When you have a DNA fragment without sequence information, you may want to find out its restriction map before any further work. The process might involve in digesting the DNA with single and double enzymes, estimating the sizes of all the restriction fragments using electrophoresis, and deducing the restriction map according to the fragment sizes. Reconstruction of restriction maps may be complicate. The difficult increases when more fragments are produced by enzyme digestion. DNAMAN use a dynamic process to find all possible combinations of restriction fragments that match the digestion patterns.
In the experiment, you should use two restriction enzymes to digest the target DNA. The size of all the fragments in single and double digestion must be estimated from electrophoresis as accurate as possible. Choose the Restriction | Map Reconstruction command to open a dialog box. Fill out the experimental data into to the table. The sums of the total fragment size of Enzyme A, Enzyme B and Enzyme A+B must be equal.
The size of the DNA fragments should be estimated accurately. You can have an error bar for the estimation. The default error is set to 10%. You may decrease it if you are confident on the estimation.
The deduced restriction map is shown in a graphic window. If more than two maps are found from the provided data, DNAMAN draws only the first two maps. The number of the possible maps is indicated at the bottom of the graphic window. In this case, the more accurate maps may be found by decreasing the error rate.
If you have more than two enzymes for digestion, perform separately the analyses of each enzyme combination. Use only two enzymes for each analysis, then construct the final map from the combination of individual maps.