Single-strand nick

DNAIigase Seals the single strand nick between the nascent chain and Okazaki fragments on lagging strand... 

DNase 1 j Under appropriate conditions, produces j single-stranded nicks in DNA. Nick translation mapping of hypersensitive sites mapping protein-DNA interactions. 

Endonucleases cleave within the chain to produce single-stranded nicks. 

The E. coli chromosome exists as a circular, folded, supercoiled duplex (a). This can be converted to a partially unfolded structure by brief treatment with RNase (c). There are 50-100 loops in the structure supercoiling may be selectively eliminated from individual loops by single-strand nicking of the DNA within the loop (b). 

The enzyme without the sigma factor, called core polymerase, retains the capability to synthesize RNA, but it is defective in the ability to bind and initiate transcription at true initiation sites on the DNA. In fact when RNA polymerase was first purified from crude extracts it was missing the a factor. The assay for polymerase involved the use of DNA with single-strand nicks. When a DNA template was used that did not have single-strand nicks, this enzyme was not active. This led to a search for a missing factor. When this factor (cr70) was added back to the purified core enzyme and the uncut DNA template, the enzyme was able to bind... 

Another isothermal amplification technique is strand displacement amplification (SDA). " After heat denaturation of DNA in the presence of four primers, dCTP, dGTP dUTP, and a modified deoxynucleotide (dATPaS), two enzymes are added, an exonuclease-deficient polymerase and a restriction enzyme. The two flanking primers that enter into exponential amplification have a restriction site added to their 5 end and get nicked by the restriction enzyme, allow-ing displacement of strands that can in turn be primed, extended, and nicked. Deoxy-ATPotS is used so that the restriction sites include a hemiphosphorothioate linkage to allow single-strand nicking, instead of cutting through double strands. 

Aside from the ability to relax (or supercoii) DNA in steps of either 1 or 2, other criteria have been used to distinguish type I and type II enzymes. One useful criterion is the catenation and decatenation of duplex circles (Liu et al., 1980). Type I enzymes, because of their inability to make double-strand breaks, can only catalyze these reactions when at least one circle bears a single-strand nick, whereas type II enzymes can perform these reactions with intact circles (Tse and Wang, 1980). 

Abasic Sites, Single-Strand Nicks, and Caps... 

The uranyl(VI) ion (UO2 ) is known to uiduce single strand "nicks in DNA on... 

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