doi.org/10.1088%2F0953-8984%2F1
4%2F14%2F202)
10. Moroz, J David; Nelson, Philip (1997), "T orsional directed walks, entropic elasticity
, and DNA twist stiffness",
Proceedings of the National Academy of Sciences, National Acad Sciences,94 (26): 14418–14422,
doi:10.1073/pnas.94.26.14418(https://doi.org/10.1073%2Fpnas.94.26.14418)
11. Vologodskii AV, Lukashin AV, Anshelevich VV, et al. (1979). "Fluctuations in superhelical DNA"(https://www.ncbi.nl
m.nih.gov/pmc/articles/PMC327745). Nucleic Acids Res. 6 (3): 967–682. PMC 327745 (https://www.ncbi.nlm.nih.gov/p
mc/articles/PMC327745) . PMID 155809 (https://www.ncbi.nlm.nih.gov/pubmed/155809). doi:10.1093/nar/6.3.967(ht
tps://doi.org/10.1093%2Fnar%2F6.3.967).
12. H. S. Chawla (2002).Introduction to Plant Biotechnology. Science Publishers.ISBN 1-57808-228-5.

General references
Bloomfield, Victor A.; Crothers, Donald M.; Tinoco, Jr., Ignacio (2000). Nucleic acids: structures,
properties, and functions. Sausalito, California: University Science Books. pp. 446–453.
ISBN 0935702490.

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