nickedstrand

Nicked strand, sometimes written as nicked strand, is a DNA strand that carries a nick, a discontinuity in the phosphodiester backbone of one strand within a double helix. This single-strand break results in exposed ends, typically a 5' phosphate and a 3' hydroxyl, and differs from a double-strand break which involves both strands.

Causes and formation. Nicks can arise naturally during cellular DNA processing, such as base excision repair or Okazaki fragment processing, or be introduced deliberately by enzymes known as nicking endonucleases. They can also occur as a consequence of DNA damage from reactive oxygen species, ionizing radiation, or mechanical stress. In many contexts, a nick is a transient intermediate that cells efficiently repair using DNA ligases to reseal the backbone.

Biological significance. In replication and repair, nicks can influence genome stability. If a nick is present on a template strand during replication, it can lead to replication fork stalling or collapse, potentially resulting in a double-strand break if not properly managed. Cells employ various pathways, including ligation, base excision repair, and homologous recombination, to restore integrity.

Laboratory uses. In molecular biology, nicks are exploited for techniques such as nick translation, where DNA polymerase replaces nucleotides starting at a nick, and for controlled strand displacement or labeling. Nicking endonucleases and nickases (such as nickase variants of Cas9) are used in genome editing and cloning to introduce single-strand breaks that favor specific repair outcomes.

See also. Single-strand break; DNA ligase; nick translation; nickase.