Nick (DNA)

Excessive rough handling in pipetting or vortexing creates physical stress that can lead to breaks and nicks in DNA.

[3] Ligases are versatile and ubiquitous enzymes that join the 3’ hydroxyl and 5’ phosphate ends to form a phosphodiester bond, making them essential in nicked DNA repair, and ultimately genome fidelity.

This biological role has also been extremely valuable in sealing the sticky ends of plasmids in molecular cloning.

Their importance is attested by the fact most organisms have multiple ligases dedicated to specific pathways of repairing DNA.

[10] Some sources of mismatched base pairs include replication errors and deamination of 5-methylcytosine DNA to form thymine.

Mut L homologues from eukaryotes and most bacteria incise the discontinuous strand to introduce the entry or termination point for the excision reaction.

Similarly, in E. coli, Mut H nicks the unmethylated strand of the duplex to introduce the entry point of excision.

[11] For eukaryotes specifically, the mechanism of DNA replication elongation between the leading and lagging strand differs.

On the lagging strand, nicks exist between Okazaki fragments and are easily recognizable by the DNA mismatch repair machinery prior to ligation.

[1] Together, the presence of a nick and a ribonucleotide make the leading strand easily recognizable to the DNA mismatch repair machinery.

[13] Nicks in DNA also give rise to different structural properties, can be involved in repairing damages caused by ultraviolet radiation, and are used in the primary steps that allow for genetic recombination.

[14] Stability is decreased as a break in the phosphodiester backbone allows DNA to unwind, as the built up stress from twisting and packing is not being resisted as strongly anymore.