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Nick Translation and End Filling - This is the oldest method of nucleic acid labelling and is still the most commonly used. This technique is quite flexible with respect to probe size, specific activity and concentration; it is particularly suited for the production of large quantities of probes for use in multiple hybridization reactions and/or where a high probe concentration is required. The procedure for nick translation is briefly described below.

1. The DNA preparation to be labelled is treated with DNase I for a very short time; this induces nicks in the DNA molecules, the positions of the nicks being random. A 'nick' is the point in one strand of a double stranded DNN molecule where the phosphodiester bond has been broken; thus each nick has a free 3'-OH group.

2. The nicked DNA sample is subjected to E. coli DNA polymerase I, which successively adds new nucleotides to the free 3' -OH group. As the new segment of DNA is synthesized in this way, the existing strand of the DNA duplex is progressively displaced and digested away by the 5' --> 3' exonuclease activity of the enzyme.

In this reaction, usually one of the deoxynucleoside triphosphates is radiolabelled, e.g., with 32p, but more or even all' the four nucleotides could be labelled. The labelled nucleotides are progressively incorporated into the newly synthesized segment; since this segment is synthesized by complementary base paring, it has the same sequence as the strand it replaces.

The process is called 'nick translation' because there is a movement (translation) of the 'nick' along the DNA duplex due to the activities of E. coli DNA polymerase I. The term 'translation' in its name does not refer to the synthesis of proteins.

Nick translation can be used with a variety of labels to generate probes suitable for most hybridization applications. It has been used to generate probes having high enough specific activity to detect single copy genes on Southern blots of mammalian DNA.

A much gentler method of DNA labelling is end filling; this method can be used with only those DNA molecules that have 5'-protruding ends. Klenow fragment is used to extend the recessed 3'-ends; this results in the filling of the single-stranded ends.

As in the case of nick translation, one of the nucleotides used for end filling is labelled with 32p. Both end filling and nick translation label DNA to such an extent that even 2 ng of DNA per band can be visualised under ideal conditions.