Supercoiled

Supercoiled refers to DNA that is twisted upon itself beyond its relaxed length, creating compact structures known as supercoils. This state arises when double-stranded DNA experiences torsional strain, typically in closed circular genomes such as plasmids and bacterial chromosomes, but also in constrained linear DNA within chromatin.

DNA can be negatively supercoiled (underwound) or positively supercoiled (overwound). Negative supercoiling promotes strand separation, facilitating transcription and replication; positive supercoiling arises ahead of moving polymerases and must be relaxed for continued elongation.

Regulation by topoisomerases: Type I topoisomerases make single-strand breaks to change linking number by increments of one, relaxing negative or positive supercoils. Type II topoisomerases cut both strands to change linking number by increments of two; bacterial gyrase generally introduces negative supercoils, helping maintain underwinding. Eukaryotic topoisomerase II and other enzymes can both relax and introduce supercoils depending on cellular needs.

Physical description: In closed circular DNA, the linking number Lk is fixed; changes in Lk are partitioned between twist Tw and writhe Wr (Lk = Tw + Wr). Supercoiling alters the spatial conformation into plectonemes or toroidal folds, which can be visualized by electrophoresis as distinct bands (supercoiled, relaxed, and nicked forms).

Biological significance: Supercoiling affects promoter accessibility, nucleosome positioning, and DNA compaction; it is actively modulated during replication, transcription, recombination, and DNA repair. Environmental conditions such as ionic strength and temperature influence supercoiling in vivo.

See also: DNA topology.