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Short answer
Supercoiled DNA is DNA that is under torsional stress: its double helix has been twisted more tightly (positive supercoiling) or less tightly (negative supercoiling) than its relaxed state. In a closed circle such as a plasmid, that stress is stored as a fixed linking number, and only enzymes that break DNA strands, the topoisomerases, can change it.
What is supercoiled DNA? Definition and scope
Deweese, Osheroff and Osheroff define the term plainly: “DNA that is under torsional stress is referred to as supercoiled”. DNA that is underwound is negatively supercoiled; DNA that is overwound is positively supercoiled. The same review notes that plasmids and bacterial chromosomes are often circular, meaning they have no free ends, which is the setting in which supercoiling is easiest to picture and to reason about.
Linking number, twist and writhe
Supercoiling is described with one bookkeeping equation. The linking number (Lk) is “the sum of the twist and the writhe”, written Lk = Tw + Wr. Twist counts how the two strands wind around each other; writhe counts how the helix axis coils on itself. When Lk is held constant, a change in one term has to be matched by an opposite change in the other, which is why torsional stress shows up as visible coiling of the molecule.
How topoisomerases change supercoiling
Because the linking number is a topological property of a closed molecule, it cannot be altered by simply bending or twisting the DNA. Topoisomerases change it by cutting the backbone, passing DNA through the break and resealing it. Two classes are described in the sources below.
- Type I topoisomerases create “transient single-stranded breaks in the double helix” and change Lk in steps of one (Deweese et al.). Sutormin et al. (2021) describe the same class as introducing a single-strand break, or nick.
- Type II topoisomerases generate “a transient double-stranded break in the DNA backbone” and change Lk in steps of two (Deweese et al.). Sutormin et al. call the cleaved fragment the G-segment.
- DNA gyrase, a type II enzyme, “is the only known topoisomerase that can actively underwind” DNA, introducing negative supercoils (Deweese et al.), and it does so using the energy of ATP hydrolysis (Sutormin et al., 2021).
Type I, type II and gyrase compared
| Enzyme class | Break made | Change in linking number | Source |
|---|---|---|---|
| Type I topoisomerase | Transient single-strand break | Steps of one | Deweese et al. |
| Type II topoisomerase | Transient double-strand break | Steps of two | Deweese et al. |
| DNA gyrase (a type II enzyme) | Double-strand break (type II) | Introduces negative supercoils, using ATP hydrolysis; the only known topoisomerase that actively underwinds DNA | Deweese et al.; Sutormin et al., 2021 |
The practical reading of the table: a single-strand nick and a double-strand cut are different events with different consequences for the linking number, so the step size an enzyme produces tells you which kind of break it must be making.
Where supercoiling matters for labs and supply decisions
Four situations bring supercoiling into routine laboratory work. This section is general context, not clinical or dosing guidance.
- Circular templates. Plasmids are usually circular, so a plasmid preparation can contain molecules in different topological states. Bitesize Bio (checked 2026-10-29) describes supercoiled, nicked and linear plasmid forms as migrating differently on an agarose gel, and notes that the supercoiled form runs faster than its true size would suggest. Treat that as a practical rule of thumb from a secondary source; the principle behind it is the topology described above.
- Cutting and cloning. Supercoiled substrates are discussed in a restriction-digest setting in our guide to restriction enzyme digest setup, and plasmid handling more broadly in gene cloning.
- Reading the gel. To interpret band patterns, see what gel electrophoresis is and the bench-level agarose gel electrophoresis protocol basics. For where plasmid DNA comes from in the first place, see DNA extraction protocol basics.
- Drug targets. Sutormin et al. report that “DNA gyrase and topoisomerase IV are the targets for many antibiotics” and that “most agents used in cancer chemotherapy are topoisomerase poisons, with etoposide being the most common.” This is why topoisomerase biology appears in microbiology and pharmacology teaching; it is background, not advice on any treatment.
Common misunderstandings
- Supercoiling is a state, not a sequence. It describes torsional stress in a molecule, not a particular base sequence.
- Negative does not mean damaged. Negative supercoiling simply means the DNA is underwound; gyrase actively creates it using ATP.
- Linking number does not drift on its own. Twist and writhe can trade off against each other while Lk stays the same; changing Lk itself requires a topoisomerase to break and rejoin strands.
- Type I and type II are not interchangeable. They differ in the break they make and in the step size, one versus two.
FAQ
What is supercoiled DNA?
DNA under torsional stress, either underwound (negative supercoiling) or overwound (positive supercoiling), as defined by Deweese et al.
What is negative supercoiling?
Negative supercoiling is an underwound state of the double helix. DNA gyrase is the only known topoisomerase that can actively produce it.
What does a topoisomerase do?
It changes the linking number of DNA by making a transient break, either in one strand (type I, steps of one) or both strands (type II, steps of two), then resealing it.
What is the linking number?
The sum of twist and writhe, Lk = Tw + Wr.
Sources
- Deweese JE, Osheroff MA, Osheroff N. Biochem Mol Biol Educ. 37(1):2-10. pmc.ncbi.nlm.nih.gov/articles/PMC2643378 (checked 2026-10-29).
- Sutormin DA et al. Diversity and functions of type II topoisomerases. Acta Naturae. 2021;13(1):59-75. pmc.ncbi.nlm.nih.gov/articles/PMC8084294 (checked 2026-10-29).
- Bitesize Bio, how to identify supercoils, nicks and circles in plasmid preps. bitesizebio.com/13524 (checked 2026-10-29; secondary source, gel behaviour only).
