Restriction site mapping

Hopple JS, Vilgalys R Phylogenetic relationships among coprinoid taxa and allies based on data from restriction site mapping of nuclear rDNA. Mycologia 1994 86 96-107. 

Restriction-site mapping in DNA may be performed by end-labelling with polynucleotide kinase as above, and subsequent partial digestion with the restriction enzyme. An overlapping series of polynucleotides with a common labelled terminus is thus formed, and size analysis of these affords a restriction map. Polynucleotide kinase may also be used to assay the number of 5 -phosphorylated termini in DNA generated as the result of the action of restriction endonuclease. In the presence of... 

Unique" Restriction Site Map of Gamma Interferon Gene... 

White, E.E., R.E. Watkins and D.P. Fowler. 1993. Comparative restriction site maps of chloroplast DNA of Picea abies, Picea glauca, Picea mariana and Picea sitchensis. Can. J. For. Res. 23 427-435. 

A restriction map shows the location of restriction sites in a given DNA sequence. 

A RESTRICTION MAP is used to identify and locate specific restriction sites on a given piece of DNA. The size of a fragment is determined by running the restriction digest on an agarose gel. Fragments separate by size—the smaller ones move farther toward the bottom of the gel. 

Figure 5-48 A physical map of the oxi3 locus of yeast mitochondrial DNA. The restriction fragments used for DNA sequencing are indicated by the arrows. The extent to which the sequences were read is represented by the lengths of the arrows. The map units are shown in the inner circle. The following symbols, together with the names of the restriction enzymes (Chapter 26), are used for the restriction sites ...

The plasmid can be cut at a number of defined sites with restriction enzymes as explained in the previous section. The map in Figure 7.5 shows the restriction sites of those enzymes that cut the molecule once or twice the unique sites are shown in bold type. 

Figure 9.2. Shuttle vector map retrieved from Riken Gene Bank. The map of shuttle vector pYAC 3/4/5 shows major restriction sites.

Figure 9.3. Restriction map produced by Webcutter. The partial restriction map shows the nucleotide sequence of human lysozyme gene submitted to Webcutter using options for all restriction endonucleases with recognition sites equal to or greater than six nucleotides long and cutting the sequence 2 6 times (at least 2 times and at most 6 times). The restriction profile (map) is returned if Map of restriction sites is selected for display. The tables by enzyme name and by base pair number can be also returned if displays for Table of sites, sorted alphabetically by enzyme name Table of sites, sorted sequentially by base pair number are chosen.

To search for an appropriate restriction enzyme and its restriction profile, subject the query DNA to Webcutter at http //www.firstmarket.com/cutter/ cut2.html. Upload the sequence file (enter drive directoryseqfilename) or paste the sequence into the query box. Indicate your preferences with respect to the type of analysis, site display, and restriction enzymes to include in the analysis. After clicking the Analyze Sequence button, the restriction map (duplex sequence with restriction enzymes at the cleavage sites), as shown in Figure 9.3, is returned if Map of restriction sites is selected for display. You may also select Table of sites, sorted alphabetically by enzyme name for display which lists number of cuts, positions of sites, and recognition sequences. 

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