Nick (DNA)

A nick is a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand typically through damage or enzyme action. Nicks allow for the much-needed release of torsion in the strand during DNA replication. Nicks are also thought to play a role in the DNA mismatch repair mechanisms that fix errors on both the leading and lagging daughter strands.

The diagram shows the effects of nicks on intersecting DNA forms. Nicking can be used to alleviate the energy created by intersecting states. By creating nicks, the DNA forms a circular shape.

Nicked DNA can be the result of DNA damage or purposeful and carefully regulated biomolecular reactions carried out in the cell. DNA can be nicked by physical shearing, over-drying or enzymes. Excessive rough handling happening in pipetting or vortexing creates the physical stress that can lead to breaks and nicks in DNA. Overdrying of DNA can also break the phosphodiester bond in DNA and result in nicks. Enzyme Nicking endonucleases can assist with this process A single-stranded break (nick) in DNA can be formed by the hydrolysis and subsequent removal of a phosphate group within the helical backbone. This leads to a different DNA conformation, where a hydrogen bond forms in place of the missing piece of the DNA backbone in order to preserve the structure.

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 end of plasmids in molecular cloning. Their importance is attested by the fact most organisms have multiple ligases dedicated to specific pathways of repairing DNA. In eubacteria these ligases are powered by NAD+ rather than ATP. Each nick site requires 1 ATP or 1 NAD+ to power the ligase repair.

In order to ligate these fragments together, the ligase progresses through three steps:

One particular example of a ligase catalyzing nick closure is the E. coli NAD+ dependent DNA ligase. LigA is a relevant example as it is structurally similar to a clade of enzymes found across all types of bacteria. LigA drives the process of the ligation by wrapping its protein clamp around the DNA and creating large protein conformational changes and remodeling of the active site.

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Wikipedia